Bowdoin Science Journal

Science

Biomimicry Within Bowdoin: The Ongoing Development of Peptoids

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To solve complex human health issues, scientists have more recently turned to biomimicry. Biomimicry, also known as biomimetics, is a field that develops synthetic materials, systems or machines that are derived from the principles of natural biological processes (Nature). Concepts within biomimetics are currently being used to design regenerative medicine and newer drugs for diseases such as cancer. In fact, within Bowdoin, Professor Benjamin Gorske, is undertaking a comprehensive research on developing methods to create drugs that attempt to inhibit signaling pathways within cancer, or interrupt the signal transduction pathways involved in the development of plaques in Alzheimer disease. 

Professor Gorske explains that these aforementioned diseases can be addressed by “controlling the signaling proteins”. By interrupting the signaling process, the underlying issue of these diseases – which are often so diverse and hard to target – doesn’t need to be treated. However, a difficulty that comes with targeting signaling proteins is that they bind to other molecules over a vast space, and are implicated in many other signaling pathways. Therefore, these proteins cannot simply be targeted by small molecular drugs, as they would be impossible to effectively block the proteins and thus are called “undruggable molecules”. Instead, Professor Gorske turns to attempting to create a biological molecule that can mimic the other molecules that bind to the target signaling protein – which are normally much bigger than current drug molecules. 

One of the targets that Professor Gorske looks into in his lab are the signaling proteins within the Hippo pathway. The Hippo pathway normally controls the size of organs by regulating cell proliferation (division of cells) and apoptosis (programmed cell death) (Cell Signaling Technology). Ultimately, this pathway controls the expression of certain genes that are involved in the proliferation process. This pathway is involved in cancer when it is disregulated, as it continuously sends a signal to the nucleus to express these genes encoding for cell proliferation, thus leading to the uncontrollable growth of cancer. The Hippo pathway involves a lot of signaling proteins that are solely involved in this signaling pathway. Most of these signaling proteins contain a WW domain – a distinct functional unit of the protein that mediates the interactions these proteins have with other molecules (EMBL-EBI). All the signaling proteins with this specific domain in this pathway generally bind to proteins with polyproline type 2 helices (PPII). Professor Gorske’s lab aims to design a molecule to contain this PPII structural component to effectively target the signaling proteins (with the WW domain) in the Hippo pathway.

Fig 1: Diagram of the Hippo Pathway. The signaling protein YAP (yes-associated protein/transcription coactivator) is an example of a molecule with the WW domain.

However, we can’t utilize naturally formed proteins with these PPII helices as the proteases in our body would find the related drugs as foreign and destroy them. Thus these helices need to be made artificially, forming molecules called peptoids. Peptoids are a class of molecules that mimic the structure and function of helical peptides (Chongsiriwatana et al., 2008). They are very biostable, relatively easy to make, and most importantly proteases don’t destroy these molecules. Thus Professor Gorske has chosen to make specific peptoids that perhaps could target these signaling proteins in his lab.

Fig 2: Comparison of the general molecular structure of a naturally-derived peptide versus an artificially-produced peptoid.

However, an issue that arose with creating these peptoids is that the peptoids often folded to form polyproline type 1 helices (PPI) rather than PPII helices. This is due to the differences in orientation of the connected amides (subunits of the peptoids). This leads to peptoids with PP1 helices being much more compressed than peptoids with PPII helices. While they do work as good lung surfactants and other antimicrobials, they are not suitable to target signaling proteins. 

Fig 3: Comparison of the 3D structure of polyproline 1 helix (PPI) and polyproline 2 helix (PPII), and the orientation of the respective amide subunits.

Through experimenting, Professor Gorske has found out in his lab that the best way to encourage amides to connect in the desired PPII orientation is through adding side chains on the amide subunits, and the side chains are additionally thionated – the carbon is double bonded to sulfur instead of oxygen. Currently, he is investigating whether adding more than one thionated residue can lead to the whole peptoid to adopt the desired PPII helical structure. 

This method of creating peptoids that Professor Gorske is working to devise can be implicated in so many uses within medicine. As peptoid drugs can mimic biological molecules, they can more precisely target the required proteins, to help inhibit or promote signaling pathways back to normal. Professor Gorske’s research is therefore crucial to the ongoing development of medicine and healthcare. 

References

“Biomimetics Articles from across Nature Portfolio.” Nature News, Nature Publishing Group, https://www.nature.com/subjects/biomimetics. 

Chen, Yu-An, et al. “WW Domain-Containing Proteins Yap and Taz in the Hippo Pathway as Key Regulators in Stemness Maintenance, Tissue Homeostasis, and Tumorigenesis.” Frontiers in Oncology, vol. 9, 2019, https://doi.org/10.3389/fonc.2019.00060. 

Chongsiriwatana, Nathaniel P., et al. “Peptoids That Mimic the Structure, Function, and Mechanism of Helical Antimicrobial Peptides.” Proceedings of the National Academy of Sciences, vol. 105, no. 8, 2008, pp. 2794–2799., https://doi.org/10.1073/pnas.0708254105. 

Embl-Ebi. “What Are Protein Domains?” What Are Protein Domains? | Protein Classification, https://www.ebi.ac.uk/training/online/courses/protein-classification-intro-ebi-resources/protein-classification/what-are-protein-domains/. 

“Hippo Signaling.” Cell Signaling Technology, 2010, https://www.cellsignal.com/pathways/hippo-signaling-pathway.

 

The Possibilities of the CRISPR-Cas9 System

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          As humans continue to further explore the fields of science, they deepen their understanding of convoluted subjects through the use of advanced technologies. One of the notable technologies today is the CRISPR-Cas9 system, a highly precise DNA editing tool that allows for genome manipulation in humans, animals, and plants. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) works with a CRISPR-associated (Cas) nuclease, which was originally derived from a genome editing system used as immune defense by bacteria. To put it simply, if infected by a virus, the bacteria captures a small piece of the invading viruses’ DNA and inserts their own DNA to create a CRISPR segment (Tavakoli et al., 2021). With this segment, the bacteria can produce RNA segments that will attach to parts of the viruses’ DNA if it attacks again. The bacteria use the Cas9 enzyme to cut the viruses’ DNA apart and incapacitate it. 

          Scientists adapted the system so it could be inputted into the human genome and edit DNA. Researchers created small segments of RNA that have a “guide” sequence which binds to a target sequence in the DNA and attaches to the Cas9 enzyme (Tavakoli et al., 2021). The guide RNA (gRNA) identifies the intended DNA sequence and the Cas9 enzyme cuts the specific location, similar to how the process occurs in bacteria. The cell’s own DNA machinery is then used to add or delete pieces of the genetic material, known as gene knock-in and gene knockout, respectively. However, it can also alter the DNA by replacing segments with more customized sequences. CRISPR activation (CRISPRa) is used to up-regulate the expression of a gene while CRISPR interference (CRISPRi) down-regulates the expression of a cell (CRISPR Guide).

Figure 1. Gene Knockout
Figure 2. Activation of Target  Gene with CRISPRa

                                       Note. Adapted from CRISPR Guide, Addgene, 2022.

          There are many potential applications in cancer immunotherapy, treatment of genetic diseases, improving plant genetic variation, and more. For example, there have been advances towards mitigating the effects of blood disorders such as sickle cell disease (SCD). In those with SCD, the misshapen red blood cells can block blood vessels, thus slowing or stopping blood flow. Effects of this fatal disease are anemia, chronic pain, strokes, and organ damage. In this instance, CRISPR technology is not used to directly rectify the disease-inducing gene variant. Instead of restoring adult hemoglobin, it works to increase the levels of fetal hemoglobin, an oxygen carrier protein that only fetuses make in the womb (Henderson, 2022). Since it’s not affected by the sickle cell mutation, it can be a substitute for the defective adult hemoglobin in red blood cells (Henderson, 2022).

Figure 3. Hemoglobin Switching in Infants

Note. Adapted from CRISPR Clinical Trials: A 2022 Update, Henderson, 2022, Copyright 2022 by Innovative Genomics Institute.

         As seen in the diagram above, SCD symptoms begin during infancy when levels of fetal hemoglobin decrease. The blood stem cells are harvested from the blood and then the genomes are edited to activate the fetal hemoglobin gene. Next, chemotherapy eliminates the disease-inducing blood stem cells from the person’s body, and the genome-edited stem cells are put back into the bloodstream through an IV, creating a new blood stem cell population that produces fetal hemoglobin (Henderson, 2022). This technique is ex vivo genome editing, where the editing occurs outside the body to prevent the risk of lingering and unwanted CRISPR components in the body. Those treated for SCD in CRISPR clinical trials show normal to near-normal hemoglobin levels with at least 30% as fetal hemoglobin (Henderson, 2022).

          It raises the following questions: is it possible to select certain features in humans that are seen as favorable or desirable? Is it possible to have almost complete manipulation of physical features or to enhance the body’s biological processes to unlock superhuman abilities only seen in movies? These human experimentations would be best measured if implemented during the early stages of life so as to let the body integrate the changes and develop properly. Perhaps we could alter ourselves to increase muscle mass, heighten athletic ability, or augment intelligence. In regard to altering the human genome, there are certain limitations as to what can and can’t be done without violating certain ethical boundaries. 

          This can be seen in the case of He Jianku, a Chinese scientist who used CRISPR to edit two embryos, both of which are now living babies. Though there was little information that only came from He himself and the Chinese government, it has been said that sometime in late 2017, He injected the two embryos with a CRISPR construct that would delete a 32-base-pair in the CCR5 gene on chromosome 3, leading to a non-functional CCR5 protein (Greely, 2019). He sought to achieve humans who could not contract AIDS because they don’t have this functioning protein (Greely, 2019). Though this theory was later proved wrong and the CRISPR construct did not fulfill his intentions, he managed to induce never before seen changes that led to the production of non-functional proteins. His actions prompted the Chinese court to convict him on the basis of deliberately violating medical regulations (Greely, 2019). Could it be argued that pushing the boundaries are necessary for scientific growth and greater human evolution? How far is too far? As CRISPR and other gene editing tools continue to develop, we can keep imagining the unnerving yet exciting possibilities that are awaiting.

 

Literature Cited

CRISPR Guide. (n.d.). Addgene. 

Greely, H. T. (2019). CRISPR’d babies: human germline genome editing in the ‘He Jiankui affair’. Journal of Law and Biosciences, 6(1), 111-183.

Henderson, H. (2022). CRISPR Clinical Trials: A 2022 Update. Innovative Genomics Institute.

Tavakoli, K., Pour-Aboughadareh, A., Kianersi, F., Poczai, P., Etminan, A., & Shooshtari, L. (2021). Applications of CRISPR-Cas9 as an Advanced Genome Editing System in Life Sciences. BioTech, 10(3), 14. 

What are genome editing and CRISPR-Cas9? (2022). MedlinePlus.

The Chronic Lyme Debate

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Second possibly only to mosquitos, ticks are the most reviled insect found in New England nature. Like mosquitos, which are notorious vehicles for viruses such as Zika and West Nile, blacklegged ticks (deer ticks) spread Borrelia burgdorferi infection, resulting in Lyme disease. Affecting over 30,000 people a year in the United States, mostly in the northeastern states, Lyme disease is a bacterial infection which causes both local and global symptoms. Early symptoms include fever, muscle fatigue, swollen lymph nodes, and, mostly notably, an erythema migrans rash. Left untreated, patients may develop facial palsy (partial facial paralysis), arthritis, central nervous system inflammation, and heart palpitations. Diagnosis of Lyme disease is based primarily on symptoms and the possibility of exposure to Lyme-carrying ticks, although laboratory tests of patient serum for anti-B. Burgdorferi antibodies may also be considered. Treatments usually consist of a several week course of antibiotics. 

Although the majority of Lyme disease patients recover after initial treatment, 5-20% of patients continue feeling symptoms such as fatigue, muscle pain, and difficulty concentrating. This disorder, called post-treatment Lyme disease syndrome, falls under a broader category of disorders referred to as “chronic Lyme disease.” Also included in this category are patients without a history of Lyme disease but with Lyme-like symptoms; patients with other recognizable disorders seeking an alternative diagnosis; and patients with positive serological results for anti-B. Burgdorferi antibodies but no past exposure to ticks or other routes of infection. 

The majority of chronic Lyme patients fall into the middle two categories: those with symptoms but no history and the misdiagnosed. Moreover, in clinical trials, traditional treatment routes for Lyme disease such as antibiotics have not been effective in alleviating symptoms. Because many of those diagnosed with chronic Lyme do not match the diagnostic criteria for traditional Lyme disease, most scientists and physicians reject the diagnosis. However, a small but very vocal group of patients and physicians fervently believe in the existence of chronic Lyme disease. They are represented by powerful advocacy groups such as the International Lyme and Associated Diseases Society (ILADS) and the Lyme Disease Association (LDA). These groups have been effective at lobbying politicians and regulators to get protections for chronic Lyme sufferers, even as the physician community become increasingly convinced of its inaccuracy.

Although Lyme disease may seem a relatively simple disease with a clear cause (tick-borne bacterial infection) and treatment plan (antibiotics), the controversy over chronic Lyme disease reveals complexities. And this particular controversy doesn’t seem to be abating. It seems that the concept of chronic Lyme disease, like the disorder it purports to describe, is here to stay.

 

Works Cited:

CDC. (2022, January 19). Lyme disease home | CDC. Centers for Disease Control and Prevention. https://www.cdc.gov/lyme/index.html 

Chronic symptoms. (2018, April 11). Lyme Disease. https://www.columbia-lyme.org/chronic-symptoms 

Feder, H. M., Johnson, B. J. B., O’Connell, S., Shapiro, E. D., Steere, A. C., & Wormser, G. P. (2007). A critical appraisal of “chronic lyme disease.” New England Journal of Medicine, 357(14), 1422–1430. https://doi.org/10.1056/NEJMra072023 

Lantos, P. M. (2011). Chronic Lyme disease: The controversies and the science. Expert Review of Anti-Infective Therapy, 9(7), 787–797. https://doi.org/10.1586/eri.11.63 

Mosquito-borne diseases | niosh | cdc. (2020, February 21). https://www.cdc.gov/niosh/topics/outdoor/mosquito-borne/default.html 

Whelan, D. (n.d.). Lyme inc. Forbes. Retrieved April 2, 2023, from https://www.forbes.com/forbes/2007/0312/096.html 

The role of info chemicals in seabird plastic ingestion

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Short-tailed Shearwater (Puffinus tenuirostris), Ryan Shaw (2009)

Plastic debris is widespread in our waters with more than a quarter of a billion metric tons of plastic suspended in its global oceans. This abundant plastic pollution is being consumed by hundreds of organisms, ranging from tiny zooplankton to giant baleen whales. Seabirds are especially at risk, with a projection model concluding that over 99% of all seabird species will have ingested plastic debris by 2050. The consumption of plastic is incredibly harmful to seabirds as it reduces the storage volume of the stomach which ultimately leads to starvation and death. In the last few years, it has been discovered that the plastic problem is much more complicated than we thought before as many seabirds rely on their sense of smell to locate their prey instead of just visually. A 2016 study has brought to light this common misconception of marine organisms consuming plastic debris solely based on visual cues and has introduced a new factor: dimethyl sulfide (DMS). 

DMS is an infochemical used by foraging organisms as a way to find prey in marine environments. The production of DMS is from the enzymatic breakdown of its chemical precursor, dimethylsulfoniopropionate (DMSP), which increases when zooplanktons eat, letting other marine organisms know of the presence of a new meal. Plastic debris is an excellent substrate for biota that produce these infochemicals due to its convenience in biofouling, which is the accumulation of organisms on a surface. Since plastic debris can be easily fouled by DMS-producing organisms, then the debris can also produce a DMS signature that is significant enough to lead seabirds and similar organisms to consume it. 

To prove this, scientists examined the sulfur signature of plastic beads from the most common types of plastic found in the ocean. These plastic beads were tested for sulfur signatures after either being exposed to marine conditions or never being exposed to these conditions. The beads exposed to marine conditions were deployed off the coast of California at the Bodega Marine Laboratory and Hopkins Marine Station at oceanographic buoys and then retrieved after approximately three weeks. After examining each plastic bead, it was found that the samples not exposed to marine conditions did not produce any DMS signature. However, every sample that was tested after marine exposure was found to have produced a DMS signature. Even after less than a month of marine exposure, these plastic samples were found to produce DMS signatures that were significant enough to be detected by seabirds.

Additionally, the study was able to predict the importance of DMS and plastic ingestion patterns within seabirds through data analysis. Plastic ingestion data was analyzed from 55 studies among 25 procellariiforms––the order under which seabirds fall––to determine that DMS responsiveness has a significant positive effect on the frequency of plastic ingestion. Additionally, plastic ingestion patterns were predicted through calculations using data from previous studies to find that DMS-responsive species ingest plastic five times as frequently as non-DMS-responsive species.

The study has challenged the frequent assumption that marine organisms consume plastic because it is visibly mistaken for prey, suggesting rather that chemical cues like DMS play a role. This plastic ingestion has many implications, one such being that the semiannual movement patterns of seabirds between the Southern and Northern Hemispheres can create contact with plastic on a global scale rather than just a regional one. Although the primary focus of this study was on seabirds, they are not the only species that respond to DMS––sea turtles, penguins, and various other organisms have been shown to use DMS and DMSP as foraging compounds and could be impacted similarly. We must start mitigating the plastic waste we produce and work towards cleaning up our oceans. While this is a huge step to take, we can begin by looking for alternatives to plastic that are safer for the environment and reduce the amount of plastic that we use in our everyday lives.


References:

Savoca, M. S., Wohlfeil, M. E., Ebeler, S. E., & Nevitt, G. A. (2016). Marine plastic debris emits a keystone infochemical for olfactory foraging seabirds. Science Advances, 2(11). https://doi.org/10.1126/sciadv.1600395 

Eriksen, L. C. M. Lebreton, H. S. Carson, M. Thiel, C. J. Moore, J. C. Borerro, F. Galgani, P. G. Ryan, J. Reisser, Plastic pollution in the world’s oceans: More than 5 trillion plastic pieces weighing over 250,000 tons afloat at sea. PLOS ONE 9, e111913 (2014).

Wilcox, E. Van Sebille, B. D. Hardesty, Threat of plastic pollution to seabirds is global, pervasive, and increasing. Proc. Natl. Acad. Sci. U.S.A. 112, 11899–11904 (2015).

Ocean plastics pollution. Ocean Plastics Pollution. (n.d.). Retrieved April 2, 2023, from https://www.biologicaldiversity.org/campaigns/ocean_plastics/?adb_sid=71bc9f17-356c-492f-9204-f0e22e2752b6

The Contraceptive Brain Drain: How Birth Control Alters Women’s Brains

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There are millions of women taking steroids every day. But how is this possible? Are they just getting really buff? It feels like we always hear stories about how performance-enhancing drugs, namely steroids, are giving world-class athletes the boost they need to beat out their competition. But women across the globe are taking steroids every day as well, in the form of hormonal birth control. Despite their widespread use, side effects of hormonal contraceptives are largely unstudied, or have been until recently. In the last ten years, several studies have come out about the effect of taking a daily dose of steroids on women’s brains and mental health, which until now has been a severely neglected area where lack of knowledge affects millions of people worldwide. 

People take hormonal birth control, or hormonal contraceptives, for a myriad of reasons, from the obvious (preventing pregnancy) to the not-so-obvious (lessening iron deficiency) and everything in between. This type of medication simply refers to methods of pregnancy prevention that act on the endocrine system. The endocrine system controls growth, development, metabolism, and reproduction via signaling molecules called hormones. Two hormones in particular, estrogen and progesterone, control the menstrual cycle and are therefore the major components of hormonal birth control. Types of hormonal contraceptives come in many forms including the pill, the patch, the implant, injections, and hormonal intrauterine devices or IUDs, but despite the wide variety in the forms this medication takes, all of them contain one or both of these two hormones. As steroids, both estrogen and progesterone affect other body systems besides the reproductive system.

To study the impacts of taking a daily dose of steroids on other areas of the body, specifically the brain, Dr. Belinda Pletzer and her colleagues conducted a study in 2010. The brain is particularly susceptible to change due to an influx of synthetic hormones because it contains a very high quantity of hormone receptors. The brain needs to act as a “sponge” for these molecules since it plays an important role in creating the appropriate responses in the rest of the body. Pletzer’s study investigated how the sponginess of the brain would affect changes in its structure by comparing images of the brains of adult men, adult women during different stages of their menstrual cycle, and adult women taking hormonal contraceptives. To perform this comparison they used a technique called voxel-based morphology on MRIs of study participants (Pletzer et al., 2010). Voxel-based morphology measures differences in the concentration of tissue and the size and shape of different areas of the brain.

Overall, they found that women taking hormonal birth control had smaller areas of gray matter, or areas of the brain that have a high concentration of the cell bodies of nerve cells, when compared to “naturally cycling women” in both their follicular and luteal menstrual phases (Figure 1). Pletzer’s study also found interesting gendered differences in gray matter volume. While men had greater gray matter overall, the volume of gray matter in the prefrontal cortex, the pre-and postcentral gyri, and the supramarginal gyrus of both naturally cycling women and women taking hormonal contraceptives was higher than the volume of gray matter in these areas in men (Figure 2). These areas are involved in decision-making and problem-solving, controlling motor function, and emotional responses. However, the higher amount of gray matter in women in these areas was overshadowed by the larger volume of gray matter in men in the hippocampus, hypothalamus, parahippocampal and fusiform gyri, putamen, pallidum, amygdala, and temporal regions of the brain during the early follicular phase (A), mid-luteal phase (B), and in women taking hormonal birth control (C) (Figure 2). Many of these areas of reduced gray matter are ones of high importance for neurophysical ability and mental health.

Additionally, a study done by Rush University Medical Center showed an association between higher levels of gray matter and better cognitive function (“Everyday Activities Associated with More Gray Matter in Brains of Older Adults”). These findings suggest that taking birth control, and the associated decrease in gray matter, could be directly causing some of the symptoms women on hormonal contraceptives experience, such as brain fog, mood changes, and even anxiety and depression. For example, a smaller hypothalamus, one of the areas of decreased gray matter, is associated with heightened irritability and depression symptoms (“Study Finds Key Brain Region Smaller in Birth Control Pill Users”). Pletzer’s research and the work of others after her on the impact of birth control on structures of the brain represent important first steps in proving a causative relationship between birth control, symptoms associated with it, and structural changes in the brain.

Although this research has made some crucial preliminary steps into researching how taking a daily dose of steroids affects the brains of women taking hormonal contraceptives, the highly complex nature of the brain and its relationship with the regulation of the rest of the body means that further research is necessary. The sheer number of people that this issue affects means that it is essential to continue researching the impacts of this widely used drug. More importantly, knowing the potentially serious negative side effects enables millions of people to make more informed decisions concerning their health and their bodies.

 

Works Cited

Rush University Medical Center. (2018, February 14). Everyday activities associated with more gray matter in brains of older adults: Study measured amount of lifestyle physical activity such as house work, dog walking and gardening. ScienceDaily. Retrieved March 11, 2023 from www.sciencedaily.com/releases/2018/02/180214093828.htm.

Lewis, C. A., Kimmig, A. C. S., Zsido, R. G., Jank, A., Derntl, B., & Sacher, J. (2019). Effects of hormonal contraceptives on mood: a focus on emotion recognition and reactivity, reward processing, and stress response. Current psychiatry reports, vol. 21, no.11, 2019, p 115. PubMed Central, https://doi.org/10.1007/s11920-019-1095-z.

Meyer, Craig H., Kinsley, Elizabeth A. “Women’s Brains on Steroids.” Scientific American, https://www.scientificamerican.com/article/womens-brains-on-steroids/. Accessed 7 Mar. 2023.

Nemoto, Kiyotaka. “[Understanding Voxel-Based Morphometry].” Brain and Nerve = Shinkei Kenkyu No Shinpo, vol. 69, no. 5, May 2017, pp. 505–11. PubMed, https://doi.org/10.11477/mf.1416200776.

Pletzer, Belinda, et al. “Menstrual Cycle and Hormonal Contraceptive Use Modulate Human Brain Structure.” Brain Research, vol. 1348, Aug. 2010, pp. 55–62. ScienceDirect, https://doi.org/10.1016/j.brainres.2010.06.019.

Sharma, Rupali, et al. “Use of the Birth Control Pill Affects Stress Reactivity and Brain Structure and Function.” Hormones and Behavior, vol. 124, Aug. 2020, p. 104783. ScienceDirect, https://doi.org/10.1016/j.yhbeh.2020.104783.

“Study Finds Key Brain Region Smaller in Birth Control Pill Users.” ScienceDaily, https://www.sciencedaily.com/releases/2019/12/191204090819.htm. Accessed 7 Mar. 2023.

What Causes Aging? An Epigenetics Study From The Sinclair Lab May Have an Answer

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Dr. David Sinclair, A.O., Ph.D. Photo from the Sinclair Lab, Harvard Medical School (2023).

Aging, also known as “senescence,” is an inevitable process in all living things. Organisms small and large eventually break down, accumulating enough wear and tear in their cells that ultimately causes the body to stop functioning as a whole. While medicine and lifestyle improvements stave off aging, identifying its fundamental causes has been more challenging. In January 2023, scientists in Dr. David Sinclair’s lab at Harvard Medical School published a paper with experimental evidence supporting what Sinclair calls the “Information Theory of Aging,” where damage to the epigenome can cause aging.

After receiving his Ph.D. in molecular genetics from the University of New South Wales, Sinclair completed his postdoctorate at MIT where he co-discovered the role of sirtuin enzymes in limiting age-related cellular damage in yeast. In addition to teaching genetics and translational medicine at Harvard Medical School since 1999, Sinclair authored the popular book Lifespan: Why We Age – and Why We don’t Have To (2019). His breakthroughs in the science of aging have earned him a great deal of attention from the public eye, resulting in appearances on several popular media outlets, including CBS’s “60 Minutes” and TIME magazine (The Sinclair Lab, 2023).

Sinclair’s newest discovery, published as “Loss of epigenetic information as a cause of mammalian ageing” in January 2023, focused on the role of epigenetics in aging. The title specifies that epigenetic information loss, rather than genetic information loss, is a cause of aging. Genetics refers to the raw molecular information sequences stored in cells as deoxyribonucleic acid (DNA), which is physically condensed inside the nucleus into pairs of chromosomes. The material inside a chromosome is known as “chromatin.” The central dogma of molecular biology states that information in DNA sequences is read by the cell in the form of messenger RNA (mRNA) through transcription, and then ribosomes in the cell read this mRNA to make proteins through translation. DNA sequences that correspond to the production of a specific molecule are genes. The prefix epi- means “on top of,” so “epigenetics” refers to mechanisms that function “above” the molecules of DNA themselves, including reading DNA sequences, regulating gene transcription, and repairing mutated DNA. Like the DNA sequence, epigenetic changes are inheritable from parents to offspring.

The differences between genetics and epigenetics influence cellular reaction to damage. Damage to genes causes mutations, which are changes in the sequence of the DNA of that gene. Cells have mechanisms of repairing mutated DNA, but failure of these mechanisms can lead to cell death, or worse, cancer. Some DNA mutations, like those where a nucleotide is deleted, are irreversible.

By contrast, epigenetic mechanisms are more easily reversed. One epigenetic mechanism is DNA methylation, where a methyl group (-CH3) is added to a cytosine nucleotide by the DNA methyltransferase enzyme. This extra functional group blocks transcription factors from binding to promoter regions nearby the methylated cytosine, in effect “silencing” the gene as it cannot be transcribed into mRNA. DNA methylation is important for differentiating cells into specific cell types by enabling cells to only express the most pertinent genes while still containing the entire genome (Moore et al., 2012). DNA methylation is reversible with the help of TET dioxygenase enzymes (Wu and Zhang, 2014). Geneticists have found DNA methylation to be a way to assess molecular aging in cells as a sort of “epigenetic clock”. By analyzing methylation patterns of the genome (the “methylome”), scientists can find the biological age as well as the rate of aging in an organism’s cells (Hannum et al., 2012).

Figure 1: Methyl groups attached to cytosine bases in a gene block the enzyme RNA polymerase from binding to the promoter region of a gene, preventing transcription. Adapted from BOGOBiology (2017)

To investigate how changes to the epigenome affect aging in mice, Sinclair used a mouse system with induced changes to the epigenome (ICE). The genetically modified mice had a higher frequency of double-strand breaks (DSBs) in the DNA, which cause changes in the epigenome as cells are required to use their mechanisms of DNA repair more often . Sinclair’s method reduced the frequency of mutations by breaking the DNA strands in a way that left more whole unpaired nucleotides in the severed strand, making it more difficult for the cell to repair the DNA strand with a different sequence than before. While ICE mice had no significant difference in mutation frequencies versus control mice, DSBs in specific locations of the genome were observed as expected (Yang et al., 2023). Thus, any apparent changes in aging in the ICE mice of this study could be ascribed to the epigenetic DSB changes rather than mutations.

Figure 2: ICE treated mice after 10 months appear to have the physical hallmarks of aging, such as hair loss and reduced body mass, early compared to CRE control mice (Yang et. al. 2023).

The haggard appearance of the ICE 10 month old mice confirmed the early aging effects of the epigenetic changes (Figure 2). At the molecular level, analysis of DNA methylation at genome sites associated with age showed that ICE cells were approximately 1.5 times “older” than the control cells. With this artificially increased age came physiological consequences. ICE mice showed diminished short-term memory retention compared to Cre-control mice, as assessed by fear conditioning tests, and the ICE mice performed half as well in a Barnes Maze test as control, indicating decreased long-term memory. Additionally, ICE mice had decreased muscle mass and grip strength after 16 months. The authors attributed the cause of this accelerated aging to increased “faithful DNA repair” from the induced DSB breaks in the ICE mice, meaning that there were not significant mutations in the repair of DSBs.(Yang et al., 2023). During DSB repair, chromatin modifying factor proteins activate and move within a cell in a process known as “relocalization,” with repeated activation of this process known to cause epigenetic changes that silence genes normally expressed in young mice. Sinclair’s lab hypothesized that the relocalization of chromatin modifiers that occurs from repeated DSB repair associated with induced epigenetic changes lead to a gradual loss of cellular function associated with aging (Yang et al., 2023).

It may seem ironic that DNA strand break repair, a process meant to keep cells functioning when critical genes are damaged, is part of what ultimately causes the death of organisms. The fact that the mechanism implemented is epigenetic rather than genetic suggests that the effects of ageing may be reversible, like epigenetic mechanisms. In fact, Sinclair has shown that it is possible to partially undo the damaging effects of aging: after inducing OSK expression, which is a set of proteins known as “Yamanaka factors,” ICE mice exhibited some signs of rejuvenation in their eyes, kidneys, and muscles. Yamanaka factors like OSK are important in the fields of aging and regenerative medicine because they are keys to the synthesis of induced pluripotent stem cells, where somatic cells can become stem cells and potentially re-differentiate into other cell types (Takahashi and Yamanaka, 2006). The OSK treatment decreased the expression of age-associated markers in the kidney and muscle cells of the mice (Yang et al., 2023).

Sinclair’s experiments have shown the epigenome to be a key front in the investigation of aging, as the reversibility of changes to the epigenome can allow it to be a more accessible interface for scientists to interact with. The plasticity of the epigenome as demonstrated from the ability of Yamanaka factors to reverse the molecular indicators of aging mice show that there may be hope for science to bring this phenomenon to human epigenomes. Indeed, the news of reversing aging in mice made rounds in the media when Sinclair’s paper was published earlier this winter, and for good reason.

Works Cited

Al Aboud, N. M., Tupper, C., & Jialal, I. (2022). Genetics, Epigenetic Mechanism. In StatPearls. StatPearls Publishing. http://www.ncbi.nlm.nih.gov/books/NBK532999/

Bannister, A. J., & Kouzarides, T. (2011). Regulation of chromatin by histone modifications. Cell Research, 21(3), Article 3. https://doi.org/10.1038/cr.2011.22

BOGObiology (Director). (2017, October 11). Epigenetics: Nature vs. Nurture. https://www.youtube.com/watch?v=Q8BMP6HDIco

CDC. (2022, August 15). What is Epigenetics? | CDC. Centers for Disease Control and Prevention. https://www.cdc.gov/genomics/disease/epigenetics.htm

David Sinclair | The Sinclair Lab. (n.d.-a). Retrieved March 5, 2023, from https://sinclair.hms.harvard.edu/people/david-sinclair

Fernandez, A., O’Leary, C., O’Byrne, K. J., Burgess, J., Richard, D. J., & Suraweera, A. (2021). Epigenetic Mechanisms in DNA Double Strand Break Repair: A Clinical Review. Frontiers in Molecular Biosciences, 8, 685440. https://doi.org/10.3389/fmolb.2021.685440

Gilbert, S. F. (2000). Methylation Pattern and the Control of Transcription. Developmental Biology. 6th Edition. https://www.ncbi.nlm.nih.gov/books/NBK10038/

Hannum, G., Guinney, J., Zhao, L., Zhang, L., Hughes, G., Sadda, S., Klotzle, B., Bibikova, M., Fan, J.-B., Gao, Y., Deconde, R., Chen, M., Rajapakse, I., Friend, S., Ideker, T., & Zhang, K. (2013). Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Molecular Cell, 49(2), 359–367. https://doi.org/10.1016/j.molcel.2012.10.016

Jin, B., Li, Y., & Robertson, K. D. (2011). DNA Methylation. Genes & Cancer, 2(6), 607–617. https://doi.org/10.1177/1947601910393957

Kulis, M., & Esteller, M. (2010). 2—DNA Methylation and Cancer. In Z. Herceg & T. Ushijima (Eds.), Advances in Genetics (Vol. 70, pp. 27–56). Academic Press. https://doi.org/10.1016/B978-0-12-380866-0.60002-2

Molecules discovered that extend life in yeast, human cells. (n.d.). EurekAlert! Retrieved March 5, 2023, from https://www.eurekalert.org/news-releases/664233.

Moore, L. D., Le, T., & Fan, G. (2013). DNA Methylation and Its Basic Function. Neuropsychopharmacology, 38(1), 23–38. https://doi.org/10.1038/npp.2012.112

Offord, Catherine. Two research teams reverse signs of aging in mice. (n.d.). Retrieved March 14, 2023, from https://www.science.org/content/article/two-research-teams-reverse-signs-aging-mice.

Takahashi, K., & Yamanaka, S. (2006). Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell, 126(4), 663–676. https://doi.org/10.1016/j.cell.2006.07.024

What is Epigenetics? The Answer to the Nature vs. Nurture Debate. (n.d.). Center on the Developing Child at Harvard University. Retrieved March 5, 2023, from https://developingchild.harvard.edu/resources/what-is-epigenetics-and-how-does-it-relate-to-child-development/

Wu, H., & Sun, Y. E. (2009). Reversing DNA Methylation: New Insights from Neuronal Activity–Induced Gadd45b in Adult Neurogenesis. Science Signaling, 2(64), pe17–pe17. https://doi.org/10.1126/scisignal.264pe17

Wu, H., & Zhang, Y. (2014a). Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions. Cell, 156(0), 45–68. https://doi.org/10.1016/j.cell.2013.12.019

Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., Chew, Y. C., Guo, W., Yang, X., Maybury-Lewis, S., Tian, X., Ross, J. M., Coppotelli, G., Meer, M. V., Rogers-Hammond, R., … Sinclair, D. A. (2023). Loss of epigenetic information as a cause of mammalian aging. Cell, 186(2), 305-326.e27. https://doi.org/10.1016/j.cell.2022.12.027

 

Ecology, Policy, and Science Communication: The Story of Biologist and Activist Erika Zavaleta

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Erika Zavaleta is an interdisciplinary scientist that has worked her career to make her research accessible, has broken down barriers for biologists of color, and is seen by many to be a trailblazer in her field. Zavaleta is a community and ecosystem biologist at the University of California Santa Cruz (UCSC) that focuses on global and regional environmental change, ecosystem functioning, and effective stewardship. She uses environmental policy, economics, anthropology, and outreach as tools to communicate her research to a larger audience as a scientist that aims to make the field accessible. She received her bachelor’s and master’s in anthropology and Ph.D. in biological sciences at Stanford University. Dr. Zavaleta is a Howard Hughes Medical Institute Professor in the Ecology and Evolutionary Biology department at UCSC. She is an appointed California Fish and Game Commission science advisor, an Ecological Society of America (ESA) “Excellence in Ecology Scholar,” ESA fellow, and a fellow of the California Academy of Sciences. Dr. Zavaleta has also co-authored over 75 papers and book chapters in the fields of conservation, ecology, and social sciences. In 2021, she received the Commitment to Human Diversity in Ecology Award from ESA due to her devotion to highlighting the voices of low-income, Indigenous, Black, and Latino backgrounds in the ecology and conservation field.

Dr. Zavaleta’s Conservation Science and Solutions Lab is interested in questions related to ecological responses to climate change, changes in biodiversity due to environmental variability, and conservation-based approaches to mediate these impacts. Some research projects currently taking place by her lab members are the impacts of land and water use changes on bat ecological communities, the impacts of community-led forestry conservation efforts in Brazil and Nepal, and the effectiveness of current conservation efforts in response to climate change. Through this research, Zavaleta’s group works to act as a link between ecology theory and research to develop and recommend effective conservation and management practices. The lab places an emphasis on collaborating with community partners, approaching research through a multidisciplinary lens, and furthering initiatives that promote inclusivity in the field of conservation and biology.

Zavaleta’s lab has supported initiatives that she founded at UCSC that provide mentorship and support for historically excluded scientists including the Doris Duke Conservation Scholars Program and the Center to Advance Mentored, Inquiry-Based Opportunities (CAMINO) in 2013 and 2017 respectively. The Doris Duke Conservation Scholars Program (DDCSP) is a national fellowship that aims to increase accessibility to the conservation field, mainly focusing on providing training and research experience for underrepresented students in science. DDCSP is carried out by five partners including the DDCSP Collaborative, the University of California at Santa Cruz, the University of Michigan, the University of Washington, and the Yale School of the Environment. CAMINO works directly with students at UCSC and provides academic and professional assistance from graduate and faculty mentors. The center pairs CAMINO scholars with funded internships where they can gain research experience regardless of their previous internships in the ecology and conservation field. Dr. Zavaleta currently serves as a faculty director for both of these programs.

Most recently, Zavaleta established a training called FieldFutures with biologist Dr. Melissa Cronin that emphasizes the importance of field-based education and research that prevent sexual harassment for scientists in the ecology and conservation field. As said on their website, “studies have shown that 64% of surveyed field researchers experienced harassment—and one in five experienced assault— while conducting fieldwork. Women, people of color, LGBTQIA+ people, and people with other marginalized identities are more likely to experience these problems.” Since fieldwork directly places scientists of all genders at greater risk of sexual violence, FieldFutures works to provide workshops that identify ways to increase prevention, provides a space for scientists to get hands-on experience in dealing with these situations, and offers protocols that can be used in the field. The “Futures” component of their name symbolizes their vision of a future for fieldwork free of sexual assault and harassment—and they are working towards getting closer to this prospect with each training.

I write about Dr. Zavaleta as a fellow Latina and future conservation biologist who not only admires her research and intellectual contributions to the field but also her dedication to making the field one that welcomes people like me. During my first and second summers as an undergraduate, I spent them as a Doris Duke Conservation Scholar at the University of California Santa Cruz (UCSC). I have heard first-hand Dr. Zavaleta’s passion for finding climate solutions, diversifying the field, and using public policy to enact impactful environmental legislation. She has not only shown her commitment to increasing diversity in the field, but she has also asserted her support for social movements around the country and pledged to incorporate their missions in her own work. In 2020 in a letter as director of DDCSP, she contended that

Science and conservation have long marginalized Black and brown voices, faces, and talents. The demographics of our country tell us that there should be five times as many scientists and professionals of color in ecology, evolution, and conservation as there are. The absence of diverse leadership in our field sustains this gap unless all of us work for change. We all have to speak up and act when we see racial inequities affect our peers, colleagues, students, and communities.

As a beneficiary of the initiatives she has passionately poured time and energy into, I can attest that programs like DDSCP have helped me and my peers realize that scientists like us—first-generation college students and people of color— can thrive in this field and use our experiences to connect to a greater audience in the scientific field. I wish to be as intentional and inclusive as Dr. Zavaleta moving forward as a scientist, educator, and science communicator and I hope that more people in this career follow her lead.

The Battle of the Medications: The Connection Between Antidepressants and Antibiotic Resistance in Bacteria

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         The consumption of antidepressant medications has skyrocketed in recent decades, reaching more than 337 million prescriptions written in 2016 in the United States alone (Wang et. al. 2019). For many individuals, these drugs are critical to maintaining everyday health as they treat many life-threatening psychiatric disorders. While their exact mechanisms differ, these medications travel in the bloodstream to the brain where they are able to influence the release of chemicals known as neurotransmitters that generate emotional states. However, while their intended target is the brain, these drugs continue to circulate throughout the body, thereby interacting with other organs and structures (Wang et. al. 2019).

         In their 2019 study, researchers led by Iva Lukic used data indicating the presence of antidepressants in the digestive tract to investigate the effect of these medications on the gut microbiome. After treating mice with different types of antidepressants, the team noticed a change in the types of bacteria present within the gut when compared to controls (Lukic et. al. 2019). This discovery that antidepressants could impact the types of bacteria present within the body ultimately led researcher Jianhua Guo to question the additional effects that these medications could have on bacteria. As antibiotics have also been shown to affect the composition of the gut microbiome, Guo began by investigating if the antidepressant fluoxetine could help Escherichia coli cells survive in the presence of various antibiotics. After finding that exposure to this medication did increase E. coli’s resistance to antibiotic treatments, Guo decided to expand his hypothesis to examine the overall connection of antidepressant usage with antibiotic resistance in bacteria.

        Collaborating with researchers Zue Wang and Zhigang Yue, Guo’s lab began by choosing five major types of antidepressant medications: sertraline, escitalopram, bupropion, duloxetine, and agomelatine. These medications differ in the ways that they prevent the reuptake of serotonin and norepinephrine in the brain, thereby allowing the researchers to examine the effects of various types of antidepressants that may be prescribed to patients. Then, E. coli bacteria were added to media containing varying concentrations of these five antidepressants. Once these cells were treated with antidepressants, the researchers began to test the cells’ resistance against antibiotics. In order to accurately reflect antibiotic use in the real world, the tested antibiotics covered the six main categories of antibiotic medications available on the market. The antidepressant-treated bacteria were then swabbed onto plates containing one of the tested antibiotics to observe cell growth. Based on the growth present on these plates, the researchers were able to estimate the incidence rate of bacterial resistance of E. coli bacteria treated with different antidepressants.

         Through this experiment, the lab observed that E. coli cells grown in sertraline and duloxetine, two antidepressants that inhibit the reuptake of serotonin, exhibited the greatest number of resistant cells across all the tested antibiotics (fig. 1). They also noted that E. coli cells exhibiting resistance to one antibiotic often demonstrate some level of resistance to other antibiotics as well. After detecting a correlation between antibiotic-resistance development and exposure to antidepressants, the lab tested the concentration dependence of this effect. While lowering the concentration of antidepressants seemed to decrease the amount of resistant E. coli cells, resistant cells continued to appear on the plates over time, suggesting that lowering antidepressant dosages only prolongs the process of developing antibiotic resistance.

Figure 1: These graphs showcase the change in the number of antibiotic-resistant E. coli cells after exposure to antidepressants over sixty days. The title of each graph indicates the tested antibiotic while the colored trend lines on the graph represent one of the five, tested antidepressants. On the y-axis of each graph, the fold change measurement is used to describe the change in the number of resistant cells that develop over time. As demonstrated by the purple and yellow trend lines, duloxetine and sertraline are associated with the greatest development of resistant cells to each of the four represented antibiotics. (Adapted from Wang et. al. 2019)

         After analyzing this data, the researchers were confronted with a question: what about anti-depressants led to the development of antibiotic resistance in bacteria? To examine this question, the lab used flow cytometry to examine what was happening within the bacterial cells. This lab technique uses a fluorescent dye that binds to specific intercellular target molecules, thereby allowing these components to be visualized. After applying this dye to resistant cells grown on the antibiotic agar plates, the researchers noticed the presence of specific oxygen compounds known as reactive oxygen species (ROS). Unstable ROS bind to other molecules within a cell, disrupting normal functioning and causing stress. Elevated cellular stress levels have been shown to induce the transcription of specific genes in bacteria that produce proteins to help return the cell to normal functioning (Wang et. al. 2019).

         ROS molecules have been shown to induce the production of efflux pumps in bacteria, leading the lab to investigate if these structures were involved in the antibiotic resistance of E. coli cells. Efflux pumps are structures in the cell membrane of a protein that pump harmful substances out of the cell. The lab mapped the genome to look for activated genes associated with the production of this protein. According to the computer model, more DNA regions in resistance bacteria coding for efflux pumps were active than in the Wild Type. The researchers then concluded that efflux pumps were being produced in response to antidepressant exposure. These additional efflux pumps removed antibiotic molecules in resistant E. coli, thereby allowing them to survive in the presence of lethal drugs.

         The antibiotic resistance uncovered in this study was significant and persistent. Even one day of exposure to antidepressants like sertraline and duloxetine led to the presence of resistant cells. Furthermore, the team demonstrated that these antibiotic-resistant capabilities often do not disappear over time; rather, they are inherited between generations of bacteria, leading to the proliferation of dangerous cells unsusceptible to available treatments. The next logical step towards validating the connection between antidepressants and antibiotic resistance would include studying the gut microbiomes of patients taking anti-depressants to look for antibiotic-resistant bacteria.

         This study reveals a novel issue that must be attended to.  In 2019, 1.27 million deaths worldwide could be directly attributed to antibiotic-resistant microbes, a number expected to grow to 10 million by the year 2050 (O’Neill 2023). These “superbugs” present a dangerously growing reality. If the correlation between antidepressant use and antibiotic resistance is left uninvestigated, superbugs will likely continue to develop even as antibiotic use is regulated and monitored to battle them. Only by taking this connection seriously will researchers be able to fully grapple with and battle the growing antibiotic resistance trends, thereby preventing common infections from becoming death sentences. 

 Sources:

CDC. (2022, July 15). The biggest antibiotic-resistant threats in the U.S. Centers for Disease Control and Prevention. https://www.cdc.gov/drugresistance/biggest-threats.html

Drew, L. (2023). How antidepressants help bacteria resist antibiotics. Nature. https://doi.org/10.1038/d41586-023-00186-y

Jin, M., Lu, J., Chen, Z., Nguyen, S. H., Mao, L., Li, J., Yuan, Z., & Guo, J. (2018). Antidepressant fluoxetine induces multiple antibiotics resistance in Escherichia coli via ROS-mediated mutagenesis. Environment International, 120, 421–430. https://doi.org/10.1016/j.envint.2018.07.046 

Lukić, I., Getselter, D., Ziv, O., Oron, O., Reuveni, E., Koren, O., & Elliott, E. (2019). Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior. Translational Psychiatry, 9(1), 1–16. https://doi.org/10.1038/s41398-019-0466-x

O’Neill, J. (Ed.). (2016). Tackling Drug-Resistant Infections Globally: Final Report and Recommendations. The Review on Antimicrobial Resistance. https://amr-review.org/sites/default/files/160518_Final%20paper_with%20cover.pdf

Thompson, T. (2022). The staggering death toll of drug-resistant bacteria. Nature. https://doi.org/10.1038/d41586-022-00228-x

Wang, Y., Yu, Z., Ding, P., Lu, J., Mao, L., Ngiam, L., Yuan, Z., Engelstädter, J., Schembri, M. A., & Guo, J. (2023). Antidepressants can induce mutation and enhance persistence toward multiple antibiotics. Proceedings of the National Academy of Sciences, 120(5), e2208344120. https://doi.org/10.1073/pnas.2208344120

The Anti-cancer and Antimicrobial Activity Associated with Sea Sponge Extracts

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Toxic Negombata magnifica sponge at Shaab el Erg reef (Red Sea, Egypt) (Alexander Vasenin, 2010)

With an ever-increasing demand for novel drug therapies, scientists are turning to marine organisms as a source of bioactive chemicals, whose properties can be harnessed for medical development. One such organism is a rather unlikely candidate: the sea sponge (phylum Porifera). Lacking a brain and a central nervous system, sea sponges rely upon specialized cells to perform their required functions. As result of their structural simplicity and sedentary existence, these ancient creatures have evolved to protect themselves against predation by means of toxic chemicals, which can prove similarly lethal to cancer cells and microbes in humans (El-Naggar et. al., 2022). A study published in Applied Sciences examined the properties of two sponge species, Negombata magnifica (finger sponge) and Callyspongia siphonella (tube sponge). This drew from the scientists’ previous study, which had indicated that all eight extracts of finger-sponge and tube-sponge studied promoted the death and inhibited the growth of cells associated with liver, breast, and colorectal cancer (El-Naggar et.al., 2022).

Whereas the earlier study had used four different solvents in the production of sponge extracts, this newerstudy examined only the methanolic extracts of Negombata magnifica (NmE) and Callyspongia siphonella (CsE). Sponge specimens were collected from the Dahab region on the Sinai Peninsula and soaked with methanol to obtain NmE and CsE. One microliter of each extract was examined for its contents of bioactive compounds via a Gas Chromatography–Mass Spectrometer (GC–MS analysis). Out of the 117 chemical compounds revealed by GC­–MS analysis, 37 were determined to be bioactive. These compounds were tested against cultured liver, breast, and colorectal cancer cell lines and ten test microorganisms representing filamentous fungi, yeasts, and Gram-positive and Gram-negative bacteria (El-Naggar et.al., 2022).

While CsE showed no antiproliferative action against the cancer cells, NmE dose-dependently impeded their growth: it induced cell cycle arrest in the liver cancer lines by inhibiting the cell division protein CDK6. It also halted mitotic progress in all three cell types by inhibiting D1 and E1 cyclins, which regulate progression through the cell cycle (Alao, 2007). Furthermore, NmE activated reactive oxygen species (ROS) production in liver cancer cells and induced apoptosis in all cell lines, via Bax (a pro-apoptotic regulatory protein) and caspase-3 (a death protease that cleaves cellular proteins) increase and BCL2 (an anti-apoptotic regulatory protein) decrease (Blanco and García-Sáez, 2018) (Ponder and Boise, 2019; Youle and Strasser, 2002). Regarding antimicrobial activity, CsE was shown to be a superior antimicrobial agent by acting against six microbial strains, whereas NmE reacted favorably to only two strains (El Naggar et. al., 2022).

Looking forward, the anti-cancer properties of NmE indicate its potential for development as an anti-cancer drug, while CsE is a promising source for antimicrobial drug discovery. Additionally, several of the compounds’ bioactivity is neither anti-cancer nor antimicrobial—for instance, both fenretinide and ethyl iso-allocholate have been attributed to anti-COVID-19 activity (Orienti, et. al., 2020; Poochi et. al., 2020). Ultimately, given that approximately eighty of the compounds have yet to be attributed to anti-cancer or anti-microbial mechanisms, the study emphasizes the importance of looking to Earth’s oceans as potential sources of bioactive compounds and harnessing the biological potential of marine organisms in the development of novel drug therapies.

References:

Alao, J.P. The regulation of cyclin D1 degradation: roles in cancer development and the potential for therapeutic invention. Mol Cancer 6, 24 (2007). https://doi.org/10.1186/1476-4598-6-24

El-Naggar, H. A., Bashar, M. A. E., Rady, I., El-Wetidy, M. S., Suleiman, W. B., Al-Otibi, F. O., Al-Rashed, S. A., et al. (2022). Two Red Sea Sponge Extracts (Negombata magnifica and Callyspongia siphonella) Induced Anticancer and Antimicrobial Activity. Applied Sciences, 12(3), 1400. MDPI AG. Retrieved from http://dx.doi.org/10.3390/app12031400

Orienti, I.; Gentilomi, G.A.; Farruggia, G. Pulmonary Delivery of Fenretinide: A Possible Adjuvant Treatment in COVID-19. Int. J. Mol. Sci. 2020, 21, 3812.

Peña-Blanco, A., & García-Sáez, A. J. (2018). Bax, Bak and beyond – mitochondrial performance in apoptosis. The FEBS journal, 285(3), 416–431. https://doi.org/10.1111/febs.14186

Ponder, K.G., Boise, L.H. (2019). The prodomain of caspase-3 regulates its own removal and caspase activation. Cell Death Discovery 5, 56. https://doi.org/10.1038/s41420-019-0142-1

Poochi, S.P.; Easwaran, M.; Balasubramanian, B.; Anbuselvam, M.; Meyyazhagan, A.; Park, S.; Bhotla, H.K.; Anbuselvam, J.; Arumugam, V.A.; Keshavarao, S.; et al. Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS-CoV-2 main protease and ACE2 protein. Food Front. 2020, 1, 168–179.

Youle, R., Strasser, A. (2008). The BCL-2 protein family: opposing activities that mediate cell death. Nat Rev Mol Cell Biol 9, 47–59. https://doi.org/10.1038/nrm2308

 

Examining the work of 2022 Nobel Prize in Physiology or Medicine Laureate Svante Pääbo

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Svante Pääbo. Max Planck Institute for Evolutionary Anthropology. Retrieved November 6, 2022. https://www.eva.mpg.de/genetics/staff/paabo/#c28042

 

 

            Have you ever wondered how humans lived on Earth before the first major civilizations formed? It turns out that we were not the only hominid species on Earth in those times: other relatives of humans, such as Neanderthals, lived and intermingled with humans. The genetic relationship between humans and these hominids is a subject of great interest to the scientific community, since the traits of our species’s distant relatives can explain genetic phenomena in modern humans. On October 3rd, 2022, the Nobel Prize Committee announced they would be awarding Swedish geneticist Svante Pääbo the prize in Physiology or Medicine “for his discoveries concerning the genomes of extinct hominins and human evolution” (NobelPrize.org, 2022). One of Dr. Pääbo’s most significant achievements leading to his prize was sequencing the Neanderthal genome. A closer look at Dr. Paabo’s work in the field of genetics elucidates how his work led to the foundation of the field of paleogenetics.

            Originally a student of Egyptology, Dr. Pääbo received a Ph.D. in molecular immunology from the University of Uppsala in 1986, but his interest in the former remained: his first Nature publication was about cloning ancient DNA from ancient Egyptian mummies (Gruber Foundation, 2022; Pääbo, 1985). Despite the possibility of degradation or contamination from the mummification process itself and from the millenia that passed since, he found that surface-level tissue samples in a one-year old boy yielded DNA that could be cloned using DNA recombination techniques (Pääbo, 1985). Since publishing this, Dr. Pääbo has made a career of refining techniques that allow the sequencing of genomes from many other types of ancient humans or hominins.
            Dr. Pääbo’s discoveries have advanced the field of paleogenomics, the study of genomes belonging to extinct species. Of primary concern is recovering ancient DNA (aDNA) from specimens in ideal physical conditions, as in dry and high-salinity environments, since in those environments long DNA molecules will not degrade as fast (Lan, 2019). Then, with techniques such as polymerase chain reaction (PCR) and Sanger sequencing, the aDNA molecules can be cloned and amplified to allow scientists to study copies of genes without needing more of the original sample (Lan, 2019). Storing individual genes from these recovered genomes in bacteria allows scientists to form “libraries” of specimen genomes. The contents of these genomic libraries can then be analyzed to fully sequence the genome of the specimen. After sequencing the genome of one species, scientists can then compare the genome to a related species to identify the differences (Genome.gov, 2020).
            In 2010, Dr. Pääbo and colleagues published “A Draft Sequence of the Neandertal Genome,” where they collected and analyzed aDNA from three individual Neanderthal specimens in Europe using the techniques described above (Green, 2010). Using data from this draft genome of the Neanderthal, they identified key genetic differences between modern humans and ancestral species. In particular, there were mutations in certain genes associated with disorders in modern humans, such as in RUNX2. Mutations of the RUNX2 gene can lead to cleidocranial dysplasia, a disorder that causes protruded frontal bones on the cranium and bell-shaped rib cages. These symptoms resemble the known skeletal morphologies of Neanderthals, which gives researchers a clue as to how humans and Neanderthals diverged genetically from each other (Green, 2010).
            The discoveries that Dr. Pääbo made in the field of paleogenomics have brought to light how molecular differences between Neanderthals and humans translate to their defining features as species. With the techniques that he developed, scientists can now examine the genomes of specimens thousands of years old without fear of contamination. Future developments in the field of paleogenomics could be expanding upon the links between Neanderthal DNA in human genomes and risk factors for diseases like COVID-19, which Dr. Pääbo himself has contributed to (Zeberg & Pääbo, 2021). Svante Pääbo’s work will help scientists uncover further links between our distant ancestors and modern humans for decades to come.



Works Cited:

Callaway, E., & Ledford, H. (2022). Geneticist who unmasked lives of ancient humans wins medicine Nobel. Nature, 610(7930), 16–17. https://doi.org/10.1038/d41586-022-03086-9


DNA Sequencing Fact Sheet. (n.d.). Genome.Gov. Retrieved November 6, 2022, from https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Fact-Sheet


Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., Hansen, N. F., Durand, E. Y., Malaspinas, A.-S., Jensen, J. D., Marques-Bonet, T., Alkan, C., Prüfer, K., Meyer, M., Burbano, H. A., … Pääbo, S. (2010b). A Draft Sequence of the Neandertal Genome. Science, 328(5979), 710–722. https://doi.org/10.1126/science.1188021


Lan, T., & Lindqvist, C. (2019). Paleogenomics: Genome-Scale Analysis of Ancient DNA and Population and Evolutionary Genomic Inferences. In O. P. Rajora (Ed.), Population Genomics: Concepts, Approaches and Applications (pp. 323–360). Springer International Publishing. https://doi.org/10.1007/13836_2017_7


Pääbo, S. (1985). Molecular cloning of Ancient Egyptian mummy DNA. Nature, 314(6012), Article 6012. https://doi.org/10.1038/314644a0

The Nobel Prize in Physiology or Medicine 2022. (n.d.-a). NobelPrize.Org. Retrieved October 16, 2022, from https://www.nobelprize.org/prizes/medicine/2022/advanced-information/


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The Nobel Prize in Physiology or Medicine 2022. (n.d.-c). NobelPrize.Org. Retrieved October 16, 2022, from https://www.nobelprize.org/prizes/medicine/2022/paabo/facts/

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