Bowdoin Science Journal

Biology

Breakthrough in Gene Sequencing and Identification of Leukemia-causing Genes in Iran

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A research group based in Iran conducted a study to confirm the legitimacy of gene sequencing technology for discovering Chronic Myeloid Leukemia causing genes within three pre-existing cancer patients. Chronic Myeloid Leukemia (CML) is an example of a monoclonal disease, meaning deriving from a single cell in this blood cell (hematopoietic).  CML represents around 15% of Leukemia in adults. Leukemia represents the most common blood cancer for adults older than 55. The blast cycle is the stage in chronic leukemia where tiredness, fever, and enlarged spleen are present. A blast crisis occurs when 20% of all blood or bone marrow has blasts or immature white blood cells. These blasts multiply uncontrollably, causing a blockage and stopping the production of red blood cells and platelets, which are necessary for survival. White cell crowding red blood cells often causes a lower immune system. This article focuses on using integrated genomic sequences to access common gene variants associated with CML, to understand the fundamental mechanisms behind the blast crisis.

Researchers used the Whole Exome Sequences (WES): integrated sequencing, chromosome sequences, and Rna sequences. Using a blood sample from the blast cycle patients, they used WES technology to identify modified, deleted, or incorrectly copied genes. Genes have extraordinary power over the way our body regulates. Sometimes cancer occurs when genes do not work as they are intended to. There are five classes of cancer-causing genes. Mutations in genes change how they activate other cells. A mutation in the process of spreading information through signal pathway components can lead cells to multiply erratically. Another class is transcription factors; proteins bind to a part of DNA to start or stop replication.  If there are modifications within those repressor/activator genes, that could lead to an unregulated abundance of cells—unsuppressed replication results in Tumors due to unregulated cell growth. It is common for some mutations in the replication process, but some proteins repair the genes; sometimes, if a gene gets mis-replicated, it can lead to other classes. 

CML cells are derived from the bone marrow and are progenitor cells, meaning they can turn into white, red blood cells or platelets, depending on the body’s purpose. The researcher’s goal with using WES on these pre-existing blast crisis patients was to discover essential variants and find similarities and differences with their gene makeup.  Researchers then divided their findings into PIF ( potentially significant findings) and PAFs(potentially actionable results). Using WES detected, 16 PIFS affected all five known classes of cancer-causing genes.  

Researchers conducted integrated sequencing on three patients using an in-house filtering algorithm to discover how leukemia develops. Discover that combining Integrated genomic sequencing and Rna sequencing is an accurate way to find and confirm leukemia variants. All patients are based in Iran; patient one was a 66-year-old female whose blast level was 25%. Patient 2 is a 55-year-old female whose blast level is 35%. And the third patient was a 45-year-old male with a 40% blast level. The percentage of blast level indicates how many white blood cells make up entirely of the person’s blood. The higher the blast level, the more immunocompromised you become, as CML’s white blood cells block up the flow of red blood cells stopping your immune system’s response. Using WES and RNA sequencing, researchers discovered multiple patient similarities and differences. Both patients one and two have abnormal karyotypes, or a person’s complete set of chromosomes,  in the form of a Philadelphia Chromosome. A Philadelphia Chromosome is when the 9 and 22 chromosomes break off and pair. A direct consequence is that chromosome 22 will be minimal, resulting in CML. Patients two and three both had multiple chromosome deletions, duplications, and modifications, all with prior research that points to the contribution in Leukemia.

 

The study affirms the importance of being able to model and analyze CML’s leukemogenesis process in terms of more timely treatment and effective management of blood-borne illness. Using gene-sequencing technology, CML’s transition to the blast phase can be detected more accurately and effectively than in previous studies.  The researchers identified variants in all classes, with an important finding that a  shared deletion was a Transcription Factor 17p, which observed that 45% of blast phase patients have such defect or mutation of a gene, creating a marker of identification and possible treatment. This study points to the importance of identifying and developing more speed-lined processes that make detection more accurate and timely. 

 

Kazemi-Sefat, Golnaz Ensieh (12/2022). “Integrated genomic sequencing in myeloid blast crisis chronic myeloid leukemia (MBC-CML), identified potentially important findings in the context of leukemogenesis model”. Scientific reports (2045-2322), 12 (1), p. Article.

The Kleptomania Connection between Serotonin and Stealing

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Although many people steal in response to economic hardship, either perceived or actual, some individuals only steal to satisfy a powerful urge. These individuals may have an impulse control disorder known as kleptomania. People with kleptomania experience a sense of relief from stealing, so they steal to get rid of their anxiety (Talih, 2011). The prevalence of kleptomania in the U.S. is estimated to be 6 people per 1000, which is equivalent to more than 1.5 million kleptomaniacs in the U.S. population ​​(Aboujaoude et al., 2004).

What exactly causes this impulse to steal? Kleptomania has a range of biological, psychological, and sociological risk factors. One of the main biological factors has to do with neurotransmitters, such as serotonin (Sulthana, 2015). Serotonin plays an important role in our bodies, contributing to emotions and judgment, and low serotonin levels have been linked to impulsive and aggressive behaviors (Williams, 2002). The serotonin system is also thought to be involved in “increased cognitive impulsivity,” as has been observed in individuals with a higher number of kleptomania symptoms (Ascher & Levounis, 2014).

Throughout the nervous system, serotonin transporters (SERT) take up serotonin that is released from neurons (Rudnick, 2007). These transporters can also be found on blood platelets and take up serotonin from the blood plasma (Mercado & Kilic, 2010). We can study these particular transporters to better understand the levels of serotonin in one’s blood and how that relates to their level of impulsiveness.

A 2010 study looked into the relationship between the platelet serotonin transporter, impulsivity, and gender. They found that while women were, in general, more impulsive than men, there was only a positive correlation between the number of transporters and impulsivity in men. This means that higher amounts of platelet serotonin transporters and lower levels of serotonin are related to more impulsivity in men, but not in women. It was also found that higher amounts of SERT transporters were linked to more “aggressive” behaviors. The authors came to the conclusion that, even though women were found to display more impulsivity than men, serotonin plays a larger role in impulsivity with men than it does with women (Marazziti et al., 2010).

Understanding the relationship between serotonin and impulsivity with kleptomania has helped pioneer specific treatments, including Selective Serotonin Reuptake Inhibitors (SSRIs). Impulsivity is linked to low levels of serotonin, so SSRIs fix this by limiting the reuptake of serotonin through the blockage of serotonin transporters, leading to the buildup of serotonin in the synapse (Sulthana, 2015). There is no cure for kleptomania, but SSRIs help to control the impulse to steal. 

Overall, kleptomania is a secretive disorder, for which many people don’t seek help due to the legal system and the social stigma around theft. Thus, very little is known about what causes kleptomania, but trying to understand it through its link with neurotransmitters has uncovered potential causes and helped develop treatments. 

 

References

Ascher, M. S., & Levounis, P. (Eds.). (2014). The behavioral addictions. American Psychiatric Publishing.

Aboujaoude, E., Gamel, N., & Koran, L. M. (2004a). Overview of kleptomania and phenomenological description of 40 patients. Primary Care Companion to The Journal of Clinical Psychiatry, 6(6), 244–247. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC535651/ 

Marazziti, D., Baroni, S., Masala, I., Golia, F., Consoli, G., Massimetti, G., Picchetti, M., Dell’Osso, M. C., Giannaccini, G., Betti, L., Lucacchini, A., & Ciapparelli, A. (2010). Impulsivity, gender, and the platelet serotonin transporter in healthy subjects. Neuropsychiatric Disease and Treatment, 6, 9–15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951061/ 

Mercado, C. P., & Kilic, F. (2010). Molecular mechanisms of SERT in platelets: regulation of plasma serotonin levels. Molecular interventions, 10(4), 231–241. https://doi.org/10.1124/mi.10.4.6 

Rudnick, G. (2007). Sert, serotonin transporter. In S. J. Enna & D. B. Bylund (Eds.), XPharm: The Comprehensive Pharmacology Reference (pp. 1–6). Elsevier. https://doi.org/10.1016/B978-008055232-3.60442-8

Sulthana, N., Singh, M., & Vijaya, K. (2015). Kleptomania-the Compulsion to Steal. Am. J. Pharm. Tech. Res, 5(3). 

Talih, F. R. (2011b). Kleptomania and potential exacerbating factors. Innovations in Clinical Neuroscience, 8(10), 35–39. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225132/ 

Williams, Julie. Pyromania, Kleptomania, and Other Impulse-Control Disorders. Enslow, 2002. 

The Power of Plant Cells: An Interview with Luis Vidali, PhD

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Walking around campus, we are surrounded by plants of various sizes — pines, grass, bushes, mosses. Despite the variety of size and characteristics, all these plants share a similar structure: their cytoskeleton. The cytoskeleton is the protein fibers found within the liquid cytoplasm of plant cells that maintain and modify their physical structure. It performs the same function in plants as the bone skeleton does in animals. But how does it function? How does a tiny seed develop into a large, sturdy tree?  

On October 11th I met with Dr. Luis Vidali, a scientist researching mechanisms in plant cell growth and reproduction, with a focus on studying the cytoskeleton of the moss species Physcomitrium patens. Born in Mexico before moving to the US to continue his studies after college, Dr. Vidali received his doctorate at the University of Massachusetts, Amherst, and is currently Associate Professor of Biology and Biotechnology at the Worcester Polytechnic Institute in Worcester, MA. 

 

Interview Transcript*: 

*At the time of the interview verbatim quotes could not be recorded. This transcript is based on notes taken during the interview and the transcript was submitted to Professor Vidali prior to publication to make sure his words were accurately represented. 

 

Luke Taylor: If you were to explain the implications of your research to the general public in a few words or sentences, what would you say? 

Dr. Luis Vidali: I study how plant cells grow, especially how plant cells take up more space as they grow. Studying the growth of plant cells is important because plants are integral to our everyday lives- from providing food, fibers, and fuels. Plants are responsible for all of these and all plants are made of microscopic cells with defined shapes. If you want to understand how plants grow, you need to understand plant cell growth.  

 

LT: Why is moss such a good model? 

LV: The model I use is Physcomitrium patens: spreading earth moss. We want plant models that grow fast and have a short reproductive cycle, to expedite the pace of researching the cells. Additionally, plants have a reproduction cycle that consists of alternation of generations, where the gametophyte is haploid (has one copy of each chromosome in its cells) and the sporophyte is diploid (has double the number of chromosomes in its cells). The generation we use is primarily the gametophyte, so it having fewer chromosomes in its cell for each generation allows us to identify mutations in its genome and find a demonstrated phenotype much faster than with diploid cells. The moss cells will eventually become identical to each other, allowing for easy control of experimentation without self-breeding techniques.  

 

LT: How do you circumvent the alternation of generations cycle with moss cells if you primarily work with the gametophyte? 

LV: The diploid sporophyte of the moss we work with makes brown capsules. We are not interested in these capsules; we are interested in the more dominant gametophyte. The reason we can circumvent the alternation of generations is because the spores develop protonemata, which are the filaments of cells growing from the moss gametophyte. We grind the moss every week to prevent the sporophyte from developing and propagating spores. The tools we use to perform this grinding are blenders not too unlike the ones in a kitchen blender, but could use a two-shaft, two-probe homogenizer as well.  

 

LT: You state that the cytoskeleton is one of the most conserved structures in plants, animals, and fungi. From what you have researched in plant cytoskeletal structure and function, which functions in plant cytoskeletons do you think may be conserved (paralleled) by fungi and animals, and which structures and functions do you believe diverged? 

LV: Conserved structures in all eukaryotic cells include the separation of chromosomes by the microtubules in the mitotic spindle, and the polarized transport of vesicles  mediated by actin. In evolution, cell division divergence includes the use of the phragmoplast exclusively in some green algae and plants. The phragmoplast is a complex including microtubules and actin which mediates the production of the cell plate during cytokinesis of the plant cell. In contrast, fungi and animal cells use actin and myosin to make the contractile ring, which squeezes the two daughter cells apart. 

 

LT: Myosin is one of the proteins of study in your lab. From my understanding, myosin is associated with animal muscle cells. How does myosin in plant cells relate to myosin use in animal cells? 

LV: Plant cells only have two classes of myosin proteins, whereas animal cells have several more classes, the most abundant one is myosin II,  (Which explains why animal muscle contraction may be the first thing to come to mind when one hears of myosin. Myosin class II in animal cells make contractile filaments with actin, whereas myosin class I mediate vesicle transportation with actin. These myosins in animal cells are related to stress fibers and their contractile nature. Plant cells lack these myosins: they only have myosin class VIII and XI. Myosin class XI is functionally homologous with myosin class V. Myosin V was present within the last common ancestor between plants and animals and mediates the transport of vesicles. The presence of myosin XI in plant cells shows the conserved nature of vesicle transportation in eukaryotic cells. In fungi, class V, I, and II myosins are present. And class II has a function like the one in the contractile ring seen in animal cells. This is an example of the phylogenetic closeness of the fungi kingdom to the animal kingdom in comparison to the plant kingdom to the animal kingdom. Myosin VIII in plant cells specifically mediates vesicle transportation of the phragmoplasts and plasmodesmata, a function specific to plant cells.   

 

LT: You have a collaboration with the department of physics at WPI. What does this entail in terms of your research and methods? Do you find the interdisciplinary nature of your research to be more enlightening about phytological research? How do you apply the principles of physics in your research?  

LV: In my lab we use biophysical and mathematical techniques to model the diffusion of vesicles and molecules in the cell. To do this, we first need to measure the diffusion coefficient of the particles. The diffusion coefficient provides information of how fast particles are moving in space and has units of µm2/s. Because the motion of particles is difficult to measure directly, we instead use the diffusion coefficient to estimate how fast particles may cover a given area in space. By using the plane of coverage as a function of time, we know it takes longer for the molecule or vesicle with a larger diffusion coefficient to cover a larger space.  In our experiments, we use reaction-diffusion calculations to measure how long vesicles bind to myosin, and we see that the vesicles bind to the myosin for very brief periods of time. These mathematical and physical models of diffusion allow us to understand the systems better and model changes in the rate of vesicle transport and secretion. 

We also use physics and mathematics to study the mechanical properties of plant cell walls. For our purposes, we model plant cell walls as a thin shell of a complex polysaccharide matrix, which behaves like a balloon. Having osmotic pressure of the plant cell will apply turgor pressure to the wall of the cells, causing it to expand and assume a more rigid form. The level we study the cell wall at is at the material rather than molecular level, generally speaking. We use an elastic model for the material properties of the cell wall, including considering tensions, stressors, and strains from the turgor pressure on the wall from osmosis. The purpose of our model is to make predictions about how the plant cell behaves, and as we continue to test these predictions, we update our model’s parameters accordingly.  

 

Related papers by Dr. Vidali and colleagues:  

Bibeau, J.P., Furt, F., Mousavi, S.I., Kingsley, J.L., Levine,M.F., Tüzel, E. and Vidali, L. (2020) In vivo interactions between myosin XI, vesicles and filamentous actin are fast and transient in Physcomitrella patens. J. Cell Sci. (2020) 133, jcs234682 doi: 10.1242/jcs.234682  

Chelladurai, D., Galotto, G., Petitto, J., Vidali, L., and Wu, M. (2020). Inferring lateral tension distribution in wall structures of single cells. Eur Phys J Plus 135, 662. https://doi.org/10.1140/epjp/s13360-020-00670-8. 

Galotto, G., Abreu, I., Sherman, C.A., Liu, B., Gonzalez-Guerrero, M., and Vidali, L. (2020) Chitin triggers calcium-mediated immune response in the plant model Physcomitrella patens. Molecular Plant-Microbe Interactions. doi: 10.1094/MPMI-03-20-0064-R 

Kingsley, J.L., Bibeau, J.P., Mousavi, S.I., Unsal, C., Chen, Z., Huang, X., Vidali, L., and Tüzel, E. (2018) Characterization of cell boundary and confocal effects improves quantitative FRAP analysis. Biophysical Journal. 114:1153-1164. doi:10.1016/j.bpj.2018.01.01. 

Living in Beaverland: The Ecology and Biogeochemistry of Beavers

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Next time you’re flying up to the Portland Jetport and the third rerun of Endgame just isn’t cutting it, look out the window. Much of the northern half of the continent is a sprawling landscape dotted with kettle lakes, winding rivers, and other vestigial scars of a world once drowned in ice. Certainly, of the processes that shaped the bedrock Bowdoin sits on, none are as immediately evident as the glaciers that covered it for seventy thousand years. Today, however, a much tinier (and cuter) force gnaws away at the landscape of modern Maine. Our waterways are a record of glaciers, true, but they’re just as much a record of the furry engineers that now inhabit them: Castor canadensis, the North American beaver. 

 

NPS / Neal Herbert, Public Domain.

 

Calling beavers “ecosystem engineers” isn’t science mumbo-jumbo: beavers quite literally show an understanding of the forces of hydrology that backdrops their dams. When a stream encounters a thin opening in bedrock that constricts its flow, its waters gurgle and bubble as it narrows through the gap. It is this gurgling that first allures a beaver to build its dam. In essence, beavers can “‘hear’ the geometry of the river basin.” There, a pioneering beaver colony lays the first branches of speckled alder that they consider too bitter for food, pointing the branches upstream to catch and anchor sediment as part of this keystone layer of wood. Layer upon layer of mud and stick convexes upstream, like the shape of the Hoover Dam, to combat increasing pressure from the pond when the dam plugs more water. As the colony gets larger, beavers build secondary and tertiary dams upstream to relieve pressure on their lodge, so that within generations, the colony will have terraformed their entire forest environment with ponds and meadows along a stairway of rivers and dams.

This process of familial expansion has impacted nearly all of the waterways in the northern United States, especially following their bounce back to pre-colonial populations. For instance, in the North Woods of Minnesota, 90% of streams flow through at least one dam, and overall, 15% of land is covered by beaver ponds or meadows. In the process, beavers unknowingly change the ecology, hydrology, and chemistry of their ponds— often by simply slowing down water. 

At its simplest, slower water cannot carry as much sediment, and in beaver habitats, this has incredible repercussions. Regions that experience alarming rates of erosion benefit from dams because streams cannot carry away soil. So, if rivers cannot carry sediment, they must deposit it instead of erode: beaver ponds carry much more sediment than other streams, increasing the amount of organic matter stored in its pond bottoms. When abandoned dams are broken through, this standing stock of nutrients encourages plant growth and a more biodiverse wet meadow after flooding settles. In the Colorado River, for instance, the distribution of sediment deposited in a dam flood influenced where a diverse plant community was able to grow.

By the same token, beaver habitats are essentially wetlands, critically changing the biogeochemical conditions around dams. Deeper waters and deeper soils foster denitrification, a form of bacterial activity that filters waters affected by nitrate pollution from things like fertilizers. Depositing more sediment also increases the carbon found in beaver ponds. Altogether, these wetland conditions increase biodiversity by a third of what’s found without beaver habitation. Because slower, sediment-laden streams downstream of dams are more likely to curve and branch, more beaver colonies can use them. With these prolific changes, the continent might truly, as environmental journalist Ben Goldfarb puts it, “better be termed Beaverland.”

Scientists have kept log (pun intended) of these benefits for quite some time— the foundational study on their role as geomorphic agents was published in 1938— but attempts to work together with the rodents in structures called beaver dam analogs (BDAs) have only caught on in recent years. In one of its earlier uses, ecosystems analyst Michael Pollock worked on the restoration of a stream that steelhead trout used in their migration inland. Before long, “beavers came and set up shop” on Pollock’s somewhat ad-hoc dams, and the results his team saw were incredible: BDAs increased habitat and reared more than three times more steelhead than an undammed stream nearby.

Despite its happy ending, Pollock argues that their study isn’t the paper to end all papers. How effectively BDAs can mimic and aid beaver dam construction still requires much more testing, and whether it’s worthwhile to reintroduce beavers at all is still debated. Nonetheless, some local governments and farmers alike who benefit from their application have begun to consider the idea of a true BDA Beaverland, so long as regulators get on board too. Whether the costs of building and maintaining BDAs are worth a beaver dam’s biogeochemical and ecological benefits are still up for talk among officials hesitant to rely on these furry rodents. But with all its controversy, you can’t deny that the impacts of Beaverland truly seem to be giving glaciers a run for their money.