Exploring Expansion of Biogas Energy Production on Homesteads, Small-Scale, and Large-Scale Farms

This project analyzes how the perception and implementation of biogas differs across large-scale farms, small-scale farms, and homesteading operations. Its end goal is to better understand the economic feasibility and practicality of biogas at different scales with the hope of establishing a more solid foundation for the sustainability community to operate on and more widespread use of biogas. Both a survey and in-person interviews were conducted during this research. The results of both indicate that existing literature does not accurately represent the state of biogas in Pennsylvania. While public perception and existing studies indicate that biogas is most effective on large-scale farms, this study finds that biogas on a micro scale is overall more affordable, accessible, and easy to maintain. With 17% of the large scale farms using biogas in Pennsylvania responding to the survey and on-site visits to two large scale farms, the results show that the cost to maintain a large biogas digester (all of which were over $1 million to build) are potentially prohibitive for the long term viability of large scale systems. In contrast, the small scale users who are building smaller household scale systems for on-site use for energy generation (all of which were under $1,000 to build) report minimum expenses necessary for maintenance.

Clonal dynamics in leukemia and microenvironments

This summer I had the opportunity to work in Dr. David Scadden’s lab in the Department
of Stem Cell and Regenerative Biology at Massachusetts General Hospital. I joined post-doctoral fellow, Trine Kristiansen, and lab tech, Samuel Keyes, on their ongoing research project studying how clonal changes in the stroma influence the leukemic cell, and differential sensitivities to
treatment from specific leukemic clones. We are specifically studying Acute Myeloid Leukemia
(AML), as it kills over 50% of the almost 18,000 adults in the U.S. diagnosed each year (Aitbekov, et al. Asian Pac J Cancer Prev, 2022). In practice, we use two methods of barcoding cells to obtain clonal information from both the stroma and leukemia: the CARLIN-Cas9 model and lentiviral integration. Both systems require a barcode library to obtain single cell resolution, and are designed to track single clones. The CARLIN model was developed by Dr. Fernando Camargo’s lab as a mouse line capable of in-vivo generation of transcribed barcodes in response to doxycycline induction. We use the CARLIN mouse model to obtain information about the
genetic diversity of the stroma. Unlike hematopoietic stem cells, stromal cells cannot be transplanted. Use of the CARLIN model allows us to barcode stromal cells without transplantation or irradiation, which might otherwise cause architectural changes in the stroma. In the CARLIN system, there are 10 guide RNAs and 10 target sites on the DNA which are always expressed. In order for the DNA to be cut to create a unique barcode, the protein Cas9 must be activated. We use an inducible system by controlling when Cas9 is activated in the
mouse by introducing doxycycline in their water or by injection. The guide RNAs bind to the Cas9 and guide it to the DNA target sites, where the Cas9 makes random cuts to produce a unique barcode per each cell. This barcode is then read out through sequencing, allowing us to identify and categorize clones. In the second barcoding system, we introduce barcodes into cells via lentiviral integration. This method allows us to control the number of barcodes made, because the diversity is determined by the random base pairs and lengths. This method involves
transplantation, but we use it for leukemia because radiation will not structurally affect it. Radiation can be used to eliminate HSCs within the marrow in preparation for transplantation. Lentiviral transduction is performed on HSCs cultured in vitro (in PVA media), which are then transplanted into the irradiated mice. The hematopoietic system is therefore replaced with barcoded cells. The barcodes are read out by sequencing before and after treatment and leukemia are introduced into the leukemia and stroma, respectively. These barcode readouts determine if certain clones are more resistant to leukemia treatment. If resistant clones are identified, treatments can be modified to target these specific clones so that relapse in AML patients is less likely.

I conducted my own in vitro experiment testing the three most common AML drugs in
clinical settings, Venetoclax, Azacitidne, and Cytarabine, on our EAS12 leukemia cell line. The
drugs were only introduced to the cells for 24 hours, because we wanted to observe the
immediate response without the possibility of resistant clones persevering throughout 24 hours of
exposure to treatment. Venetoclax takes longer to kill leukemic cells, so this experiment could be
done with a longer drug exposure time next.

From the data that I was able to obtain this summer, I was able to conclude that the AML
treatments are successful in killing the leukemic cells, the combination of Venetoclax (300 nM)
and Azacitine (3 uM) was the most successful treatment in three groups of different cell
numbers, and we had successful barcoding of our EAS12 cells that were injected into our mice
on July 14.

Exploring Variations in Strength and Mechanical Properties of Lumbar Vertebrae in Eulipotyphla

This study examines potential strength variations among lumbar vertebral units, driven by functional trade-offs. Microindentation testing is employed to elucidate mechanical property discrepancies across distinct vertebral units. Hypothetically, shrew lumbar vertebrae features will be correlated with mechanical attributes, including stiffness and load-bearing capacity. We are predicting that the vertebrae may show adaptations in strength with a trend of increasing strength as one descends the vertebral column. This could be driven by the need to balance the mechanical demands of supporting weight and providing stability with the requirement for flexibility and mobility in the lower lumbar region. In other words, the transition from weight-bearing to facilitating movement prompts a distribution of strength to address these functional trade-offs, consequently yielding the observed pattern.

Exploring Variations in Strength and Mechanical Properties of Lumbar Vertebrae in Eulipotyphla

This study examines potential strength variations among lumbar vertebral units, driven by functional trade-offs. Microindentation testing is employed to elucidate mechanical property discrepancies across distinct vertebral units. Hypothetically, shrew lumbar vertebrae features will be correlated with mechanical attributes, including stiffness and load-bearing capacity. We are predicting that the vertebrae may show adaptations in strength with a trend of increasing strength as one descends the vertebral column. This could be driven by the need to balance the mechanical demands of supporting weight and providing stability with the requirement for flexibility and mobility in the lower lumbar region. In other words, the transition from weight-bearing to facilitating movement prompts a distribution of strength to address these functional trade-offs, consequently yielding the observed pattern.

The effect of temperature on metabolism and oxidative damage in a lizard, Sceloporus consobrinus

Ectotherm metabolic rates positively scale with temperature. As metabolism increases, mitochondria produce more reactive oxygen species, consequently increasing oxidative damage to biomolecules such as DNA. While a recent study in ectotherms produced the expected positive relationship between temperature and metabolism, it also revealed a surprising inverse relationship between metabolic rate and oxidative damage. Our study investigates the effect of temperature manipulation on metabolism and oxidative damage in three geographically distinct populations of Sceloporus consobrinus across a latitudinal thermal gradient. Adult female lizards from each population were collected and exposed to two separate 23.5 hour temperature treatments in the lab: 18°C and 37°C. Metabolic rates were measured at each temperature, and blood samples were collected before and after each temperature exposure. Following DNA extraction and digestion, the oxidative damage biomarker 8-hydroxy-2′-deoxyguanosine (8-OHdG) was quantified for each individual using liquid chromatography with tandem mass spectrometry. As expected, our findings show that metabolic rates are higher at warmer temperatures. Further, while we did not see a change in 8-OHdG levels after the 37°C treatment, the 18°C challenge resulted in an increase in 8-OHdG levels in two of the three populations. Interestingly, lizards from the northernmost population showed resistance to oxidative damage during the cold thermal challenge. This may be due to an altered thermoregulatory strategy or a mechanism to reduce temperature-related oxidative damage. As climate change continues to amplify temperature extremes and may disproportionately impact ectotherms, it is important to understand the influence that temperature has on organismal performance.

Telomere dynamics in Tree Swallows: exploring the effects of temperature and microbiome

As the climate is rapidly changing, many species are facing a more unpredictable and thus challenging environment. Particularly, frequent cold weather swells, known as cold snaps, have posed a significant thermoregulatory challenge that is suspected to shorten telomeres–the non-coding, protective, terminal caps on chromosomes–and ultimately reduce organismal lifespan. However, it is unknown how the composition of the gut microbiome affects an organism’s ability to face these thermoregulatory challenges. Here, we investigated the effect of temperature and antibiotics on telomere length in the widely distributed and tractable Tree Swallow (Tachycineta bicolor). Wild nestlings were reared in captivity from days five to twelve post-hatch under both cold (31ºC) and control (35ºC) conditions and further divided into two groups: antibiotic treated and non-antibiotic treated. Blood samples from twelve days post-treatment were analyzed using the telomere restriction fragment assay. While there was no significant temperature by antibiotic interaction, both warmer temperatures and antibiotic treatment resulted in individuals with longer telomeres. These findings suggest that more variable and colder climates early in the breeding season are likely to have a detrimental impact at the cellular level. Though we predicted that the administration of antibiotics may result in more telomere loss, the longer telomere average for the antibiotic treated nestlings suggests the connection between temperature challenges and the gut microbiome is complex and deserving of further research.