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The Use of Stem Cells to Treat Alzheimer’s Disease
By Tara Nguyen, Human Development, ’25
Alzheimer’s disease (AD) is a neurodegenerative disease that causes cognitive and motor functions to worsen over time, eventually leading to the loss of day-to-day function [1]. AD is the fifth leading cause of death in individuals aged 65 and older. Other causes of death within the top five, such as stroke and cardiac arrest, have decreased in numbers since 2000 while deaths from AD have increased by over 145% [2]. In 2022, an estimated $321 billion was spent on long-term and hospice care for AD patients older than 65 years, an increase from $234 billion as recently as 2019 [1-2]. This piece will cover the pathogenesis of AD and how stem cell research is contributing to finding a successful treatment for AD.
One of the foremost signs in the pathogenesis of AD is the accumulation of amyloid-beta (Aβ) peptides, 39-43 residue amino acids derived from the irregular activity of the amyloid-beta precursor protein (APP) [3-4]. The Aβ peptide forms plaque deposits in areas of the brain that control memory function such as the medial temporal lobe and the neocortical structures [4-5]. The impacts of plaque deposits in these areas of the brain include impaired memory, attention, thought, and perception.
The other most common sign in the development of AD is the occurrence of neurofibrillary tangles (NFTs), which occur due to the misfolding of tau proteins. Tau is an important microtubule protein that takes on six distinct isotypes, each with its own precise function. This protein is important in maintaining the stability of the microtubule system, which contributes majorly to axonal transport [6]. In axonal transport, motor proteins use microtubule systems to transport proteins between neurons. Without stable microtubule systems for this transport, the development, function, and survival of nerves are inhibited [7]. Hyperphosphorylation of the tau protein leads to its overexpression and aggregation, meaning that the microtubule system which tau maintains will no longer be stable. This means that nerve transport, development, function, and survival will be impacted, and NFTs will propagate in the neuronal space of patients with AD. Furthermore, the overexpression of hyperphosphorylated tau proteins can lead to the damage and loss of neurons [6].
Most cells in the human body are specialized cells, such as those that make up the nervous system or the cells that function in the liver. However, there are cells that have regenerative abilities and, unlike specialized cells, are not restricted to one specific function: stem cells. Stem cells provide opportunities for research into regenerative medicine due to their ability to specialize into different cells of various functions rather than only into one. Specifically, multipotent stem cells (MSCs) can specialize into cells from one particular organ or system. For example, neural stem cells (NSCs) are MSCs in the central nervous system that have the ability to differentiate into all nervous system cells. While these cells are indeed stem cells, they only have the potency to specialize into neural system and related cells.
In 2009, a study focusing on NSCs was completed at the University of California, Irvine’s Department of Neurobiology and Behavior Institute for Memory Impairments and Neurological Disorders by Mathew Blurton-Jones et al. This study used transgenic mice models that expressed features of Alzheimer’s Disease, such as pathogenic forms of APP and phosphorylated tau proteins [8]. However, instead of targeting these pathogenic hallmarks of AD, researchers transplanted NSCs into the hippocampus of these mice [8].
Despite there being no change to the amounts of APP present or the tangles in phosphorylated tau proteins, this study found that cognitive function of these mice improved through brain-derived neurotrophic factor (BDNF), which mediates the survival and growth of neurons in the central nervous system [8]. While the hallmarks of AD were still present in these mice, they were able to regain some cognitive function.
Another study done by I.S. Kim et al, in cooperation with the Yonsei University College of Medicine in South Korea in 2015, used stem cells to investigate potential therapeutic effects in AD. Like the study by Blurton-Jones et al, this study utilized NSCs in a transgenic mouse model. The transgenic mouse model had a neuronal disease state that resembles that of Alzheimer’s Disease with features including damaged neurons, an excess of APP, and phosphorylated tau proteins [9].
This study found that non-engineered human NSCs, when inserted into this transgenic mouse model, inhibited the phosphorylation of tau in the model by interfering with the related signaling pathways [9]. As previously discussed, the overexpression of phosphorylated tau is one of the causes of damaged neurons, a primary cause of AD. The researchers hope that a similar effect may show in humans, since the insertion of human NSCs into the transgenic mouse model was able to limit one of the factors and indicators of the development of AD [9].
Further studies are needed to determine whether or not stem cells can prove truly useful in the treatment of AD. Studies that have been approved and published thus far have shown a hopeful light towards the usefulness of stem cells in the modeling and treatment of AD. The works of Matthew Blurton-Jones et al. and I.S. Kim et al. provide a stepping stone towards a working treatment to inhibit, or even reverse, the effects of AD. Some next steps may include researching a possible solution for Aβ plaques, or finding solutions to consider both NFTs and Aβ plaques, and these studies may, hopefully, help the process of developing a successful treatment for AD in humans.
References:
- “2019 Alzheimer’s Disease Facts and Figures.” Alzheimer’s & Dementia 15, no. 3 (2019): 321–87. https://doi.org/10.1016/j.jalz.2019.01.010.
- 2022 alzheimer’s disease facts and figures. (2022). Alzheimer’s & Dementia, 18(4), 700–789. https://doi.org/10.1002/alz.12638
- Breijyeh, Zeinab, and Rafik Karaman. 2020. “Comprehensive Review on Alzheimer’s Disease: Causes and Treatment” Molecules 25, no. 24: 5789. https://doi.org/10.3390/molecules25245789
- Danielle G. Smith, Roberto Cappai, Kevin J. Barnham, The redox chemistry of the Alzheimer’s disease amyloid β peptide, Biochimica et Biophysica Acta (BBA) – Biomembranes, Volume 1768, Issue 8, 2007, Pages 1976-1990,ISSN 0005-2736, https://doi.org/10.1016/j.bbamem.2007.02.002. (https://www.sciencedirect.com/science/article/pii/S0005273607000387)
- Rukmangadachar LA, Bollu PC. Amyloid Beta Peptide. [Updated 2022 Aug 29]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2022 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK459119/
- Cheng Ying, Bai Feng, The Association of Tau With Mitochondrial Dysfunction in Alzheimer’s Disease. Frontiers in Neuroscience, Volume 12, 2018, https://www.frontiersin.org/articles/10.3389/fnins.2018.00163 https://doi.org/10.3389/fnins.2018.00163, ISSN 1662-453X
- Sleigh, J.N., Rossor, A.M., Fellows, A.D. et al. Axonal transport and neurological disease. Nat Rev Neurol 15, 691–703 (2019). https://doi.org/10.1038/s41582-019-0257-2
- Blurton-Jones, M., Kitazawa, M., Martinez-Coria, H., Castello, N. A., Müller, F.-J., Loring, J. F., Yamasaki, T. R., Poon, W. W., Green, K. N., & LaFerla, F. M. (2009). Neural stem cells improve cognition via BDNF in a transgenic model of alzheimer disease. Proceedings of the National Academy of Sciences, 106(32), 13594–13599. https://doi.org/10.1073/pnas.0901402106
- Lee, IS., Jung, K., Kim, IS. et al. Human neural stem cells alleviate Alzheimer-like pathology in a mouse model. Mol Neurodegeneration 10, 38 (2015). https://doi.org/10.1186/s13024-015-0035-6
Engineering Photosynthesis
By Saloni Dhopte, Genetics and Genomics ‘23
If there’s one flowchart I remember from my middle school science textbook, it’s the one for photosynthesis.
Plants are autotrophs- they make their own food using sunlight and carbon dioxide from the air. This process, called photosynthesis, is responsible for supplying most of the oxygen in the Earth’s atmosphere and maintaining all life on Earth. Naturally, such an important job is highly complex and involves a lot of sub-processes, each with their own key players. One such sub-process is the Calvin cycle. One of the main stages of the Calvin cycle is the fixation of carbon by an enzyme known as RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), which converts atmospheric carbon into organic compounds, a process known as carboxylation. Turns out, this enzyme is more important than our middle school science textbooks originally let on.
In 2021, global carbon emissions reached a staggering 37.12 billion metric tons [1]. Through photosynthesis, plants used to be able to sequester enough carbon dioxide from the atmosphere into the soil to balance our emissions. Now, with the advent of modern agriculture, industry, and fossil-fuel-heavy lifestyles, that balance has been lost. Among other things, an increase in the carbon dioxide concentration in the atmosphere will result in a further rise in temperature, proving to be detrimental to life on Earth [2]. While recollections of the Calvin cycle and its components may trigger unpleasant memories for biology majors, some scientists sought to look at this process from a new perspective and apply it to fight global warming. Various researchers are working to enhance the Calvin cycle, particularly by engineering RuBisCO in order to ‘improve’ photosynthesis and increase plants’ carbon sequestration potential [3].
But why RuBisCO? Its job is the rate-limiting step in photosynthetic carbon fixation [4]. In addition to carboxylation, it also is responsible for the addition of oxygen (oxygenation) to CO2 to produce one molecule of 3-phospoglyceric acid (3-PGA) and one molecule of 2-phosphoglycolate (2-PG). Thus, researchers want to engineer RuBisCO such that its oxygenation activity is limited, so most of the plant’s resources are used to increase carbon fixation. Researchers from the Universitat de les Illes Balears-INAGEA in Spain engineered specific amino acids in the large and small subunits of the RuBisCO enzyme to increase its overall carbon dioxide fixation efficiency. They also engineered carbon dioxide concentrating mechanisms (CCMs) of C4 plants (which have a relatively faster fixation efficiency) into C3 plants (which have a relatively slower fixation efficiency) to promote maximal carboxylation activity. However, the plants that were transformed with this engineered enzyme were unable to grow as fast as wild-type plants [5].
Another interesting method of engineering photosynthesis involves the use of artificially manufactured nanoparticles. Current chloroplast synthetic biology techniques suffer from low rates of chloroplast transformation (introducing a foreign gene into the plant cell organelle), fewer species are compatible with chloroplast transformation, and labor-intensive phenotype screening. Nanotechnology, on the other hand, allows for faster delivery of biomolecules to plants, with minimum off-target effects. The use of this technology has supported plant science research in a broad range of areas including plant signaling, stress communication, and environmental monitoring. Buriak et al. used nanotechnology to engineer photosynthesis for increased carbon fixation [6]. Nanoparticles were introduced into the plant via leaf infiltration, and they capture carbon dioxide in the form of bicarbonate, thus increasing the amount of carbon dioxide that interacts with RuBisCO [6]. The researchers were successful in increasing the carboxylation efficiency by 20% in vitro. The in-planta effects still remain to be investigated.
Most recently, the Innovative Genomics Institute (IGI)– founded by Nobel Prize winner Dr. Jennifer Doudna– announced the next step in photosynthesis engineering. With the support of an $11 million grant from the Chan Zuckerberg Initiative (CZI), they have assembled a team of scientists from universities across the country including UC Berkeley and UC Davis [7]. Each research group is set to tackle the problem of increasingly inadequate carbon fixation by plants relative to the growing carbon emissions. They aim to enhance the natural carbon sequestering abilities of plants to match climate change. IGI scientists will be focusing on CRISPR-Cas9 genome editing– a technique that utilizes the mechanism of bacteria’s natural immune system to target specific sequences in a host genome and incorporate desired edits [7].
Current methods of increasing the carbon fixation rate of plants often lead to carbon dioxide being released back into the atmosphere via the respiration of the soil microbes. Thus, along with working towards increasing the efficiency of carbon dioxide removal from the atmosphere, the IGI scientists aim to develop methods of retaining the carbon in the soils. This has many benefits because carbon is nourishing for the soil, and increasing water retention. Scientists such as Dr. David Savage, Dr. Krishna Niyogi, and Dr. Pamela Ronald plan on employing genome editing techniques on rice to improve the efficiency of carboxylation [7]. Dr. Peggy Lemaux and Dr. Myeong-Je Cho are working on developing high-efficiency genome editing protocols for sorghum (a type of grass used in cereals and animal feed), in an effort to improve its ability to remove carbon dioxide from the atmosphere [7]. Drs. Jill Banfield and Jennifer Pett-Ridge are developing methods to measure the carbon fixed by these edited plants and also studying the microbial communities in the soil that will be responsible for the long-term maintenance of carbon [7]. Thus, with these three distinct project areas, IGI strives to fight global warming and create a better tomorrow. So if any freshmen or sophomores are reading, pay attention to the Calvin cycle in your introductory biology courses–, it is key to the future of engineering photosynthesis.
Greater glider populations are decreasing in Australia while selective logging regimes power on
By Adam Vera, Applied Chemistry ’23
The greater glider (Petauroides volans) in a hollow-bearing Eucalyptus tree
Australia’s eucalypt forests along the eastern coast were once abundant with the country’s iconic arboreal marsupial, the greater glider (Petauroides volans). Native to the Central Highlands of Queensland and New South Wales, it has long been recognized as the cute and clumsy acrobat of the treetops—it can glide over 100 meters! It can serve as an indicator of ecosystem health, as it is usually the first species to leave an area exposed to environmental harm, such as wildfire, disease, or anthropogenic disruption. This unique trait makes them an umbrella species: when they are protected, many other species are as well. The core habitats of the greater glider are the hollows that form in old-growth Eucalyptus trees. Hollow-bearing trees are essential because they serve as protection from predators and harsh weather, and they provide ready access to the eucalyptus buds and leaves that they eat. These marsupials of Australia have long embodied the land; sadly, like many other species around the world, they are facing endangerment and vulnerability due to anthropogenic (human activity) action. Their populations are already decreasing which suggests an increase in environmental harm and a decrease in non-use land value [1].
Bushfires have increased in both intensity and quantity in eastern Australia, most notably in 2020 [4]. Global temperature and humidity are factors that can increase rates of bushfires due to increased greenhouse gas emissions and the warming effect they have on the atmosphere [4]. Bushfires have resulted in the habitat destruction and forced migration of many species, including the greater glider, due to the reduction in hollow-bearing trees. Climate change has not been the only factor negatively impacting the glider; selective logging regimes have been steadily removing hollow-bearing trees ideal for the glider. Intensive logging and forest clearing in the site regions of the glider have targeted tall, straight, unburnt trees for harvest since the 1960s to accommodate early machinery [1]. Trees that are targets for loggings are often old-growth because they are well established and durable. Unfortunately, they are also frequently hollow-bearing and therefore habitats for the glider. Selective logging has not slowed down for the protection of this species, nor has it avoided known habitat areas. Without a change, the greater glider will become extinct. Increase in public support for a reduction of selective logging will raise awareness of the unjust treatment of native species and improve the lives of the gliders .
The extinction of the greater glider grows imminent as selective logging destroys habitats. The Department of Climate Change, Energy, the Environment and Water within the Australian government added the species to its endangered species list in July of 2022 [2]. A study performed by researchers at the University of Wollongong, Australia in 2018 proved a positive relationship between logging intensity (measured as acres of old growth forest logged) and glider abundance. They did so by cross-referencing forest sites that had been logged and the presence of the gliders within them, determined via in-person ground monitoring. The removal of 60 cubic meters of hollow-bearing trees (m3) per hectare (10,000 m3) cut the predicted abundance in half at a site within northern New South Wales [2].
“Predicted occurrence of the glider in the Central Highlands of Victoria with respect to the Number of Hollow-Bearing Trees”
In comparison, another team at the Australian National University discovered, using similar methods, the predicted occurrence of the glider in a site in the Central Highlands of Victoria had dropped roughly 30% from 2000 to 2015, as shown to the left [3]. This is consistent with a near 50% loss of hollow-bearing trees per site due to selective logging over the same time frame. The greater glider is an umbrella species because of its innate ability to indicate harmful changes in a local environment, as previously stated. With the loss of this species, many other wildlife species will not receive enough advanced warning about such harmful changes, leaving them vulnerable. Additionally, its predators may experience food shortages and have to relocate, disrupting local ecosystems and creating imbalance in food webs. Furthermore, the lack of management on logging means the decrease in trees is likely to continue, possibly resulting in the extinction of the greater glider.
Wildfires and selective logging regimes are reducing the number of suitable habitats per acre for the greater glider at an increasing rate, as shown in the figure above [2]. These two variables must be controlled in order to protect the species and reduce habitat disturbance. The team from the University of Wollongong suggested fire managers use prescribed fire to reduce the spread of unplanned wildfires. If used, they must be on only low to moderate fire condition days, as well as at a safe distance from known habitats of the gliders [2]. Another active management strategy suggested by both teams is the reduction of selective logging. While easier said than done, it is essential that logging managers not harvest in areas of high species population, as well as not overharvest old growth, hollow-bearing trees in a small, dense area [3]. In the meantime, artificial hollows can be used as temporary habitats [3]. By following these solutions, the species population in eastern Australia will begin to recover and have suitable, comfortable habitats.
“A greater glider at the Australian Conservation Foundation.”
The benefits of preserving this species include the protection of an iconic Australian marsupial, the protection of other species under its umbrella, and the upholding of the standard for how to treat endangered species. The greater glider still inhabits eastern Australia, and can once again live in robust populations with the support of government and concerned citizens.
References:
- McLean, C., Kavanagh, R., Penman, T., & Bradstock, R. 2018. The threatened status of the hollow-dependent arboreal marsupial, the Greater Glider (Petauroides volans), can be explained by impacts from wildfire and selective logging. Forest Ecology and Management, 415-416: 19-25. https://doi.org/10.1016/j.foreco.2018.01.048
- Threatened species list. EPBC Act List of Threatened Fauna. (n.d.). December 2, 2022, www.environment.gov.au/cgi-bin/sprat/public/publicthreatenedlist.pl#mammals_endange red
- Lindenmayer, Blanchard, W., Blair, D., McBurney, L., Taylor, C., Scheele, B. C., Westgate, M. J., Robinson, N., & Foster, C. 2021. The response of arboreal marsupials to long‐term changes in forest disturbance. Animal Conservation, 24(2): 246–258. https://doi.org/10.1111/acv.12634
- Dunne, Daisy. 2020. Explainer: How climate change is affecting wildfires around the world. Carbon Brief, n.p. https://www.carbonbrief.org/
Feeding 8 Billion People: Engineering Crops for Climate Resiliency
By Shaina Eagle, Global Disease Biology ’24
Feeding the world’s 8 billion– and growing– people [2] is an Augean task that requires cooperation between farmers, scientists, government agencies, and industry stakeholders across the globe. Agriculture and climate are deeply intertwined and climate conditions play a critical role in determining agricultural productivity and have a significant impact on global food security. The climate crisis poses immense challenges to food security and the farmers whose livelihoods depend on crop production. As the consequences of the climate crisis increase and intensify, developing resilient agricultural systems is essential to ensuring that our food and those who grow it can adapt without further depleting carbon and water resources.
Climate-smart agriculture identifies technologies that can best respond to the impacts of climate change, such as increasing temperatures and heat waves, changing rainfall patterns, severe storms, drought, and wildfires that adversely affect crop yield and quality [1]. Agronomists, plant biologists, and farmers are working to develop crops that will increase sustainable production and better withstand a changing climate via various genetic techniques.
Clonal Seeds
A team including a UC Davis Assistant Professor of Plant Sciences, Imtiyaz Khanday, genetically engineered rice seeds that reproduce clonally, or without sexual reproduction, in order to maintain the desirable traits found in the F1 generation (Vernet et al. 2022). They developed a breeding technique that allows for high-frequency production– or the ability to produce a large quantity in a short amount of time in a cost-effective manner– of hybrid rice using synthetic apomixis. Apomixis, a type of asexual reproduction in plants, allows for the production of seeds without fertilization, which can be useful in hybrid breeding programs. The study used CRISPR/Cas9 gene editing to introduce mutations in the genes responsible for sexual reproduction in rice. These seeds were planted and produced the F1 generation of plants, which were genetically stable and had high yield potential. Subsequent generations were clonally propagated from the F1 plants. In agriculture, high-frequency production has the ability to produce a large number of crops or seeds using advanced breeding techniques. High-frequency production is important for meeting the increasing demand for food and other agricultural products, as well as for improving the efficiency and profitability of farming operations.
The study suggests that this technique could be a valuable tool for plant breeders to produce high-quality hybrid rice seeds with more efficient and cost-effective methods. Clonal propagation can help maintain desirable traits as the climate crisis threatens agriculture, such as disease resistance, yield potential, or drought tolerance that might otherwise be lost through sexual reproduction. It is a faster alternative to sexual reproduction methods such as cross-breeding, which can take several generations and require extensive testing to identify desirable traits.
De Novo Domestication
De novo is a Latin term that means “from the beginning” or “anew”. In the context of genetics and plant breeding, de novo refers to the creation of something new or the starting point for the development of a new organism or trait. De novo domestication, for example, refers to the process of identifying and selecting wild plants with desirable traits and developing them into new crops that are better adapted to agricultural use. This approach differs from traditional domestication, which involves selecting and breeding plants that have already been used by humans for thousands of years. Eckhardt et al. highlight the potential benefits of de novo domestication, including the creation of new crops that are better adapted to changing environmental conditions, and the conservation of genetic diversity by using previously unexploited wild species.
A study by Lemmon et al. (2021) aimed to create a domesticated tomato variety with desirable traits by introducing mutations into genes related to fruit size and shape via CRISPR-Cas9. While there are many tomato cultivars available, they often have limitations in terms of yield, quality, or other traits that are important for consumers and growers. Therefore, there is a need to develop new tomato varieties with improved characteristics, and the de novo domestication of a wild tomato variety using genome editing offers a potential solution to this challenge. The domesticated variety has several desirable traits, including larger fruit size, smoother fruit shape, reduced seed count, and prolonged fruit shelf life. Additionally, the domesticated tomato plants have increased branching and produced more fruit per plant compared to the wild-type tomato plants.
Kaul et al. (2022) conducted a de novo genome assembly of rice bean (Vigna umbellata), a nutritionally rich crop with potential for future domestication. The study revealed novel insights into the crop’s flowering potential, habit, and palatability, all of which are important traits for efficient domestication. Flowering potential refers to the crop’s ability to produce flowers, which is important for seed production and crop yield. Understanding the genetic basis of flowering potential can help breeders select plants that flower earlier or later, depending on their needs. Habit refers to the overall growth pattern of the plant, such as its height, branching, and leaf morphology. Understanding the genetic basis of habit can help breeders select for plants that are more suitable for specific growing conditions or cultivation methods. Palatability refers to the taste and nutritional value of the crop, which are important factors for its acceptance as a food source. Identifying genes involved in carbohydrate metabolism and stress response can help breeders develop crops with better nutritional value and resistance to environmental stressors. Overall, these traits are desirable because they can contribute to the development of a more productive, nutritious, and resilient crop. The researchers also identified genes involved in key pathways such as carbohydrate metabolism, plant growth and development, and stress response. Climate change is expected to have a significant impact on crop yields, water availability, and soil fertility. One NASA study found that maize yields may decrease by 24% by 2030 [3]. Understanding the genetic basis of stress response and carbohydrate metabolism can help breeders develop crops that are more resilient to environmental stressors, such as drought, heat, and pests. Furthermore, identifying genes involved in plant growth and development allows breeders to introduce desirable traits, such as earlier flowering or increased yield. This is important for domestication because it can help accelerate the process of crop improvement and make it easier to develop new varieties with desirable traits. Overall, the genes identified in the study provide a foundation for developing crops that are better adapted to changing environmental conditions and more suitable for cultivation, which is crucial for ensuring food security in the face of climate change.
Genetically enhancing common crops
Molero et al. (2023) identified exotic alleles (germplasm unadapted to the target environment) associated with heat tolerance in wheat through genomic analysis and conducted breeding experiments to develop new wheat with improved heat tolerance. The exotic alleles were obtained from wheat lines that originated from diverse regions around the world, including Africa, Asia, and South America. The identified alleles increased heat tolerance in wheat under field conditions, and the effect was consistent across multiple environments. The authors obtained these lines from the International Maize and Wheat Improvement Center (CIMMYT) and used genomic analysis to identify the specific exotic alleles associated with heat tolerance. These alleles were then incorporated into breeding programs to develop new wheat varieties with improved heat tolerance.
The authors used genomic analysis to identify these alleles, which had diverse functions, including regulating heat shock proteins, osmotic stress response, and photosynthesis. The study provides evidence that the use of multiple exotic alleles could lead to the development of wheat varieties with improved heat tolerance under field conditions. The authors crossed the heat-tolerant lines carrying the exotic alleles with local commercial varieties to develop new breeding populations. They then evaluated the heat tolerance of these populations under field conditions to identify the lines with improved heat tolerance. The selected lines were further evaluated in multiple environments to confirm their performance and stability. Heat tolerance was measured by exposing the plants to high temperatures under field conditions and evaluating their performance. Specifically, they conducted experiments in three different environments, including a dry and hot irrigated environment, a semi-arid rainfed environment, and a temperate irrigated environment, all of which are known to impose high-temperature stress on wheat. The authors evaluated multiple traits related to heat tolerance, including yield, plant height, spike length, and the number of spikes per plant.
They also measured physiological traits such as chlorophyll fluorescence, canopy temperature, and photosynthetic activity. By evaluating these traits, they were able to identify the wheat lines with improved heat tolerance. By combining both phenotypic and genomic analyses, they were able to identify the wheat lines and alleles with the greatest potential for improving heat tolerance in wheat under field conditions. This demonstrates the potential for the use of exotic alleles in plant breeding to improve crop performance and address the challenges of climate change.
Porch et al. (2020) report the release of a new tepary bean germplasm (seeds or plant parts that can be passed onto the next generation and are helpful in breeding efforts) called TARS-Tep 23, which exhibits broad abiotic stress tolerance, as well as resistance to rust and common bacterial blight. Tepary bean (Phaseolus acutifolius) is a drought-tolerant legume crop that is native to the southwestern United States and northern Mexico. Tepary beans are generally grown in arid and semi-arid regions of North America, including the Sonoran Desert, Chihuahuan Desert, and the Great Basin. They are also grown in parts of Central and South America. According to FAO statistics, the total world production of tepary beans in 2019 was around 4,000 metric tons. Rust and common bacterial blight are two diseases that can affect the growth and productivity of tepary beans. Rust is a fungal disease that causes orange or brown spots on the leaves and stems of plants, leading to reduced photosynthesis and yield loss. Common bacterial blight is a bacterial disease that can cause wilting, necrosis, and reduced yield in affected plants.
The researchers conducted field trials and laboratory experiments to evaluate the performance and traits of TARS-Tep 23 under different conditions. Laboratory experiments involved inoculating TARS-Tep 23 with rust and common bacterial blight pathogens, then comparing the performance and traits with other tepary beans under these conditions. Field trials were carried out under conditions such as normal rainfall, drought, and heat stress. The results showed that TARS-Tep 23 had higher yields and better growth under drought and heat stress compared to other tepary bean varieties. It also showed high resistance to rust and common bacterial blight. The release of TARS-Tep 23 provides a valuable resource for breeding programs and can contribute to enhancing the productivity and sustainability of tepary bean cultivation. Developing climate-resistant germplasm is a critical resource for crop improvement and biodiversity cultivation, and it is used by plant breeders and researchers to develop new varieties with desirable traits such as disease resistance, stress tolerance, and improved yield.
Conclusion
The urgent need to address the challenge of climate change and its impact on global food security cannot be overemphasized. The world is already experiencing food shortages due to the adverse effects of climate change, and this problem is likely to worsen in the future unless appropriate measures are taken. Significant strides are being made in the research and development of new agricultural and genetic technologies that can engineer crops for climate resiliency. These technologies offer hope for a more sustainable future by enhancing food production, increasing resilience to extreme weather conditions, and mitigating the impact of climate change. However, it is essential to recognize that research and development efforts should not only focus on genetic engineering but should also involve all levels of the food production process, including better management practices, more efficient use of resources, and improved supply chain management. Only by taking a comprehensive approach can we hope to achieve a sustainable and resilient food system that can withstand the challenges of climate change.
References
[1] Eckardt, Nancy A, Elizabeth A Ainsworth, Rajeev N Bahuguna, Martin R Broadley, Wolfgang Busch, Nicholas C Carpita, Gabriel Castrillo, et al. “Climate Change Challenges, Plant Science Solutions.” The Plant Cell 35, no. 1 (January 2, 2023): 24–66. https://doi.org/10.1093/plcell/koac303.
[2] Frayer, Lauren. “Earth Welcomes Its 8 Billionth Baby. Is That Good or Bad News… or a Bit of Both?” NPR, November 15, 2022, sec. Goats and Soda. https://www.npr.org/sections/goatsandsoda/2022/11/15/1136745637/earth-welcomes-its-8-billionth-baby-is-that-good-or-bad-news-or-a-bit-of-both.
[3] Gray, Ellen. NASA’s Earth Science News. “Global Climate Change Impact on Crops Expected Within 10 Years, NASA Study Finds.” Climate Change: Vital Signs of the Planet. Accessed May 30, 2023. https://climate.nasa.gov/news/3124/global-climate-change-impact-on-crops-expected-within-10-years-nasa-study-finds.
[4] Jägermeyr, Jonas, Christoph Müller, Alex C. Ruane, Joshua Elliott, Juraj Balkovic, Oscar Castillo, Babacar Faye, et al. “Climate Impacts on Global Agriculture Emerge Earlier in New Generation of Climate and Crop Models.” Nature Food 2, no. 11 (November 1, 2021): 873–85. https://doi.org/10.1038/s43016-021-00400-y.
[5] Jia, Huicong, Fang Chen, Chuanrong Zhang, Jinwei Dong, Enyu Du, and Lei Wang. “High Emissions Could Increase the Future Risk of Maize Drought in China by 60–70 %.” Science of The Total Environment 852 (December 2022): 158474. https://doi.org/10.1016/j.scitotenv.2022.158474.
[6] Liu, Weihang, Tao Ye, Jonas Jägermeyr, Christoph Müller, Shuo Chen, Xiaoyan Liu, and Peijun Shi. “Future Climate Change Significantly Alters Interannual Wheat Yield Variability over Half of Harvested Areas.” Environmental Research Letters 16, no. 9 (September 1, 2021): 094045. https://doi.org/10.1088/1748-9326/ac1fbb.
[7] McMillen, Michael S., Anthony A. Mahama, Julia Sibiya, Thomas Lübberstedt, and Walter P. Suza. “Improving Drought Tolerance in Maize: Tools and Techniques.” Frontiers in Genetics 13 (October 28, 2022): 1001001. https://doi.org/10.3389/fgene.2022.1001001.
[8] Molero, Gemma, Benedict Coombes, Ryan Joynson, Francisco Pinto, Francisco J. Piñera-Chávez, Carolina Rivera-Amado, Anthony Hall, and Matthew P. Reynolds. “Exotic Alleles Contribute to Heat Tolerance in Wheat under Field Conditions.” Communications Biology 6, no. 1 (January 9, 2023): 21. https://doi.org/10.1038/s42003-022-04325-5.
[9] Ozias-Akins, Peggy, and Joann A. Conner. “Clonal Reproduction through Seeds in Sight for Crops.” Trends in Genetics 36, no. 3 (March 2020): 215–26. https://doi.org/10.1016/j.tig.2019.12.006.
[10] Raphael Tiziani, Begoña Miras-Moreno, Antonino Malacrinò, Rosa Vescio, Luigi Lucini, Tanja Mimmo, Stefano Cesco, Agostino Sorgonà. “Drought, heat, and their combination impact the root exudation patterns and rhizosphere microbiome in maize roots.” Environmental and Experimental Botany, Volume 203, 105071. 2022. https://doi.org/10.1016/j.envexpbot.2022.105071.
[11] Underwood, Charles J., and Raphael Mercier. “Engineering Apomixis: Clonal Seeds Approaching the Fields.” Annual Review of Plant Biology 73, no. 1 (May 20, 2022): 201–25. https://doi.org/10.1146/annurev-arplant-102720-013958.
[12] Vernet, Aurore, Donaldo Meynard, Qichao Lian, Delphine Mieulet, Olivier Gibert, Matilda Bissah, Ronan Rivallan, et al. “High-Frequency Synthetic Apomixis in Hybrid Rice.” Nature Communications 13, no. 1 (December 27, 2022): 7963. https://doi.org/10.1038/s41467-022-35679-3.
[13] Yu, Chengzheng, Ruiqing Miao, and Madhu Khanna. “Maladaptation of U.S. Corn and Soybeans to a Changing Climate.” Scientific Reports 11, no. 1 (June 11, 2021): 12351. https://doi.org/10.1038/s41598-021-91192-5.
Tau Proteins for Early Diagnosis of Alzheimer’s Disease: A Literature Review
By Yoonah Kang, Neurobiology, Physiology, and Behavior ’24
Author Bio : I am a third year student studying Neurobiology, Physiology, and Behavior. I always enjoyed biology in middle school and high school. I became interested in neurobiology through the AP psychology class in high school because I really enjoyed the section about the biology behind psychological phenomena. This paper was originally written for the UWP 104F class, writing in health professions. I was interested in Alzheimer’s Disease because it is a disease that affects many people around the world, but there is still no cure/treatment for it. While reading articles about Alzheimer’s, I found out that the best course for longevity is early diagnosis which allows for early intervention. So I focused on a way that can allow for easier ways to diagnose patients. I hope the readers understand that Alzheimer’s is very complex, and there is still a lot to learn, but also there has been a lot of research to further our knowledge about AD.
Introduction:
As the population over 65 years of age increases, the prevalence of Alzheimer’s Disease in the United States is projected to triple to 14 million by 2060 [1]. Alzheimer’s disease (AD) is a progressive neurodegenerative disease that begins with mild memory loss and can ultimately lead to death. It is characterized by the accumulation of amyloid-β and tau neurofibrillary tangles in the brain [2]. These characteristics can be measured to determine the onset of Alzheimer’s at earlier stages. Currently, treatments only delay the onset and progression of symptoms. Early diagnosis is important because it identifies the disease before it causes irreversible damage and improves treatment efficacy. Early diagnosis can also aid research for new drugs that reverse the pathological effects of AD before it becomes irreversible. It is possible to detect biomarkers involved in AD early because “neurodegenerative processes … start up to 20-30 years before symptom onset” [3].
Aggregation of Tau proteins is a major distinguishing feature of AD. Neurofibrillary tangles (i.e. tau protein aggregates) inside neuronal axons block transport of nutrients and disturbs essential functions, which leads to damage and destruction of neurons in the brain [4]. Under normal conditions, Tau proteins are highly soluble (able to be dissolved) and are directly attached to microtubules to support the intracellular transport of proteins and organelles. In the brains of AD patients, Tau proteins are hyperphosphorylated and dissociate from microtubules, which “initiates the conformational change from natively unfolded tau into [insoluble] paired helical filament tau inclusions (protein aggregates) and neurofibrillary tangles” [5]. The dissociation of Tau proteins from microtubules leads to instability and breakdown of microtubules, which leads to neuronal dysfunction.
Currently, the evaluation of cerebrospinal fluid biomarkers (CSF) and positron emission tomography (PET) scans are widely used as diagnostic criteria for AD. The presence of the three main CSF biomarkers, Aβ42, T-tau, and P-tau, are established as diagnostic criteria for AD [6]. For example, a patient suspected of having AD may get their tau-PET or CSF p-tau checked to confirm diagnosis. However, drawing blood and evaluating blood biomarkers is less invasive than CSF biomarkers, which require a lumbar puncture, and are more cost-effective than PET scans. Retrieving biomarkers via blood is also more accessible at hospitals and local clinics because it does not require specialized instruments. This literature review focuses on the detection of abnormally high concentrations of tau proteins in blood to diagnose Alzheimer’s disease.
Methodology:
I used the UC Davis library website to access the databases PubMed and APA PsycInfo. I searched a combination of the following terms: “Alzheimer’s”, “Alzheimer’s Disease”, “blood biomarker”, “blood”, “biomarker”, “tau”, “diagnosis”, “early diagnosis”, “literature review”, and “meta-study”. I chose articles between 2014 to 2022 because research of tau blood biomarkers is a recent field with new advances each year.
Initially, I chose articles with titles such as “fluid biomarkers in diagnosis of Alzheimer’s” to understand the overall use of biomarkers in diagnosing AD. Reading meta-studies about blood biomarkers helped narrow my topic to tau proteins in blood. Afterwards, I skimmed literature reviews to find sections about tau proteins. I also read articles that specifically focused on tau proteins and their use in diagnosis of Alzheimer’s. I read titles and abstracts to rule out articles that only included biomarkers such as CSF biomarkers, microRNA, platelets, apolipoprotein B, or amyloid β peptides.
Results and Discussion:
Biomarkers that originate from the brain, such as tau proteins, are present at low concentrations in the systemic blood circulation because of the blood-brain barrier, which filters molecules moving in and out of the brain. However, in the 2021 article “Blood Biomarkers in Alzheimer’s Disease”, Miren Altuna-Azkargorta and Maite Mendioroz-Iriarte point out that “researchers have described blood-brain barrier dysfunction in patients with AD.” This dysfunction allows passage of molecules between the CSF and blood [3]. Brain protein concentration is low in blood because components of blood are complex and contain various other proteins and proteases, which mix with and hydrolyze (break down) proteins from the brain [7]. Therefore, more sensitive instruments are required to measure tau protein levels accurately and consistently.
However, there is an ongoing debate on the plausibility of t-tau in blood being used to diagnose AD. Lei Feng et al.’s 2021 article, “Current Research Status of Blood Biomarkers in Alzheimer’s Disease: Diagnosis and Prognosis,” reviews the various biomarkers in blood for AD diagnosis. In the section about t-tau proteins, they state that “t-tau may lack diagnostic specificity for AD because of its elevation [in concentration] in a series of pathologies, such as epilepsy and corticobasal degeneration” [7]. Another article, “Review: Tau in Biofluids – Relation to Pathology, Imaging and Clinical Features”, written by Henrick Zetterberg in 2017, is skeptical of blood plasma t-tau proteins because they lack specificity for AD and have a shorter half-life than CSF t-tau [8]. Since levels of t-tau are elevated for other neurodegenerative diseases, these tests may yield a false positive result for AD.
However, Bob Olsson et al. are hopeful about the prospects of plasma t-tau being used to diagnose AD. In their 2017 meta-analysis, “CSF and Blood Biomarkers for the Diagnosis of Alzheimer’s Disease: a Systematic Review and Meta-analysis,” they perform a systematic review of eleven research papers that assess t-tau in blood, including a total of 271 AD patients and 394 controls. With the combined data, the authors conclude that there is a significant difference in t-tau levels in blood between AD patients and control. Even though this association between elevated t-tau levels and AD has been found, Olsson et al. admit that there is large variation among the few studies available. Therefore, more studies must be done to establish a clearer association between t-tau and AD [6].
In 2016, Niklas Mattsson et al. published “Plasma Tau in Alzheimer Disease”, which looks at a total of 1284 participants between two cohorts: BioFINDER, which is in Sweden, and ADNI, located in the United States and Canada. The authors compare levels of tau proteins in blood plasma between patients with AD, patients with mild cognitive impairment (MCI), and people with normal cognition. With the cohort of patients in the ADNI program, the researchers found that there was an increase in plasma tau in AD patients, but they were not able to replicate these results with the BioFINDER cohort [9]. Varying results between the cohorts can suggest that association between plasma tau and AD is low, but it should be noted that this study was carried out across different locations with different handling protocols, inclusion criteria and technologies [9]. These confounding variables may have affected the results of this study.
Recent studies using ultrasensitive immunoassay methods show more promising results for detecting tau proteins. Leian Chen et al.’s article, “Plasma Tau Proteins for the Diagnosis of Mild Cognitive Impairment and Alzheimer’s Disease: a Systematic Review and Meta-analysis,” reviews 56 studies and summarize which technologies are effective at detecting an elevation in tau protein concentration, from people with normal cognition to MCI to AD patients. They find that immunomagnetic reduction technique (IMR) and Single molecule array (Simoa) assay methods detect differences in p-tau181, p-tau217, and p-tau231 levels across all three groups [2]. More specifically, blood “p-tau217 [is] more sensitive than p-tau181 and p-tau231 … because p-tau217 is more tightly related to the formation of Aβ plaques in the brain” [2], which is a distinguishing feature of AD. IMR is also consistent in detecting differences in t-tau levels between normal, MCI, and AD groups [2]. This shows that new technologies are starting to show more consistency in data reproduction of blood biomarkers, which prior research lacked. However, elevated plasma p-tau181 and p-tau217 levels are also found in other diseases like chronic kidney disease, hypertension, myocardial infarction, and stroke [2] – similar to tests for t-tau. Future research could focus on differentiating p-tau protein levels indicated by AD versus other diseases.
Two articles observe p-tau181 for early diagnosis of AD. Joyce R. Chong et al. wrote the article, “Blood-based High Sensitivity Measurements of Beta-amyloid and Phosphorylated Tau as Biomarkers of Alzheimer’s Disease: A Focused Review on Recent Advances,” in 2021, and it looks at studies that observe p-tau181 using Simoa immunoassay platform. They find that plasma p-tau181 can “differentiate between AD and non-AD neurodegenerative diseases” because it is associated with other AD-specific pathologies such as “NFT burden, grey matter atrophy, hippocampal atrophy, cortical atrophy brain, metabolic dysfunction and cognitive impairment” [10]. The study also reports that “the earliest increases in plasma p-tau181 occurred shortly before PET and CSF Aβ markers reached abnormal levels” [10]. Another article, written by Syed Haris Omar and John Preddy in 2020, titled “Advantages and Pitfalls in Fluid Biomarkers for Diagnosis of Alzheimer’s Disease,” looks at a study that used IMR to observe p-tau181. Omar and Preddy conclude that plasma p-tau181 can differentiate between AD and cognitive decline due to age because there is an increase in the ratio of p-tau181 to t-tau from control to patients with mild AD: 14.4% and 19.5%, respectively [11]. Therefore, developing more accurate detection methods of plasma p-tau181 may allow for earlier diagnosis of AD than current diagnosis procedures, which uses PET scans and CSF biomarkers, because it is an AD specific biomarker.
Even though plasma tau currently cannot be used to diagnose Alzheimer’s Disease, recent studies show promising use in preclinical settings. In 2022, Rik Ossenkoppele et al. published the article “Tau Biomarkers in Alzheimer’s Disease: Towards Implementation in Clinical Practice and Trials.” Ossenkoppele et al. looked at tau pathology identified through PET, CSF, and plasma. The authors recommend using plasma p-tau as a “screening method to identify preclinical Alzheimer’s disease among cognitively unimpaired individuals,” but a “positive result should be confirmed using tau-PET or CSF p-tau” [5]. In “Plasma Tau Association with Brain Atrophy in Mild Cognitive Impairment and Alzheimer’s Disease,” Kacie D. Deters and her colleagues also highlight plasma tau’s use as a screening tool rather than a diagnostic tool for “cognitively normal or mildly symptomatic older adults” [12]. Currently, there is more research confirming the reliability of tau-PET and CSF p-tau in diagnosing AD compared to plasma tau. However, PET scans and collecting CSF samples for all patients suspected to have AD is not cost-effective and may not be available in clinical settings without special instruments to perform these tests. Since collecting blood samples is easier, checking for plasma p-tau in the pre-clinical phase can narrow down the patients who will need the more invasive procedures.
Conclusion:
The research on plasma tau proteins is new and has made significant progress in the past decade, but more research must be done on this topic. A more uniform way of measuring tau proteins must be established so studies can be replicated and yield similar results. Because these are recent advances, longitudinal studies are much needed. The progress of tau proteins in blood should be monitored in patients with AD to observe their effects in disease progression. In the near future, research on tau proteins can be used to develop drugs to treat AD.
Preliminary evidence for differential habitat selection between bird species of contrasting thermal-tolerance levels
By Phillips.
Author’s note: Since coming to college, I have wanted to conduct research on the environmental impacts of agriculture and contribute to efforts to make farming work for both people and nature. In pursuit of this goal, I signed up as an intern with Daniel Karp’s agroecology lab in my freshman year and stayed with them for my entire undergrad. During this internship, I worked alongside several Ph.D. students, such as Katherine Lauck and Cody Pham, who research the cumulative effects of land conversion and climate change on native avifauna at Putah Creek. I was so inspired by their work that I decided to conduct an independent project investigating similar phenomena. Specifically, I was curious about how birds respond to temperature across multiple landscapes, and how this pattern of behavior might influence their choice of habitat. While reading this paper, I would like you to consider the broader implications of the findings as they pertain to species conservation in the context of climate change.
Abstract
Increasing frequency and severity of temperature spikes caused by climate change will disproportionately impact heat-sensitive species. However, certain types of vegetation may protect animals from temperature spikes. Heat-sensitive species can retreat to shaded microhabitats when temperature increases, allowing them to avoid detrimental effects on fitness. Here, we examined habitat selection and behavioral responses to temperature of Western Bluebirds (Siailia mexicana) and Northern Mockingbirds (Mimus polyglottos). We conducted transect surveys and collected behavioral data on bird movement for two months in riparian forest and perennial cropland in the Central Valley of California, where breeding season temperatures are often above 35°C. Bluebirds were observed more frequently in shaded riparian forest, while mockingbirds were observed more frequently in exposed agricultural fields. Correspondingly, bluebirds became less active at higher temperatures, while mockingbirds exhibited no response. Together, our results imply that heat-sensitive species may be more likely to select natural or semi-natural habitats and change their behaviors when temperatures spike. The results of this study imply that the combined effects of anthropogenic land development and climate change may be more destructive for heat-sensitive species than for heat-tolerant species.
Introduction
Climate change is increasing the frequency and intensity of temperature spikes across the world [1]. Many species will likely experience increased mortality due to these extreme conditions [2–4], with heat-sensitive species experiencing especially detrimental effects [5,6]. However, thermally-buffered habitats could mitigate the impact of heat spikes on organisms, as certain habitat features, like vegetative cover, have been shown to cool local temperatures through shading and evapotranspiration [7,8]. Landscapes with high amounts of thermally-buffered habitats, such as closed-canopy forests, have been shown to have less dramatic temperature extremes than open habitats [9,10]. Furthermore, it has been shown that animals in these thermally-buffered habitats are less likely to be impacted by rising global temperatures [11,12]. As such, organisms that are sensitive to temperature extremes may preferentially select for these habitats, and therefore may be able to avoid potentially lethal effects. Birds have been observed to retreat to shaded habitats when temperatures spike [13]. However, it is unclear whether heat-sensitive species specifically select for thermally-buffered habitats, or if heat-tolerant species persist in non-buffered habitats. Therefore, we sought to understand how the habitat selection of bird species may be associated with their behavioral responses to temperature.
Bird populations in North America are in rapid decline [14], and are predicted to continue declining with climate change [15]. As such, determining the habitat requirements of birds in response to increasingly extreme temperatures could be crucial to their conservation. We conducted behavioral surveys of birds in the Central Valley of California to address two questions: 1) does habitat selection differ between Western Bluebirds and Northern Mockingbirds, and 2) are behavioral responses to temperature different between these species? We hypothesized that birds species which exhibit significantly different behavior during high temperature will preferentially select habitats with more vegetation cover.
Methods
Experimental design
We selected two sites along Putah Creek in the Central Valley of California. In this system, temperatures often reach 35°C during the hottest months of the year. These sites contain a combination of riparian (forest existing along a river bank) and agricultural land and are approximately five miles apart from each other. At each site, the two focal land cover types–riparian forest and perennial agriculture–were present within one half-mile of each other (Figure 1). We obtained observations along four 100 meter (m) transects. In the riparian areas, we placed transects along regions of the sites where vegetation was sparse enough that birds could be observed, as dense vegetation made it difficult to track the individual birds. In the agricultural areas, we placed transects along areas that were close enough to the crops that birds could be spotted. Transects were placed approximately 50 meters apart from each other.
We focused on Western Bluebirds (Siailia mexicana) and Northern Mockingbirds (Mimus polyglottos) due to their high abundance at Putah Creek. Additionally, we chose these species because they forage on the ground rather than in the air, and therefore were easier to observe with the naked eye.
Figure 1. Our two study sites were in close proximity to both riparian and agricultural habitats along Putah Creek. At each site, we observed birds along a total of 16 transects (depicted in red).
Data collection
We conducted our surveys from late April to early July 2022, the height of the breeding season for our study species. We visited each site at least once a week, in either the morning or early afternoon. During each visit, I would walk along the transects. Once a bird of either target species was spotted, I would track the bird for two minutes and record all behaviors displayed, along with the amount of time spent engaging in each behavior. These behaviors included “foraging” (searching for, chasing, or eating an insect), “moving” (locomotion with wings or legs), “resting” (standing or sitting motionless), “singing” (repetitive vocalization for more than three seconds), “preening” (use of beak to position feathers), and “disputing” (fighting between birds that occurs due to territorial disputes). I recorded temperature and wind speed each hour using a Kestrel 2000 Weather Meter.
Data analysis
We ran Fisher’s exact tests to determine if mockingbirds and bluebirds preferentially selected different landscape types across sites. The variables in this model included ‘species,’ and ‘landscape type,’ which was defined as either “Agriculture” or “Riparian.” We ran the model across both sites and did not distinguish between the two separate sites depicted in Figure 1.
Then, we implemented multiple linear regression models examining the relationship between the time spent engaging in various behaviors and temperature for each species. We considered the time spent engaged in a particular behavior to be the percentage of time during the two-minute observation period in which the individual bird exhibited that behavior (i.e., time spent moving, foraging, resting, preening, singing, or disputing).
To account for the effects of spatial autocorrelation (or the tendency of areas which are close together to provide similar data values), we first included a site covariate in our models. We additionally attempted to control for the effects of a natural circadian rhythm on behavior by including a time-of-day covariate. As temperature and time were highly correlated (r = 0.696 for bluebird observations and 0.548 for mockingbird observations), we included these covariates using a temperature residual approach. Specifically, we regressed time against temperature and obtained residual values, representing whether temperatures were hotter or cooler than the average expected temperature at any given time of day. We then ran a multiple linear regression including the effects of temperature residuals, time of day, and site on bird behavior.
Results
Landscape preference
Bluebirds and mockingbirds exhibited significantly different habitat preferences. Bluebirds preferentially resided in riparian areas, whereas mockingbirds preferentially resided in agricultural landscapes across both sites (Fisher’s exact test, p = 4.583E-15; Figure 2).
Figure 2. Mockingbirds (n=34) are observed to reside in agricultural landscapes more frequently than riparian landscapes. Bluebirds are observed to reside in riparian landscapes more frequently than agricultural landscapes (n=35).
Changes in patterns of behavior
We found that temperature negatively affected the amount of time that bluebirds spent moving (Linear regression, p = 0.0077, F = 8.069, df = 1, 33; Figure 3; Supp. 1). However, temperature did not significantly affect mockingbird movement (Linear regression, p = 0.297, F = 1.125, df = 1, 32; Figure 3; Supp. 1).
Results were broadly similar after including ‘site’ as another effect in the model to account for multiple observations at the same location. Specifically, temperature still did not affect mockingbird movement (Multiple regression, p = 0.635, F = 0.577, df = 3, 30; Supp. 3) and marginally affected bluebird movement (Multiple regression, p = 0.0682, F = 2.622, df = 3, 31; Supp. 3). However, one of the sites had very few bluebird observations (n=4); when this site was removed from the model, temperature again negatively affected bluebird movement (Linear regression, p = 0.0123, F = 7.138, df = 1, 29; Supp. 2).
The last model we ran tested the effects of both temperature residuals and time of day on bird behavior. Using these models, temperature again did not have a significant effect on the behavior of mockingbirds but did have a marginal effect on bluebird movement (p = 0.07; Supp. 4).
For all of the models, resting, foraging, disputing, singing, and preening of bluebirds and mockingbirds exhibited no significant association with any environmental variable (Supp. 1, Supp. 2, Supp. 3, Supp. 4).
Figure 3. Bluebirds (left) are observed to reduce the percentage of time they spend moving as temperature increases. Mockingbird movement (right) did not significantly decline with rising temperature. The black points represent individual bird observations, the solid lines represent the linear model predictions, and the gray bands represent the 95% confidence intervals.
Discussion
Our results suggest that bluebirds select for shaded riparian habitats, while mockingbirds select for exposed agricultural habitats. Correspondingly, the temperature-altered patterns of movement in bluebirds suggest that they are sensitive to heat and may potentially select for thermally-buffered habitats as a result. In contrast, a lack of observed heat sensitivity in mockingbirds suggests that persistence in open habitats could in part be driven by thermal tolerance. While more data are required to make definitive conclusions, considering only patterns at our site with sufficient data, we found significant evidence for temperature-altered patterns of movement. Together, these results suggest that temperature sensitivity could drive patterns of habitat selection.
Previous research also suggests that habitats with low vegetative cover (i.e., without thermally-buffered microclimates) are likely to contain heat-tolerant species [16,17]. For example, Wilson et al. 2007 demonstrated that populations of leaf-cutter ants (Atta sexdens) residing in cities took 20% longer to succumb to high temperatures than ants dwelling in rural areas. In Brans et al. 2017, it was observed that water fleas (Daphnia magna) from urban areas were more tolerant to high temperatures than rural populations, partially because they had smaller body sizes. Both studies imply that organisms must have high heat tolerance to live in habitats with low vegetative cover. This is similar to our finding that mockingbirds, a heat-tolerant species, were more likely to reside in unvegetated agricultural landscapes than were bluebirds, a heat-sensitive species. However, while the previous studies provide evidence that organisms become heat-tolerant in these landscapes due to natural selection, our findings suggest that behavioral differences between heat-tolerant species and heat-sensitive species may also cause unvegetated landscapes to become dominated by heat-tolerant species.
Additionally, we demonstrate that riparian and other thermally-buffered habitats could be crucial to the persistence of heat-sensitive species. Other studies have shown that vertebrates are more likely to exhibit heat-related mortality in habitats with low vegetation cover [12,18]. For example, Zuckerberg et al. 2018 demonstrated that avian survival in small grassland patches was negatively associated with temperature, while survival in large grassland patches was not. Additionally, Lauck et al. 2023 showed that temperature spikes are associated with a decline in bird reproduction across the continental United States for organisms living in agricultural areas, but not for organisms living in forests. These results suggest that vegetation protects vertebrates from heat stress. Although the mechanisms of this protection are not clear, one potential explanation is that vegetation provides shaded areas that animals can use as refuges to avoid lethal temperatures [7]. Additionally, it has been shown that plants regulate local temperatures through evapotranspirative cooling [8], potentially playing a role in protecting vertebrates from heat spikes.
One caveat of our study is that bluebird responses were only marginally significant under multiple regression models that included time of day as a covariate. Associations between bird behavior and time could either be due to circadian rhythms or temperature shifts; it is difficult to statistically disentangle the effects of temperature and time of day. However, the significant results from the models including only temperature imply that bluebirds do indeed alter their behavior in response to environmental factors that likely include temperature.
Conclusion
Our findings provide preliminary evidence that Western Bluebirds are temperature-sensitive and preferentially select vegetated habitats, while Northern Mockingbirds do not preferentially select vegetated habitats. To obtain enough data to provide definitive evidence of these patterns, the methods could be repeated for several more years and across more sites. Nonetheless, the results from this study suggest that anthropogenic land development will be more destructive for heat-sensitive species than for heat-resistant species. As such, we suggest incorporating thermally-buffered habitats such as groups of trees or hedgerows in working landscapes to mitigate the negative impacts of anthropogenic land development on heat-sensitive organisms.
Interview: John Davis
By Isabella Krzesniak.
INTRODUCTION
John Davis is a 5th year Ph.D. candidate in the Integrative Genetics and Genomics graduate group at UC Davis. He works in the Maloof Lab and uses bioinformatics to analyze genetic variation among native California wildflowers in the Streptanthus clade in different environments and uses data to create gene models.
The project he is working on has two main goals. First, he aims to create genomic resources for Streptanthus clade species through reference genomes and transcriptomes, which can be used to analyze differential gene expression in different individuals. Second, he aims to examine the germination niche of Streptanthus clade species, the conditions required for them to germinate and the gene networks expressed during this life stage.
These models have many applications concerning adaptation in the wake of climate change; for instance, they can help ecologists make informed decisions such as whether a crop will function well in a given region as the climate warms. Davis’ work is part of a collaborative study between the Maloof, Gremer, Strauss, and Schmitt labs in the Department of Plant Biology.
What does your research consist of and what are its potential applications?
We’re looking at how plant populations persist in different environments. So even though it’s wildflowers that are closely related, you can also look at how they differ in terms of survival in different environments. If you have an environment that’s great for one crop, but it’s either getting wetter or hotter, the crop might not survive very well. But if you know which genes it has or how it functions, you can move it to a different location or potentially just bring in a different crop that will function well in that region. From an ecological standpoint, it’s a matter of which species will survive and which ones will die off. Underlying all of it are what genes the plant has.
What work are you doing with the project in particular?
The main thing I’m doing right now is building genomic references. We’re trying to do gene expression studies, but if we don’t know what the genes are, we can’t compare the differences in gene expression. So, one of the things I’m doing is building these reference genomes and transcriptomes to determine which genes are in the species. And then from there, I hope to build gene models, construct coexpression networks, and predict germination based on gene expression profiles. To analyze the data, I use Python, Linux, Excel, and R. Another thing I’m doing is building transcriptomes which are collections of just the genes that are expressed. Then, ideally, my goal would be to develop gene networks that would basically tell us which species have these genes that are needed to survive in these environments and which ones don’t.
Why are you studying Streptanthus in particular and what exactly are you doing as part of the study?
The Streptanthus clade has a well-documented phylogeny of closely-related species. Adding genomic resources will improve our ability to perform genetic analyses.
After seed collection, what steps do you take to analyze your data?
We took our seeds and sent them to a collaborating company where they extracted the RNA and then prepared RNA-seq libraries (where they extracted the RNA and then prepared the data), which were then sent to the UC Davis Genome Center where they were sequenced. and then the Genome Center sends us back the sequence reads. We have those reads, we use those to assemble transcripts and to also do gene expression analysis, where we start relating and making models to compare gene expression to different climate variables like precipitation, temperature, and elevation. They’re all correlated.
What kind of models do you employ for data analysis?
It’s just basic linear models and other types of models. You have your variable, which in our case would be germination proportion, and that is a function of gene expression. Gene expression is affected by temperature, genotype, and precipitation, so it’s just models on models.
Has the project been successful?
We did what we set out to accomplish with the funding. Right now, the final bit of sequencing data is coming in and then we’re actually starting to dive into it and produce actual results.
What are the difficulties of working with plants?
I love genetics and genomics stuff and I just fell into working with plants. Plants are the hardest compared to bacteria and humans. Plant genomes are ridiculous and weird things happen all the time. Humans are diploid–we’re boring. I finished working on a project with Brassica napus. It’s an allotetraploid (having four sets of chromosomes derived from different species), which is a hybrid of two different plants, Brassica rapa and Brassica oleracea, so it has two separate diploid genomes in itself. You have the two genomes that are crossing over with each other through homeologous exchange. So when you’re going try to assemble that genome, you don’t know if it came from the Rapa genome or the Oleracea genome. I think strawberries are up to eight copies of each chromosome, so it makes it a lot harder when you’re trying to find alleles. When you’re doing an experiment where you’re trying to knock out alleles of a genome, you have to knock out every copy in each chromosome. Whereas in humans, you only have to knock out two of them to make it homozygous. But in a strawberry, you have to knock out all six of those mutations. Plants just seem like the hardest of the group. And then you have pine trees where genomes have 22.5 gigabases (20 billion base pairs) and humans only have 3.2 gigabases.
How has extreme weather (wildfires, flooding) over the past years affected the study?
So one of the struggles of our project is that we’re looking at how the climate affects germination, but at the beginning of our project, there were droughts like crazy and wildfires, and that affects the genetics of the population and what survives and what doesn’t.
You’re trying to do all these environmental studies that look at the long-term effects compared to now, but when you’re a grad student on a grant, the grant only lasts four to five years. But, how do you take four to five years of data and project it out decades ahead without having data from decades prior? It just gets difficult when you only have four seasons that you can collect data from, and two of those are on fire and one of them is flooding. None of this seems like normal conditions historically. So it can make it a little bit tough to tease out what’s long-term variation in genetics in response to what’s happening in the environment right now.
What makes ecological, as opposed to transgenic research, difficult?
With our studies, we don’t knock out any genes or use any transgenics. Ours is all ecology. That’s the difficulty of our project. With Arabidopsis (a model organism in plant biology), the genes are pretty much homozygous and it’s a lot easier. In our case, all the seeds are collected in the wild, so they’re going to be heterozygous. We can try to make more of the seed by breeding the greenhouse to expand our seed stock, but we can only do so much since it takes up space to make more seed. The field is always going to be changing too. When you collect seeds from one year, the genetics could be completely different from the genetics of the next year.
Why don’t you use transgenics in your studies?
You don’t want to dive into transgenics (organisms whose genes have been altered) because there’s so much pushback against it. These are all natural California species and you don’t want to put something in the environment that can outcompete the natural population.
We’re trying not to affect the study environment that we’re looking at. When we do seed collections, we don’t take from at-risk populations of the certain species, and when we collect seeds, we only take a percentage of the seeds from each plant. We don’t want to affect the growth for the next season, so ultimately, we’re trying to do the minimum amount of disruption to the environment that we’re studying. We potentially hope to use our results for rehabilitation efforts. We’ll be able to tell which ones need more help to survive and which ones are fine.
Canine Cloning: History and Recent Trends
By Sara Su, Animal Science and English ’24
INTRODUCTION
In 1996, Dolly the sheep was the first mammal to be successfully cloned [1, 2]. Since then, 22 other animal species have been cloned, including rats, mice, cattle, goats, camels, cats, pigs, mules, and horses [3-12]. Among these, about 19 species have clones surviving to adulthood. In 2005, the first cloned dog to survive to adulthood was named Snuppy, who was derived from somatic cells from the ear-skin of a male Afghan hound. He was the 15th animal to be cloned and lived to the age of 10 [13]. He was cloned using Somatic Cell Nuclear Transfer (SCNT), a common method that involves removing the nucleus from an oocyte (egg cell) and replacing it with a nucleus from a somatic cell, typically a fibroblast [14]. Fibroblasts are a type of stromal cell found in connective tissues such as the skin and tendons – they are often used in cloning because they are relatively easy to culture. After nuclear transfer, this reconstructed oocyte, which is similar to a fertilized egg, is then activated and transferred into the oviduct of a surrogate female, usually in groups of 10-15 cells. After pregnancy is confirmed, viable offspring are born via C-Section [13-16]. Though SCNT is the most viable method of cloning so far, it remains very inefficient and the live birth ratio is extremely low [13, 17, 18]. Nearly 30 years after Dolly, little is understood about cloning, which presents unique challenges to different species; this review will discuss the relevance of the canine model in regards to human health, canine-specific challenges in using SCNT for cloning, as well as recent trends among successfully cloned dogs.
The Interest in Dogs as a Medical Model
Overall, dogs have become increasingly relevant as a medical model for human diseases in the 21st century. This is because many heritable canine diseases are orthological to human ones, which means they share similar traits and functions [19]. The dog genome is found to be closer to the human genome than the mouse genome – while mice are commonly used as medical models for humans, canine models have also proven to be useful for comparative studies due to their relatively long life, larger size, and similar tissue functions[20]. There are at least 350 shared genetic diseases between dogs and humans discovered so far, affecting a variety of systems such as the dermatological, lysosomal, hematological/immunological, and muscular/skeletal systems [21]. All of these contribute to the rising application of canine medical models to study disease mechanisms for well-known conditions such as Alzheimers and diabetes, while also being able to explore clinical therapies for rare genetic diseases that would otherwise be difficult to study. Other fields of study using canine colonies include but are not limited to: organ transplants, drug development, non-invasive biomarker generation, and psychological disorders [19-24].
Dog-Specific Challenges in Cloning
There are a few species-specific reasons why dog cloning remains inefficient. Cloning efficiency, defined as the ratio of live offspring coming from the number of transferred reconstructed oocytes, is usually not more than 3% across all species, regardless of the age or type of donor cell. Additionally, the average cloning efficiency between breeds does not differ significantly [21]. For canines, cloning efficiency is higher than many other reported species, at 2% [25]. However, this is still an extremely low number, and a specific challenge when it comes to dogs is the viable maturation of oocytes in vitro [13, 26]. It should be noted that the pregnancy rate can be increased by increasing the number of reconstructed oocytes injected into surrogates, but cloning efficiency itself is not changed. Another issue with canines is the vast number of breeds within the species – it is difficult to select for compatible nuclear/oocyte donors, in addition to adequate surrogate selection [21]. Finally, a widespread issue with cloned individuals is postnatal care – although survival is pretty much guaranteed for clones that are born healthy, cloned animals are just as vulnerable to disease and poor management as any other species [21]. Dolly the sheep died early from such an instance, rather than complications directly related to cloning. Overall, there is insufficient knowledge of the nuances of canine reproductive systems, including a lack of comprehensive protocols regarding oocyte maturation in culture and specific methods of post-natal clone care, leading to further difficulties in dog-specific cloning.
Snuppy and His Clones
As previously stated, the first dog to be successfully cloned and survive to adulthood was a male Afghan hound named Snuppy, short for Seoul National University Puppy. Snuppy was born in 2005, and was the only survivor out of 123 recipient surrogates. Snuppy was cloned from fibroblast cultures derived from the biopsy of the ear-skin of an Afghan hound named Tai. He was confirmed to be genetically identical to Tai through the use of canine-specific biomarkers [27]. For this experiment, 3 out of 123 surrogates resulted in pregnancies, 2 were carried to term, and 1 survived to adulthood – the other puppy died on day 22 due to aspiration pneumonia after experiencing neonatal respiratory distress. Although the efficiency of cloning is very low in the first place, this particular experiment had a cloning efficiency rate much lower than expected – 2 puppies were born to 123 surrogates, or 1.6% [13]. Snuppy ended up living to be 10 years old, while his donor Tai lived to be 12 years old – both individuals died of cancer-related causes, but were generally healthy until then. It should be noted that the median lifespan of Afghan hounds is reported to be 11.9 years, so their lifespans were not out of the norm [28].
In 2017, Snuppy was cloned. This time the cloning efficiency and success rates were much higher and resulted in 3 clones who are still alive today. Rather than using fibroblasts, this experiment used adipose-derived mesenchymal stem cells (ASCs). Then, ASCs were cultured with Dulbecco’s Modified Eagle Medium(MDEM), a technique that increases oocyte fusion rate in SCNT[29]. This experiment resulted in pregnancy and delivery rates of 42.9% (3 dogs out of 7 recipients) and 4.3% (4 clones out of 94 embryos). Compared to Snuppy’s 2.4% (3 out of 123) and 0.2% (2 from 1,095), these changes in technique correlated in a huge jump in overall efficiency [13, 28].
Other studies have also been published exploring the viability of cloned working dogs. For dogs, SCNT can be used regardless of sex, age, and breed [13, 30]. It was recently concluded that cloned dogs have similar behavior patterns to their cell donors, and can lead healthy lives with life spans comparable to naturally bred dogs [21, 29]. Overall, about 20% of dog breeds recognized by the American Kennel Club have been successfully cloned, which is highly successful compared to other mammals [21]. Though more research is needed to improve dog cloning efficiency, it has already been proven that clones of drug detection dogs[31] and cancer-sniffing dogs[33] outperform naturally bred dogs, scoring higher averages on qualification tests for these services [32-33].
CONCLUSION
To conclude, both studies regarding the creation of Snuppy and the subsequent cloning of his cells demonstrate great potential for the common use of canine clones in the modern world. Multiple obstacles regarding canine cloning were recognized and overcome, though the cloning efficiency rate can be further improved by obtaining greater knowledge of the canine reproductive system. Additionally, it was proven that clones who are born healthy aren’t at a larger risk for diseases or a shortened lifespan – they are comparable to the average puppy. All of this contributes to the feasibility of cloning working dogs – studies are already exploring the possibility of using clones of dogs that perform drug- and disease- detection, knowing that the physical qualifications for such jobs are strongly linked to specific genetic traits.
REFERENCES
- Wilmut I, Schnieke AE, McWhir J, Kind AJ, Campbell KH. Viable offspring derived from fetal and adult mammalian cells. Nature. 1997 Feb 27;385(6619):810-3. doi: 10.1038/385810a0. Erratum in: Nature 1997 Mar 13;386(6621):200. PMID: 9039911.
- Campbell KH, McWhir J, Ritchie WA, Wilmut I. Sheep cloned by nuclear transfer from a cultured cell line. Nature. 1996 Mar 7;380(6569):64-6. doi: 10.1038/380064a0. PMID: 8598906.
- Zhou Q, Renard JP, Le Friec G, Brochard V, Beaujean N, Cherifi Y, Fraichard A, Cozzi J. Generation of fertile cloned rats by regulating oocyte activation. Science. 2003 Nov 14;302(5648):1179. doi: 10.1126/science.1088313. Epub 2003 Sep 25. PMID: 14512506.
- Wakayama, T., Perry, A., Zuccotti, M. et al. Full-term development of mice from enucleated oocytes injected with cumulus cell nuclei. Nature 394, 369–374 (1998). https://doi.org/10.1038/28615
- Kato Y, Tani T, Sotomaru Y, Kurokawa K, Kato J, Doguchi H, Yasue H, Tsunoda Y. Eight calves cloned from somatic cells of a single adult. Science. 1998 Dec 11;282(5396):2095-8. doi: 10.1126/science.282.5396.2095. PMID: 9851933.
- Cibelli JB, Stice SL, Golueke PJ, Kane JJ, Jerry J, Blackwell C, Ponce de León FA, Robl JM. Cloned transgenic calves produced from nonquiescent fetal fibroblasts. Science. 1998 May 22;280(5367):1256-8. doi: 10.1126/science.280.5367.1256. PMID: 9596577.
- Baguisi, A., Behboodi, E., Melican, D. et al. Production of goats by somatic cell nuclear transfer. Nat Biotechnol 17, 456–461 (1999). https://doi.org/10.1038/8632
- Wani NA, Wernery U, Hassan FA, Wernery R, Skidmore JA. Production of the first cloned camel by somatic cell nuclear transfer. Biol Reprod. 2010 Feb;82(2):373-9. doi: 10.1095/biolreprod.109.081083. Epub 2009 Oct 7. PMID: 19812298.
- Shin, T., Kraemer, D., Pryor, J. et al. A cat cloned by nuclear transplantation. Nature 415, 859 (2002).
- Polejaeva, I., Chen, SH., Vaught, T. et al. Cloned pigs produced by nuclear transfer from adult somatic cells. Nature 407, 86–90 (2000). https://doi.org/10.1038/35024082
- Woods GL, White KL, Vanderwall DK, Li GP, Aston KI, Bunch TD, Meerdo LN, Pate BJ. A mule cloned from fetal cells by nuclear transfer. Science. 2003 Aug 22;301(5636):1063. doi: 10.1126/science.1086743. Epub 2003 May 29. PMID: 12775846.
- Galli, C., Lagutina, I., Crotti, G. et al. A cloned horse born to its dam twin. Nature 424, 635 (2003). https://doi.org/10.1038/424635a
- Lee BC, Kim MK, Jang G, Oh HJ, Yuda F, Kim HJ, Hossein MS, Kim JJ, Kang SK, Schatten G, Hwang WS. Dogs cloned from adult somatic cells. Nature. 2005 Aug 4;436(7051):641. doi: 10.1038/436641a. Erratum in: Nature. 2005 Aug 25;436(7054):1102. Erratum in: Nature. 2006 Mar 9;440(7081):164. Erratum in: Nature. 2006 Oct 12;443(7112):649. Shamim, M Hossein [corrected to Hossein, M Shamim]. PMID: 16079832.
- Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006 Aug 25;126(4):663-76. doi: 10.1016/j.cell.2006.07.024. Epub 2006 Aug 10. PMID: 16904174.
- Kim GA, Oh HJ, Park JE, Kim MJ, Park EJ, Jo YK, Jang G, Kim MK, Kim HJ, Lee BC. Species-specific challenges in dog cloning. Reprod Domest Anim. 2012 Dec;47 Suppl 6:80-3. doi: 10.1111/rda.12035. PMID: 23279471.
- Moon, P. F., Erb, H. N., Ludders, J. W., Gleed, R. D. & Pascoe, P. J. Perioperative management and mortality rates of dogs undergoing cesarean section in the United States and Canada. J. Am. Vet. Med. Assoc. 213, 365–369 (1998).
- Malin K, Witkowska-Piłaszewicz O, Papis K. The many problems of somatic cell nuclear transfer in reproductive cloning of mammals. Theriogenology. 2022 Sep 1;189:246-254. doi: 10.1016/j.theriogenology.2022.06.030. Epub 2022 Jun 30. PMID: 35809358.
- Tsunoda Y, Kato Y. Recent progress and problems in animal cloning. Differentiation. 2002 Jan;69(4-5):158-61. doi: 10.1046/j.1432-0436.2002.690405.x. PMID: 11841470.
- Gurda BL, Bradbury AM, Vite CH. Canine and Feline Models of Human Genetic Diseases and Their Contributions to Advancing Clinical Therapies . Yale J Biol Med. 2017 Sep 25;90(3):417-431. PMID: 28955181; PMCID: PMC5612185.
- Parker HG, Kim LV, Sutter NB, Carlson S, Lorentzen TD, Malek TB, Johnson GS, DeFrance HB, Ostrander EA, Kruglyak L, 2004: Genetic structure of the purebred domestic dog. Science 304, 1160–1164.
- Olsson PO, Jeong YW, Jeong Y, Kang M, Park GB, Choi E, Kim S, Hossein MS, Son YB, Hwang WS. Insights from one thousand cloned dogs. Sci Rep. 2022 Jul 1;12(1):11209. doi: 10.1038/s41598-022-15097-7. PMID: 35778582; PMCID: PMC9249891.
- Sargan, D.R. IDID: Inherited Diseases in Dogs: Web-based information for canine inherited disease genetics. Mamm Genome 15, 503–506 (2004). https://doi.org/10.1007/s00335-004-3047-z
- Zhang J, Chen X, Kent MS, Rodriguez CO, 2009: Establishment of a dog model for the p53 family pathway and identification of a novel isoform of p21 cyclin-dependent kinase inhibitor. Mol Cancer Res 7, 67–78.
- Zhang J, Chen X, Kent MS, Rodriguez CO, 2009: Establishment of a dog model for the p53 family pathway and identification of a novel isoform of p21 cyclin-dependent kinase inhibitor. Mol Cancer Res 7, 67–78.
- Yanagimachi R. Cloning: experience from the mouse and other animals. Mol Cell Endocrinol. 2002 Feb 22;187(1-2):241-8. doi: 10.1016/s0303-7207(01)00697-9. PMID: 11988333.
- Lange-Consiglio, A. et al. Oviductal microvesicles and their effect on in vitro maturation of canine oocytes. Reproduction 154, 167–180. https://doi.org/10.1530/REP-17-0117 (2017).
- Lee JB, Park C; Seoul National University Investigation Committee. Molecular genetics: verification that Snuppy is a clone. Nature. 2006 Mar 9;440(7081):E2-3. doi: 10.1038/nature04686. PMID: 16528814.
- Kim MJ, Oh HJ, Kim GA, Setyawan EMN, Choi YB, Lee SH, Petersen-Jones SM, Ko CJ, Lee BC. Birth of clones of the world’s first cloned dog. Sci Rep. 2017 Nov 10;7(1):15235. doi: 10.1038/s41598-017-15328-2. PMID: 29127382; PMCID: PMC5681657
- Kim GA, Oh HJ, Lee TH, Lee JH, Oh SH, Lee JH, Kim JW, Kim SW, Lee BC. Effect of culture medium type on canine adipose-derived mesenchymal stem cells and developmental competence of interspecies cloned embryos. Theriogenology. 2014 Jan 15;81(2):243-9. doi: 10.1016/j.theriogenology.2013.09.018. Epub 2013 Oct 21. PMID: 24157230.
- Kim MJ, Oh HJ, Hwang SY, Hur TY, Lee BC. Health and temperaments of cloned working dogs. J Vet Sci. 2018 Sep 30;19(5):585-591. doi: 10.4142/jvs.2018.19.5.585. PMID: 29929355; PMCID: PMC6167335.
- Choi J, Lee JH, Oh HJ, Kim MJ, Kim GA, Park EJ, Jo YK, Lee SI, Hong DG, Lee BC. Behavioral analysis of cloned puppies derived from an elite drug-detection dog. Behav Genet. 2014 Jan;44(1):68-76. doi: 10.1007/s10519-013-9620-z. Epub 2013 Dec 17. PMID: 24343203.
- Kim MJ, Park JE, Oh HJ, Hong SG, Kang JT, Rhim SH, Lee DW, Ra JC, Lee BC. Preservation through cloning of superior canine scent detection ability for cancer screening. J Vet Clin 2015;32:352–355.
- Lee SH, Oh HJ, Kim MJ, Kim GA, Setyawan EMN, Ra K, Abdillah DA, Lee BC. Dog cloning-no longer science fiction. Reprod Domest Anim. 2018 Nov;53 Suppl 3:133-138. doi: 10.1111/rda.13358. PMID: 30474338.
Is Rejuvenating Research Akin to the Fountain of Youth?
By Barry Nguyen, Biochemistry & Molecular Biology
Authors note: I have always been interested in the aging research field. So much so, I watched ALL 8 podcasts episodes of Dr. David Sinclair’s aging podcast during the summer (which can be found on Spotify–highly recommend). A lot of the discussion is centered around developments in rejuvenating research and the various biological pathways associated with aging that can be activated depending on one’s lifestyle.
As we age, not only does our outward appearance change, but the biological clock hidden within our cells does too. The biological clock, an intrinsic feature shared among cells, allows for partial genetic reprogramming, creating an opportunity to defy the concept of time and aging [2]. This recent development of gene therapy is our closest bet to finding the Fountain of Youth.
About a decade ago, Shinya Yamanaka had shared the Nobel Prize for discovering a cocktail of proteins with the potential to revert somatic cells back into stem cells. These transcription factors are Oct 4, Sox2, Klf4, and cMYC and are now known as Yamanaka Factors [1]. Typically referred to as OSKM genes, the Yamanaka Factors play a significant role in regulating the developmental signaling network necessary for stem cell pluripotency (defined as the capacity to differentiate to virtually all types of cells) and therefore can revert the identity of virtually any cells in the body.
Recent advancements in the study of aging at the molecular level have been significant according to Dr. Diljeet Gill, a postdoctoral researcher at the Salk Institute’s Reik Lab, which conducts research on rejuvenation.“These developments have led to techniques that enable researchers to measure age-related biological changes in human cells,” says Dr. Gill [3].
Scientists have identified two defining phenomena of the aging process to assist in characterizing signs of aging. The first is the epigenetic clock, which describes the chemical tags present throughout the genome. The second hallmark is the transcriptome, which encapsulates all the gene readouts produced by the cells.
As an organism ages, the epigenetic markers become widely different. Epigenetic modifications are an intrinsic biological feature of aging, with older organisms showing a significantly different epigenetic profile than younger organisms [1]. Because Yamanaka Factors are able to alter the epigenetic landscape of somatic cells, reprogramming-induced rejuvenation strategies using the OSKM genes are made possible. Furthermore, an animal’s epigenome can be entirely reset by chemically modifying DNA and proteins that help regulate gene activity. Essentially, this form of gene editing allows scientists to revert the aging of cells.
Cells that have undergone cellular reprogramming not only appear younger, but also function like young cells. In a new study conducted in a collaboration between Dr. In Izpisua and the Altos Lab at the Salk institute have found that mice receiving long-term treatments of Yamanaka factors expressed a gene expression and metabolism profile that resembled that of much younger mice [2].
Results of the study may open up a future of therapeutic possibilities. Researchers observed notable effects in the APBA2 gene, a gene associated with Alzheimer’s Disease and the MAF gene, a gene associated with cataract development, in their transcriptional profile; both displayed a more youthful, more abundant level of transcription, meeting one of the criteria of reverse aging. The results were promising and, according to Dr. Gill, “proved that cells can be rejuvenated without losing their function and that rejuvenation looks to restore some function to old cells.” Moreover, Professor Reik, the group leader, stresses that future work can move towards targeting rejuvenating genes to reduce effects of aging.
The prospects of this new facet of aging research are extraordinary. However, it should be noted that yamanaka factors have the capacity to induce Teratomas, a germ cell tumor. Despite a limit in studies investigating the extent to which Yamanaka Factors can induce cell tumors, the ability for Yamanaka Factors to induce pluripotency and stem cell-like properties allow cells to reach a cancer-like state. Cancers are typically characterized as uncontrolled cell division. Furthermore, the differentiated cell’s ability to revert to pluripotency significantly increases the possibility for cells to take on cancer-like states.
Nevertheless, studies within this field are exciting, and researchers are united by a common goal of identifying methods to slow or even reverse the processes that lead to disease. As research continues, society is at a rapid pace in reaching a point where predicting, preventing, and even treating diseases through cellular rejuvenation becomes a reality.
References:
- Cellular rejuvenation therapy safely reverses signs of aging in mice. Salk Institute for Biological Studies. (2023, January 5). Retrieved February 5, 2023, from https://www.salk.edu/news-release/cellular-rejuvenation-therapy-safely-reverses-signs-of -aging-in-mice/
- Fan, S. (2022, April 4). Scientists used cellular rejuvenation therapy to rewind aging in mice. Singularity Hub. Retrieved February 5, 2023, from https://singularityhub.com/2022/04/06/scientists-used-cellular-rejuvenation-therapy-to-re wind-aging-in-mice/
- Garth, E. (2022, May 12). Research reverses aging in human skin cells by 30 years. Longevity.Technology – Latest News, Opinions, Analysis and Research. Retrieved February 5, 2023, from https://longevity.technology/news/research-reverses-aging-in-human-skin-cells-by-30-ye ars/
- Two research teams reverse signs of aging in mice | science | AAAS. (n.d.). Retrieved February 5, 2023, from https://www.science.org/content/article/two-research-teams-reverse-signs-aging-mice
The Fungus Among Us: Fungal Presence in Cancerous Growths
By Mirabel Sprague Burleson, Biological Sciences ‘24
Cancer can contaminate nearly every tissue in the human body, arising from complex and diverse mutations that impact many genes. It’s incredibly widespread and lethal and is currently one of the most common causes of death in the United States, second only to heart disease by a small margin [1]. Despite the immense resources poured into cancer research, it remains a major issue in modern medicine. One barrier to the advancement of cancer treatments is finding a way to successfully treat cancer cells without harming the healthy cells surrounding them. Common treatments such as chemical and radiation therapy damage normally functioning cells, resulting in dangerous and debilitating side effects.
In order to develop a treatment that is capable of successfully isolating cancer cells, researchers must understand the hallmarks of cancer. Knowing the distinct characteristics of cancerous cells, such as abnormal division rate, increased mobility, and irregular organelles, allows researchers to develop treatments that attack these specific biological targets. Modern research focuses on determining unique bacterial presence in cancerous cells, as bacteria are an easy target for many treatments.
Recent studies on bacterial presence in cancer found metabolically active cancer-specific communities of bacteria in tumor tissues, which lead to their inclusion in updated cancer hallmarks [2]. In the wake of these findings, Narunsky-Haziza et al. (2022) conducted a study to determine if fungi could also be detected in tumor tissues [3]. Fungal presence in cancer cells could provide a new target for treatments.
The Narunsky-Haziza et al. study sources samples from four independent cohorts: The Weizmann Institute of Science (WIS), The Cancer Genome Analysis (TCGA), Johns Hopkins University, and the University of California at San Diego (UCSD) [3]. Narunsky-Haziza et al. took 17,401 tissue, blood, and plasma samples across 35 cancer types from these four cohorts. 104 samples made of a waxy substance called paraffin and 191 DNA-extraction negative controls were added to the WIS cohort samples to account for potential contamination by environmental fungi or fungal DNA introduced during handling and processing (other cohorts’ samples had adequate controls for fungal presence) [3,4,5]. These samples were then reexamined by Narunsky Haziza et al. for fungal presence with internal transcribed spacer 2 (ITS2) amplicon sequencing [3].
The ITS2 region of nuclear ribosomal DNA is considered one of the best DNA barcodes for sequencing because of its variability between even very closely related species and the ease of amplification [6]. ITS2 amplicon sequencing allows researchers to examine the ITS2 region and identify variations between samples. Narunsky-Haziza et al. use this method to cross-examine known fungal sequences and the sequences found in the samples to identify the different fungal nucleic acids present in the samples’ mycobiomes (fungal microbiome) [3].
Using ITS2 amplicon sequencing, this study found that while tumor bacterial richness is much higher than fungal richness, there was a clear presence of fungi in the samples examined [3]. Fungi were detected in all 35 cancer types examined, although not all individual tumors were positive for fungal signals [3]. Most fungi were found to be within cancer and immune cells, similar to bacterial presence [3]. Interestingly, significant correlations were found between specific fungal presence and tumor types, immunotherapy, age, and smoking habits; however, whether this is correlated or casually associated is yet to be determined [3]. Also, an unexpected significant positive correlation between fungal and bacterial richness was found in bone, breast, brain, and lung samples, though not in any of the others [3].
This study does present several caveats. For one, differences in sample preparation, sequencing, bioinformatic pipelines, and reference databases exist between the four cohorts, which affect bacteriome analyses. Another potential issue is that although there was a large number of samples included, the stages of cancer across samples were different for all four of the cohorts, which created high variability in the data [4,5]. The WIS and TCGA cohorts also showed high variation in mycobiome richness, which Narunsky-Haziza et al. suspect is likely due to the negative controls introduced to the WIS cohort as well as potential split reads found in the TCGA cohort [3,4,5]. A split read is a sequence that partially matches the reference genome in at least two places, but has no continuous alignment to it. Split reads can indicate a difference in structure between the sample and the reference genome.
Additionally, while four different staining methods were used to find fungal presence and tumor-specific localization patterns, they proved to have differing sensitivities across cancer types. As all of the staining methods used can only detect certain subsets of the fungal kingdom, a relatively high false-negative rate can be expected. In contrast, although each cohort used negative controls, some false-positive results are inevitable [3].
Although this study successfully broadened the cancer microbiome landscape, these findings do not establish any causality in the presence of fungal nucleic acids. Narunsky-Haziza et al. hope that this first pan-cancer mycobiome atlas will serve as a key player in informing future cancer research to help characterize new information for cancer diagnostics and therapeutics [3]. While it remains unclear if fungal DNA plays a role in cancer development or severity, with further research, fungal presence could prove to be a helpful biomarker and potentially provide advancement in cancer treatments for the benefit of patients worldwide.