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The impossible story of an African pioneer in colonial America

August 19, 2019

Anthony Johnson's place in American history significant, says ASU historian

Anthony Johnson arrived in Virginia in 1621Source: "1619: Virginia's First Africans" (Hampton History Museum, www.HamptonHistoryMuseum.org/1619), various sources. He farmed other people’s land in the new English colony before he acquired land of his own and wealth. He married Mary, had children — two daughters and two sons — and passed on his own property to his heirs before his death in 1670. 

In the romanticized belief in hard work, values and upward mobility, Anthony Johnson’s life could have been the definition of the American dream. 

Except it wasn’t. 

Anthony Johnson was born in AngolaSource: Virginia Humanities, “Site of 17th Century Estate of Anthony and Mary Johnson,” AfroVirginia, http://afrovirginia.org/items/show/388, various sources, a west coast country in south central Africa almost 7,000 miles from the coast of Virginia. He is believed to have arrived in the English settlement by ship under the name “Antonio” but not of his own volition. Johnson was one of millions of people of African descent forcibly brought to the Americas and enslaved for almost 250 years in the United States. His harrowing journey through the Middle PassageThe Middle Passage refers to the stage of the triangular Atlantic slave trade in which millions of enslaved Africans were forcibly packed onto ships and transported to the Americas as human cargo. Many died during the passage. Their bodies were thrown into the Atlantic Ocean. and traumatic transitions to survive cruelty and hardship in a foreign land was not unlike the experiences of many others.

Except it was. 

Calvin Schermerhorn

“This is the beginning of African America in English America,” said Calvin Schermerhorn, a scholar of African American studies in the School of Historical, Philosophical and Religious Studies at Arizona State University. “It is very much a part of our national story to know that the people who arrived in Virginia did not arrive in a position to build a city upon a hill. They arrived and were immediately exploited and put to unpaid labor. So to have an achievement story like Anthony Johnson’s emerge from this period is remarkable and merits more reflection on the narratives that compose our history.” 

Although Anthony Johnson is recorded as having arrived in Virginia in 1621, Schermerhorn and other historians believe he had likely seen the colonial peninsula before — in August 1619, around the date marked for this year’s 400-year commemoration of the day “20 and odd AfricansVirginia colonist John Rolfe documented the arrival of the ship The White Lion and “20 and odd” Africans in a journal that has been cited repeatedly in academic literature and textbooks. Rolfe is also known for his marriage to Pocahontas of the Native American Powhatan tribe in Virginia.,” reportedly disembarked the English ship The White Lion at Virginia’s Old Point Comfort. 

Piecing together research and literature by genealogists and fellow scholars, Schermerhorn says it is likely that Anthony and his future wife, Mary, also from Angola, were being held captive on a second English ship called The Treasurer that docked on the Virginia coastline a few days after The White Lion in 1619. Five more people of African descent were traded for supplies for The Treasurer. The remaining captives, including Anthony and Mary, were taken to Bermuda and likely labored on a tobacco estate before Anthony was shipped to Virginia for a permanent stay. 

Upon his landing in Virginia in 1621, Anthony was put to work on Bennett’s Welcome, a plantation Schermerhorn describes as a fortified compound with 60-odd people, mostly indentured servants, working the land. The plantation suffered numerous casualties during the Powhatan Attack of 1622 in which Native Americans fought to remove colonists from their lands. Anthony was among a handful of survivors. Then, as fate would have it, Mary arrived at the Bennett plantation later that same year. The two married and later gained freedom. They would establish themselves in Virginia’s Northampton County in the 1640s, patenting 250 acres of land in the colonial settlement where they grew corn and tobacco and assembled a workforce of indentured laborers — and enslaved people.   

“Here are people who arrived under these circumstances and did the impossible,” Schermerhorn said. “They somehow slipped the chains; rose into a property-owning class; passed on property to their children; sued their white neighbors over property and other injustices — and won.” 

The Johnsons’ legal battle over a black bound worker named John Casor was among their more controversial victories. When Casor, who initially worked on Johnson’s property, left the Johnsons to work as a contracted indentured servant for Johnson’s white neighbor, Johnson sued his neighbor for Casor’s return, claiming he still “owned” Casor. The Northampton Court agreed with Johnson in a 1655 appeal ruling after initially siding with Johnson’s neighbor and Casor was ordered returned to Johnson. The ruling made John Casor the first person of African descent in Virginia to be declared a slave as the result of a civil case. 

Handwritten court ruling for Anthony Johnson and his servant John Casor

Handwritten court ruling for Anthony Johnson's case over his servant. (March 8, 1655) Image courtesy Library of Virginia, Northampton County: Deeds, Wills

“For a time class trumped race,” said Schermerhorn, referring to Anthony and Mary Johnson’s notable standing in the community along with a handful of other African-descended people who had also managed to gain freedom and become successful property owners in their own right. Schermerhorn adds that the court could have decided against the Johnsons in the Casor case but decided that it was more important to preserve the economic system, which depended heavily on keeping people enslaved, by enforcing servitude for life against Casor. 

“At that moment, it was more important that Casor was enslaved than the fact that Johnson, a man of African descent, was an enslaver,” Schermerhorn said. In making this point, Schermerhorn noted the existence of underinformed arguments of convenience that seek to either revere or blame Anthony Johnson for establishing slavery in Virginia. Schermerhorn says historical records show that African-descended people had been punished with servitude for life well before the Casor case. 

“Anthony Johnson probably didn’t see himself as black or African,” Schermerhorn said. “He saw himself as Angolan and probably didn’t consider John Casor as someone in his group.” That said, Schermerhorn says there were other Angolans in the neighborhood who also owned property and may have been even more exceptional in wealth and status than Anthony and Mary Johnson. The Johnsons’ story, however, has attracted more attention than the others due in part to a number of extraordinary circumstances that played out in the courts — the Casor case being one of them and Mary and her daughters petitioning and winning tax-exempt statuses for life — a social standing reserved exclusively for white women at the time. 

Where most accounts of the Johnsons’ remarkable history drops off after Anthony’s death in 1670, Schermerhorn cites research that seems to track the movements of Mary Johnson and her sons after racist practices became more common and even legitimized by the passage of several laws in Virginia. 

“The family was pushed to the margins,” Schermerhorn said, citing the research of genealogist Paul HeineggPaul Heinegg's research includes the two-volume work "Free African Americans of North Carolina, Virginia, and South Carolina from the Colonial Period to about 1820." . When Anthony died, the courts seized his land in Virginia, claiming he did not leave a will and that because he was “Negro” he was alien and not eligible to own land. Johnson’s sons John and Richard had to defend themselves against the language that was also used against them in the attempts to seize the property they owned.  

The family reportedly moved to Somerset County, Maryland, where Anthony had leased a plot of land before he died. Mary lived into her 90s, and bequeathed land animals to her grandchildren, according to Schermerhorn. He says further research suggests Johnson descendants also moved to Delaware and then to North Carolina, demonstrating the family’s resilience time and again in an increasingly unwelcoming society. 

Research has also provoked a number of questions relative to how the trajectory of American culture and values might have been different for descendants of the Johnsons and other African-descended Americans had it not been for the deliberate and conscious decision to stratify society through race-based slavery. 

“On the 400th anniversary of the arrival of the first Africans in Virginia, we have to look at the origins of the chasm of the widening racial wealth gap in present day United States,” Schermerhorn said. “The history of the Johnson family is significant in that they saw American society in its infancy. They saw the opportunities; they grasped the opportunities; they made good on the promise that we usually think of as the American Dream — pulling oneself up by the bootstraps and succeeding through perseverance and playing by the rules. They illustrate the possible.

“They also illustrate a moment after 1619 when America could have been different,” Schermerhorn added. “There is no necessary historical pathway that involves race-based slavery, yet this is what the Johnsons witnessed and endured when this system came to rob them of their property and seize what they had worked hard for.” 

This, Schermerhorn says, “is part of our founding story” and one that needs to be retold regularly, beyond commemorative anniversaries and the month of February February is the month designated to observe important people and events in the history of African diaspora. It is known as Black History Month or African American History Month.“because the story of African America is — without hyphenate — American history.”

Top photo: Anthony Johnson Clerical Signature (Somerset County Court Land Records), Wikimedia Commons/Triangular Trade by Semhur and Francois Nancy, Wikimedia Commons

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ASU ecologist says state’s rivers are facing rocky waters

August 15, 2019

Heather Bateman studies how human land use affects vertebrate populations, habitats and riparian systems

An Arizona State University professor said the state’s rivers are only going to see shortages in the future, which will have a direct impact not only on humans, but wildlife and their habitats.

Two factors are driving this: climate change and human population growth.

“The Southwest will face major challenges in the future by needing to balance anthropogenic water consumption with water that nature needs,” said Heather Bateman, an associate professor with ASU’s College of Integrative Arts and Sciences. “We might need to set priorities as a state or region on which ecosystems should hold the right to maintain their hydrologic flows.”

ASU Now spoke to Bateman, a field ecologist who studies terrestrial wildlife such as birds, reptiles, and amphibians, on this troubling development and what it will mean for the future of Arizona’s river system.

Question: How does nature use water?

Answer: Water is rare in the arid southwestern United States. Rivers and their floodplain habitats make up less than 3% of the total land area. These habitats, called riparian areas, are interfaces between aquatic and terrestrial systems. Riparian areas support trees and woody vegetation that require shallow groundwater. These forests offer a cooler and more humid microclimate, compared to the surrounding Sonoran Desert. Most wildlife relies on riparian areas at some point during their life cycle. This means that animals use the habitat for migration or commuting, to find food and mates, and some species will only raise their young there. Several species of fish and wildlife that have state and federal projection are found exclusively in streams and riparian areas. Unfortunately, because these areas have been modified and diminished, species needing these areas have declined in numbers and are of conservation concern.

Q: How is Phoenix’s burgeoning population straining our rivers and ecosystems?

A: Phoenix is the fifth largest city and Maricopa County is among the fastest growing in the U.S. This means that the demand for water by humans will likely increase for consumption, municipal, industrial and agriculture uses. As industry changes and land use changes, water use will also fluctuate. For example, converting an alfalfa field to residential homes will save water, but converting desert to residents will consume more water.   

Q: What will this potential shortage do to our state’s riparian system?

A: Having less water in streams means that groundwater in riparian areas will lower and trees and woody vegetation needing this will die back. Sometimes the timing of high flow events is very important. For example, cottonwood and other trees set seeds to be released during the season when water flow is high. These floods scour river banks and deposit the seeds in suitable substrate. Without floods, these plants cannot recruit, or produce the next generation. When these flood-adapted plant species die back, other plants will take their place and a different suite of wildlife will start to use these areas. Our research has found that in highly modified rivers, non-native plants that don't need floods become established. We find lower diversity of lizards, amphibians and small mammals in these modified areas. Interestingly, even intermittent waters are important resources in the desert. If these arroyos and washes don't flow during monsoon or winter rainy seasons, those habitats can also experience decreases in biodiversity.

Q: Are there examples where resource managers have done a good job keeping the state’s rivers flowing?

A: Some natural resource agencies have asked the state for permission to keep water in the stream, sort of a water right, and not be withdrawn for other uses. The process involves documenting how flows in rivers are important for maintaining diverse habitat and wildlife and that this is a beneficial use of water. As I mentioned before, some areas might be worth prioritizing for keeping water in the stream for important areas. Arizona has only two streams with the federal designation of Wild and Scenic. The Wild and Scenic Rivers Act was signed into law over 50 years ago and was used to prioritize areas deemed to have significant natural resource value. In the U.S., less than 1% of our rivers have this protection. 

Q: What does this possible shortage mean for future wildlife?

A: When streams become de-watered or lose their high flows, I mentioned that the forest composition can change. Species needing more water will be replaced by more drought-tolerant species. Same can happen with the wildlife. Animals that need plants or water for feeding and nesting will be replaced by species that are more tolerant of a wider range of conditions. These generalist species can be found in other habitats and the uniqueness of riparian areas will decline.  

Q: What can Arizona residents do to improve our water and rivers?

A: Go visit these areas. Take a walk along a stream and listen for birds and see if there are flowers and pollinators around. Feel the coolness of these areas as they provide shade from the sun. I find these areas to be inspirational and not only are they good for the wildlife, but they are good for us too. Three streams come into Phoenix, which is why we call it the Valley. These streams are water sources for humans too. Pay attention to how decision-makers handle water issues. For example, how might a border wall that blocks stream flow affect the San Pedro? The headwaters of the San Pedro are in Mexico and the stream flows north into Arizona. This stream also has an important conservation designation. Without headwater flows, there is less water to support vegetation, and less vegetation to support wildlife or future human growth. Besides, it's good for people to connect with nature. I hope that people can see Phoenix as a river city.

Top photo: Heather Bateman, an associate professor with ASU’s College of Integrative Arts and Sciences, stands outside the Boyce Thompson Arboretum in Superior, Arizona. Photo by Deanna Dent/ASU Now 

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Study reveals how phone phishing catches its prey

August 14, 2019

New ASU research identifies how scammers use social engineering to exploit victims' vulnerabilities

Consumers have increasingly become victims of telephone scams — including the recent proliferation of Social Security number suspension ploys — to gain access to their personal information. But what aspects of these calls makes us willing to hand over our private details?

Adam Doupé, an Arizona State University assistant professor of computer engineering, and his team conducted a study to evaluate the effectiveness of scam calls, determine what factors can influence their success and identify what areas research should be addressed to safeguard against them.

Findings of the study were presented at the USENIX Security Symposium this week in Santa Clara, California.

Voice “phishing” is a form of phone fraud that uses social engineering principles to trick recipients into sharing sensitive personal information. Scammers use visual cues, like an altered caller ID and alarming voice content, to persuade a target to comply.

Video by Deanna Dent/ASU Now

The researchers examined the visual and voice attributes of these calls to determine what characteristics encourage information sharing in order to design solutions that can help protect consumers. The team evaluated 150 successful, real-world samples and created its own IRS and human resources phishing scams, including an IRS tax lawsuit, an unclaimed tax return, a payroll withholding event and an HR bonus.

For the test scams, the team used the following components:

  • IRS scams used spoofed area codes originating in Washington, D.C., or a toll-free number; HR scams used the local business area code.
  • Caller IDs replicated a government or business.
  • Male and female voices, either synthesized or a prerecorded human, all repeated the same message.
  • A variety of accents were used.

The scam scenario that generated the greatest breach of personal security, 20% (of 60 people who continued with the call), used a company human resources caller ID with a synthesized American male voice. The second largest, at more than 17% (of 58 people who continued with the call), used a phone number that looked like a company number, but did not have an identifiable caller ID. 

The research included 10 specific experiments fielded to 3,000 recipients during a single work week in late March 2017. 

“Overall, the results were quite surprising: 3.7% of people possibly entered their Social Security numbers into an automated telephone scam,” Doupé said. “However, the most effective telephone spam campaign, which tricked 10.33% of the callers, was specifically targeted at people in their workplace, in what is known as a ‘spearphishing scam.’”

ASU Assistant Professor Adam Doupe

Assistant Professor Adam Doupé. Photo by Deanna Dent/ASU Now 

The experiment spoofed the caller ID of the phone call to appear to come from an internal employer system and used a company-specific scam scenario — an approaching payday. 

After the initial announcement about the nature of the call, the recipient was asked to enter the number “1” to continue to the next message, followed by a request to enter the last four digits of their Social Security number. The study notes that in the real world, the last four digits of a Social Security number, together with the recipient’s phone number, presents a pathway to financial and identity fraud.

Those who entered their Social Security digits were then presented with a “debriefing survey” which explained the experiment and inquired about the recipient’s motivation for responding. The ending message provided researchers’ contact information. (No Social Security numbers were actually collected during the test.)

Across all 10 experiments to a total of 3,000 recipients, 256 (8.53%) continued listening to the scam announcement, and 112 (3.73%) called back in response to a voicemail. Among those who listened to the entire announcement, 148 (4.93%) entered at least one digit of their Social Security numbers.

In the survey, 35 (1.17%) said they were convinced by the scam, and for those who heard the final message and responded to the survey, 27 (1.23%) stated they were not convinced. Both messages involved a threatened payroll withholding.

The most significant finding is that impersonating an internal entity, like an HR department, had a significant effect on the success of a phone phishing scam. Individuals who entered a Social Security sequence and responded to the follow-up survey indicated that the company caller ID was a convincing factor, though the majority remained suspicious and exercised vigilance in protecting their personal information.

Most recipients of the tax-related calls who completed the survey said they already knew the IRS would not make calls like those in the test, with some indicating that a foreign accent added to their suspicions.

"This study shows that telephone scams are quite effective, and therefore countermeasures should be developed to counteract effective techniques, such as spoofing caller ID," Doupé said. “Users must be educated on the dangers of telephone scams, and that caller ID cannot be trusted.”

The paper, “Users Really Do Answer Telephone Scams,” was presented at the 28th USENIX Security Symposium on Aug. 14, by Huahong Tu (University of Maryland), Adam Doupé and Gail-Joon Ahn (Arizona State University), and Ziming Zhao (Rochester Institute of Technology).

Terry Grant

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Generations helping each other out in the classroom

August 14, 2019

MLFTC professors comb through mountains of educational data to offer up analysis on immigrant students and learning

Third-plus generation students — those born in the U.S. to U.S.-born parents — attend better-resourced schools compared to first- and second-generation students from immigrant families. But analysis reveals that these students who attend schools that do not serve immigrants are more likely to demonstrate lower academic achievement than their peers who do. In other words, attending school with immigrant student peers may actually improve the academic performance of third-plus generation learners.

Margarita Pivovarova and Jeanne M. Powers, professors in Mary Lou Fulton Teachers College, spent a few years researching the issue. Their resulting article, “Does Isolation from Immigrant Students Benefit or Harm Third-Plus Generation Students?” was recently published in Education Policy Analysis Archives, a peer-reviewed journal.

It’s the third such analysis from Pivovarova and Powers, who combed through mountains of educational data, tested research methodologies and looked at the relationship between academic achievement and isolation in third-plus generation students and their immigrant peers.

ASU Now spoke to Pivovarova and Powers about their analysis, school climates and diversity of cultures and experiences for immigrants.

Brunette woman in pastel colored dress

Margarita Pivovarova

Question: What prompted you to write this analysis?

Margarita Pivovarova: This study could not have been more personal to me. I am a first-generation immigrant and a parent of a first-generation student who experienced the transition to the U.S. educational system, and social and cultural environment when he was in high school. I observed the influence of these contexts firsthand for more than 10 years, first when we immigrated to Canada and later when we moved to the U.S. However, when writing the paper and doing the analysis, I abstracted from what I actually knew from my experience and my son’s experience. I was curious to learn whether our individual impressions are aligned with the average and to what extent. Dr. Powers and I were also driven by intellectual curiosity. We wanted to see if we could assess some of the claims widely circulated in media about immigration, and specifically that immigrants harm natives. Since these claims often guide public policies, we thought as researchers and social scientists, we should test them using actual data.

Jeanne M. Powers: Some of my earlier research is on school segregation so when we started working on this paper I was interested in understanding the extent to which third-plus immigrant students were exposed to, or in this case isolated from, immigrant students. This paper is actually the third in a series of papers; in the first paper we looked at the isolation of U.S.-born students, which is second- and third-plus-generation students combined. In the first paper and an additional paper, our findings highlight how it is important to distinguish between second- and third-plus-generation students. While second- and third-plus generation students have similar achievement, second-generation students’ families and schools more closely resemble those of their first-generation peers than their third-plus-generation peers.

Q: What are some of the academic challenges third-plus-generation students face today that are unique to them but not their predecessors?

MP: Academic challenges are not unique to third-plus-generation students. The rapid expansion of technology and subsequent changes in the formats and frequency of assessments affect all students regardless of their generational status. I would say that there are other challenges that third-plus-generation students face that are unique to their cohort. These include the extent of immigration and increasing racial and cultural diversity. But perhaps more importantly, all students have to negotiate the role of media, and specifically, social media that forms and shapes their perceptions of immigration and their immigrant peers. 

JMP: Another challenge that all students share that we couldn’t address directly but is worth noting is the underfunding of public schools in the past 10 years. The vast majority of all students regardless of generational status attend public schools. In an expansion of this project using multiple years of the same data (the U.S. data from the Program for International Student Assessment) we found that while 15-year-olds in 2015 are more racially diverse and are less affluent on average than 15-year olds in 2000, some of the indicators we might associate with declines in funding, such as class size, have increased during this period.

Q: To what extent are third-plus generation students isolated from their immigrant peers and how does this make a difference in academic achievement?

MP: Our findings suggest that 1 in 10 of third-plus-generation students in U.S. high schools are not exposed to either first- or second-generation immigrant peers. This implies that they are not exposed to a large population of U.S. residents who themselves or whose parents were born outside of the U.S. and represent a diversity of cultures and experiences. We find that on average, these 10% of third-plus-generation students have lower test scores compared to their third-generation peers in schools that serve immigrant students. This finding was consistent even when we accounted for students’ backgrounds and the characteristics of their schools. However, we also have to warn our readers that correlation is not causation and our study only describes patterns observed in real-world data about students rather than draws causal links between generational status and academic achievement. In our related studies we found that third-plus-generation students outperform their immigrant peers when we do not consider factors that are associated with academic achievement like family background and school contexts. But once all of these factors are taken into account, these differences in achievement disappear. Given the research on peer effects in schools, we can say that isolation might not be beneficial and may even be harmful because students in isolated schools do not have an opportunity to interact with their higher-achieving immigrant peers. 

JMP: Our findings also reflect the concentration of immigrant students in urban areas. Most immigrant students (both first- and second-generation) attend schools in metropolitan areas. Once differences in the backgrounds of students attending urban schools are accounted for, students attending urban schools have higher achievement than students who attend schools in other areas. Some of these differences may be related to school resources such as access to teachers with training in their subject areas and lower student-teacher ratios. This may point to the under-resourcing of rural schools, although that is an issue that needs to be addressed more specifically in another study.

Woman in glasses and colored necklace

Jeanne M. Powers

Q: Your analysis notes that third-plus-generation students are more likely to attend schools with lower concentrations of poverty and have parents with higher educational attainment than their immigrant peers, and yet they achieve less. Why?

MP: Here we have to distinguish between an average third-plus-generation student and a third-plus-generation student who attends an isolated school. For the third-plus-generation students who are isolated from their immigrant peers, the situation is different. The average achievement in isolated schools is lower even though these schools as a group have more teaching resources and lower levels of poverty. Their parents, conversely, are less likely to have college degrees. The patterns we observe in this study and a related paper may reflect what has been termed as an “immigrant paradox” — when students from immigrant backgrounds have higher achievement compared to their third-plus-generation peers despite not having the same resources. We also have to mention that our study is not without caveats. For instance, we cannot see how the apparent “lower” achievement of third-plus-generation students would translate to outcomes later in life such as college attendance, employment and earnings. We can only speak about this one point of time when we observed 15-year-old students in their respective high schools.

JMP: We should also emphasize that we are comparing two groups of third-plus-generation students: students who attend schools that serve immigrant students, and students who attend schools that do not serve immigrant students. We saw this as an interesting way to test the assumptions that underlie recent federal immigration policies and proposals. We think it is important to consider the extent to which these assumptions are supported or challenged by empirical analyses. Our study suggests the latter.

Q: What are some of the positive findings you discovered with third-plus-generation students?

MP: The vast majority of third-plus-generation students, indeed 90% of third-plus-generation students attend schools where they interact with their first- and second-generation peers. It is only a small, although substantive share who might miss out on important experiences that would shape their views of and attitudes about immigration.

JMP: All students benefit from positive school climates. Our findings suggest that when students are engaged at their schools, academic achievement — in this case mathematics achievement — is higher. Similarly, when teachers are responsible for smaller numbers of students (the teacher of the average third-plus-generation student was responsible for 125 students), student achievement was higher.

Q: Who do you hope will read your analysis and how should they use or implement it?

JMP: One of the goals of the analysis was to test an assumption driving federal immigration policy — that immigrants harm U.S. citizens — in this case students. We found that third-plus-generation students who attended schools that did not serve immigrants had lower achievement than their peers who attended schools with immigrant students. On the other hand, there are well-documented benefits from exposure to a diverse set of peers, and public schools are one of the primary places where youth can potentially interact with a broad range of peers, including but not limited to immigrant students.

MP: Policy analysis and those who write reports about the state of education in the U.S. should draw attention to ways that context matters, once again!. A lot of what we observe is a joint product of what is happening inside families, schools and neighborhoods. And there is no need to blame undesirable outcomes on only one of the links in the chain. Rather, we should better understand the intricate nature of these interactions.

Q: Is this the last chapter in your research on immigration and academic achievement? Or do you have long term plans for this project?

JMP: Our next project uses multiple years of PISA data to look at the possible associations between features of the state policy context, specifically the political climate for immigration, and the achievement of immigrant students over time. For example, do immigrant students have higher achievement when they attend schools in states where there are larger concentrations of immigrant students? Conversely, is student achievement lower when students attend schools in state with a more negative climate for immigrants? Is the isolation of third-plus-students’ generation students associated with the political climate for immigration? Using multiple years of data will help us address changes over the period when many states were actively enacting laws such as Arizona’s SB1070 that targeted immigrants and addressed multiple areas of public life (e.g., employment, identification, drivers’ licenses).

MP: Immigration debates are not going away any time soon and most likely are to become even more intense as the 2020 presidential campaign unfolds. As Dr. Powers mentioned our next project, we plan to contribute to these debates with evidence on the academic experiences of both immigrant students and their native peers.

Top picture courtesy of Getty Images/iStockphoto

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New drug targets early instigator of Alzheimer’s disease


August 14, 2019

More than a hundred years after they were first identified, two ominous signposts of Alzheimer’s disease remain central topics of research — both formed by sticky accumulations of protein in the brain. Amyloid beta solidifies into senile plaques, which congregate in the extracellular spaces of nerve tissue, while tau protein creates tangled forms crowding the bodies of neurons.

Plaques and tangles, considered classic hallmarks of Alzheimer’s, have been the objects of fierce debate, sustained research and many billions of dollars in drug development. Yet therapeutic efforts to target these pathologies, which are consistently associated with cognitive decline in both humans and animal models, have met with dispiriting failure. DYR219 is a powerful new drug developed by Travis Dunckley and his colleagues and described in the new study. Its strength lies in the fact that it can target both of the leading pathologies associated with Alzheimer's disease — plaques (caused by the protein amyloid beta) and tangles (caused by the tau protein). Further, DYR219's activity can occur early in the progression of the disease, before the formation of these pathologies, offering a better chance of preventing the advance of Alzheimer's and its destruction of cognitive function. DYR219 inhibits a kinase known as DYRK1. In Alzheimer's and other neurodegenerative diseases, DYRK1 phosphorylates both the tau and amyloid beta proteins—key steps in the formation of plaques and tangles in the brain. Graphic by Shireen Dooling Download Full Image

Travis Dunckley, a researcher at the ASU-Banner Neurodegenerative Disease Research Center, and Christopher Hulme, medicinal chemist at the Arizona Center for Drug Discovery based at the UA College of Pharmacy, are exploring a small molecule drug known as DYR219. The promising therapy, while still in the experimental stages, may succeed where other treatments have failed and could be effective against a range of neurodegenerative illnesses in addition to Alzheimer’s. 

Rather than directly attacking the visible hallmarks of Alzheimer’s, namely the plaques and tangles caused by the disease’s relentless progression, the new drug acts by inhibiting an early pathway believed to be critical in the formation of both plaques and tangles.

Dunckley says that targeting the early-stage events leading to plaque and tangle formation represents an important advance in the field. “If you can block that process early, you can delay the downstream aggregation and formation of the pathologies.”

By preventing or delaying the development of Alzheimer’s disease pathologies, DYR219 or a similar drug may halt the progression of Alzheimer’s in its tracks, before it damages the brain beyond repair.

The new small molecule acts by inhibiting DYRK1, a particular neuroactive enzyme known as a kinase. Researchers like Dunckley and Hulme have been studying DYRK1 and exploring its crucial importance not only in Alzheimer’s disease but a broad range of neurodegenerative maladies.

The new study recently appeared in the journal Molecular Neurobiology.

Two faces of DYRK1

Although the activity of DYRK1 is believed to be a key factor in the formation of plaques and tangles, it is vital to the brain during early embryonic development, where it is involved in a host of processes, including signaling pathways linked with cell growth and proliferation, as well as the differentiation of cells into mature neurons and the formation of dendritic spines essential for the transmission of nerve impulses. 

Christopher Hulme, graduate assistant Chris Foley and Travis Dunckley.

From left: Christopher Hulme, graduate assistant Chris Foley and Travis Dunckley. Hulme and Dunckley's recently formed company Iluminos has developed compounds that may help treat neurodegenerative diseases like Alzheimer’s. A new study describes a small molecule kinase inhibitor that has shown effectiveness in blocking or delaying the development of plaques and tangles — pathologies caused by accumulations of amyloid and tau proteins in the brain.


In the mature brain, however, DYRK1’s activities can turn hostile, initiating pathologies associated with Alzheimer’s, dementia with Lewy bodies and Parkinson’s disease. The dysfunction of DYRK1 is also a central feature of Down syndrome. Patients with this disorder are highly prone to developing Alzheimer’s early in life, often in their 40s or 50s.

The DYRK1 kinase carries out its harmful role in the brain through a process known as phosphorylation. When DYRK1 encounters a protein known as APP (amyloid precursor protein), it attaches a cluster of oxygen and phosphorus atoms, known as a phosphate group. DYRK1 also phosphorylates tau.

Too much phosphorylation of these critical proteins can have disastrous effects in the brain. The hyperphosphorylation of APP is believed to increase the formation of amyloid plaques, while tau hyperphosphorylation leads to neurofibrillary tangles. Inhibition of these processes could interrupt the sequence of events leading to plaque and tangle formation and block or delay the onset of Alzheimer’s.

“The reason I’m excited about this, especially in the face of a lot of the recent high-profile clinical trial failures, is that this is really a different approach to treating the disease,” Dunckley said, noting that previous efforts to target plaques and tangles directly have failed to provide any benefit to cognitive function. “What we’re trying to do is restore the normal phosphorylation of APP and tau, so that you don’t get those downstream pathologies.”

Working upstream

In earlier research, Dunckley, Hulme and colleagues showed that using a small molecule drug to inhibit DYRK1 in hybrid mice bred to develop AD-like symptoms reduced the load of amyloid plaque in their brains and improved cognitive performance.

The new study explores early DYRK1 inhibition as a potential preventive measure against Alzheimer’s, with impressive results. “We showed a robust and significant delay in the onset of amyloid and tau pathology,” Dunckley said.

Researchers speculate that one reason anti-plaque and anti-tangle therapies have shown promise in mice yet consistently failed in humans is the nature of disease progression in the two very different brains. In hybrid mice, plaques and tangles can develop quickly, before Alzheimer’s has caused significant neurodegeneration and cell loss in the brain. Treating plaques and tangles in this case can help the remaining healthy neurons resume normal function. In human Alzheimer’s, however, plaques and tangles are typically accompanied by advanced neuronal devastation. It’s simply too late in the course of the disease to derive any benefit from targeting the amyloid and tau pathologies alone.

Connection with Down syndrome

Inhibition of DYRK1 has also shown promise in the treatment of Down syndrome. The DYRK1 gene is localized on chromosome 21, in the Down syndrome critical region. Overexpression of DYRK1 appears intimately involved with the learning defects characteristic of this disease and its inhibition has been shown to improve cognitive performance in mice.

Dunckley believes a DYRK1 inhibitor like the one described in the new study could first be used to treat pathology and cognitive impairment in Down syndrome patients, before its eventual application for Alzheimer’s.

Those living with Down syndrome carry a gene defect on chromosome 21 that allows for rapid and definitive diagnosis. The fact that this pool of patients will go on to develop Alzheimer’s with high probability makes them ideal subjects for clinical trials involving DYRK1-inhibiting drugs. Such an approach promises to avoid the pitfalls currently involved in testing preventive treatments for Alzheimer’s disease, which would need to be administered years or even decades before the onset of symptoms in patients of uncertain prognosis.

Targeting an enigmatic killer

The ability of DYRK1 inhibitors to halt or significantly delay both major Alzheimer’s-associated pathologies caused by amyloid beta and tau offers renewed hope for effective treatment of Alzheimer’s and may hold the key to addressing other devastating afflictions linked to hyperphosphorylation by DYRK1.

Hulme expresses excitement about rapid advancements in this area.

“A challenging in-house design effort driven by several UA graduate students over the last seven years, most recently Christopher Foley, has successfully unearthed newer drugs that are incredibly selective, much more stable and much more potent,” he said. “If such drugs deliver on their early promise, they may eventually be used as a common prophylactic against neurodegenerative diseases, perhaps like current medications for the prevention of heart disease.”

The pressing need for an effective Alzheimer’s disease therapy could not be more acute. Dementia currently affects nearly 50 million people, striking a new victim somewhere in the world every three seconds. The majority fall victim to Alzheimer’s disease, the most common form of dementia, which accounts for around 75% of cases. Barring major advances in treatment, the number of cases is projected to skyrocket to 131.5 million by mid-century.

On a more hopeful note, because Alzheimer’s is primarily a disease of old age, it has been estimated that a therapy capable of delaying the onset by just five years would cut the number of cases globally by half. The research outlined in the current study offers an innovative approach to this urgent medical crisis. 

Richard Harth

Science writer, Biodesign Institute at ASU

480-727-0378

ASU study shows positive lab environment critical for undergrad success in research

Undergraduate researchers with LEAP Scholars program publish findings


August 14, 2019

Getting involved in research as an undergraduate can have significant benefits, such as enhancing a student’s ability to think critically, increasing their understanding of how to conduct a research project and improving the odds that they’ll complete a degree program in science, technology, engineering and math (STEM).

And, for students who participate in research over several years, the benefits are even greater. They often develop greater confidence in their research skills along with an ability to solve problems independently, and they are more likely to pursue a career in STEM. Undergraduate students work with a faculty mentor Undergraduate students work in a neuroscience lab with faculty member Janet Neisewander. Photo by Samantha Lloyd/ASU VisLab

But many undergraduates drop out of their research experience before graduation or even during their first year working in a biology lab. Until now, there has been no research as to why.

In a study published today in PLOS ONE, a group of 14 undergraduate Arizona State University co-authors addressed this question as part of a class project. Led by School of Life Sciences Associate Professor Sara Brownell, graduate student Logan Gin and University of Central Florida Assistant Professor Katelyn Cooper, students with the LEAP Scholars program surveyed more than 750 life sciences undergraduates doing research in 25 public institutions across the U.S. They found that 50% of students who participated in the study had considered leaving their undergraduate research experience more than 50% of those students ultimately decided to leave. 

They also found that the most important factors that influence whether a student decides to continue working in research included a positive lab environment and enjoying their everyday research tasks, as well as flexible schedules, positive social interactions and feeling included. Students also persisted with their research when they felt they were learning important skills and perceived the work was important to their career goals.

“We often assume that all undergraduate research experiences are positive for students, but this study shows that this is not the case. If 50% of students consider leaving their undergraduate research experience, then that means that we have a structural problem with how we are integrating students in undergraduate research,” senior author Brownell said. “We can empower students with more knowledge about undergraduate research to help them choose a suitable lab, but we also need to find ways to make our research labs more positive environments for all students.”

Other factors, such as race, gender, GPA and college generation status, also play a role in what factors influence students to persist in their research experiences. Men were more likely than women to stay in research because they consider it important for their future careers. Men were also more likely to leave their research experience because they didn’t enjoy their specific lab tasks, while women were more likely to consider leaving because of a lack of flexibility in the lab. 

Underrepresented minority students were more likely to leave their research work because they felt they were not learning important skills, while white students were more likely to stay in research because they enjoyed their everyday lab tasks. And, students with lower GPAs were more likely to stay in research because they were unsure about future research opportunities, while those with higher GPAs were more likely to leave research because they did not enjoy the everyday lab tasks. 

“We were excited to identify factors that disproportionately affected underrepresented and marginalized students’ decisions to leave research. It will be challenging to identify solutions, but identifying these issues is a critical step in developing a more diverse and inclusive scientific community,” Gin said. 

ASU LEAP Scholars

LEAP Scholar students present their research findings on undergraduate persistence in a research lab at a spring SOLUR Symposium. Left to right: Leilani Pfeiffer, Barierane Akeeh, Deanna Elliott, Luis Guiterrez, Rebecca Mello, Carolyn Clark, Rachel Scott. (Not all researchers pictured.)




 

For faculty members who invest time and resources to train undergraduates to work in their labs, this study provides important insight that can be used to shape their student lab experiences, develop support policies and improve mentor and mentee relationships. 

“What was most surprising to us was the importance of the lab environment and the interactions among people in the lab,” lead author Katelyn Cooper said. “When we hire faculty members to run research labs, we often are looking for the smartest people with the best research ideas. However, this study highlights that if we want to maximize the success of undergraduates in research, we need to be selecting for supportive faculty who can create positive working environments.”

Brownell and her co-instructors lead ASU’s LEAP Scholars program, a four-semester scholarship program funded by the National Science Foundation to help community college transfer students get involved in undergraduate science research. Because many transfer students need to work a job while attending college, the LEAP program provides scholarships and mentors so they can work in a research lab instead and focus full time on their coursework.

Sandra Leander

Manager, Media Relations and Marketing, School of Life Sciences

480-965-9865

ASU researchers use new tools of data science to capture single molecules in action


August 14, 2019

In high school chemistry, we all learned about chemical reactions. But what brings two reacting molecules together? As explained to us by Albert Einstein, it is the random motion of inert molecules driven by the bombardment of solvent molecules. If brought close enough together, by random chance, these molecules may react.

Capturing the motion of single molecules is achieved by a method known as fluorescence correlation spectroscopy (FCS). The catch? It takes many detections of light particles – photons – emitted by single molecules to get a clear picture of molecular motion.    man and woman sitting at a table looking at a paper ASU professors Steve Presse and Marcia Levitus Download Full Image

As an illustration, think of a political poll. At any given time in a campaign cycle, polls are used to predict the outcome of an upcoming election. But how many voters must we interrogate to get an accurate prediction and, given how time-sensitive polling information is, how quickly can we probe the nation’s political leanings? Asking every voter in every state would yield accurate results but be too costly in time and dollars. For practical reasons, we need to take a sample of voters and efficiently exploit all information contained in that sample. The voters in this illustration are our proverbial photons here.

“Single-molecule fluorescence techniques have revolutionized our understanding of the dynamics of many critical molecular processes, but signals are inherently noisy and experiments require long acquisition times,” explained Marcia Levitus, an associate professor in the School of Molecular Sciences and the Biodesign Institute at Arizona State University.

FCS takes too long, and the chemistry we care about learning might already be done by the time we try to observe it. Furthermore, exposing samples to the laser for long periods of time may result in the photochemical damage of molecules under study, preventing the widespread use of FCS in biological research.

A paper published in Nature Communications by ASU Associate Professor Steve Presse and collaborators now addresses these issues using tools from data science and, more specifically, Bayesian nonparametrics – a type of statistical modeling tool so far largely used outside the natural sciences.

This work leverages new tools from data science in order to make every photon detected count and refine our picture of molecular motion.

“New mathematical tools make it possible to think about old but powerful experiments in a new light,” said Presse, lead author on the study and joint professor in the Department of Physics and School of Molecular Sciences.

A molecule, whose path traced out in time is shown by the blue line, occasionally wanders into a brightly lit green region. Within this region, the molecule is excited and begins emitting light of a different wavelength that we can distinguish from the green light. This emitted-light reports back on the behavior of the molecule. 

Levitus added, “Old strategies limited our ability to probe anything but slow processes, leaving a vast number of interesting biological questions involving faster chemical reactions out of reach. Now we can begin asking questions on processes resolved in short order.” 

Presse’s team includes Sina Jazani, a graduate student, and Ioannis Sgouralis, a postdoctoral associate at the ASU Center for Biological Physics. The experimental collaborators and co-authors of the paper include Levitus, Sanjeevi Sivasankar, an associate professor at the University of California, Davis' Department of Biomedical Engineering and his graduate student Omer Shafraz.

Communication specialist, School of Molecular Sciences

 
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News21 journalism students from 19 universities investigate disaster recovery

August 13, 2019

The Carnegie-Knight News21 program, a national multi-university reporting initiative headquartered at Arizona State University’s Walter Cronkite School of Journalism and Mass Communication, released a major multimedia investigation Aug. 13 about disaster recovery in the United States.

Thirty-seven journalism students from 19 universities traveled to 25 states, Puerto Rico and the U.S. Virgin Islands, conducting hundreds of interviews and reviewing thousands of pages of government documents, data and state and federal statutes for “State of Emergency.” 

“This deeply reported project brought to the forefront the lasting and troubling consequences of natural disasters and recovery, particularly for people living in remote, impoverished and storm-prone communities,” said News21 Executive Editor Jacquee Petchel, a Pulitzer Prize-winning investigative journalist. “What we found were thousands of people still coping with the aftermath, months and even years after the fact.”

While hurricanes Katrina, Sandy, Harvey and Maria were each a disaster of shattering magnitude, there are hundreds of smaller disasters that garner only a fraction of the national attention and billions of federal dollars. A News21 analysis of Federal Emergency Management Agency data over the past two decades shows that small disasters accounted for more than 60% of all federally declared disasters between 2003 and 2018. Yet they received at least $57.8 billion less in public assistance from FEMA. 

The federal government also provided less individual assistance to survivors in communities with smaller disasters. Since 1999, 651 declared disasters did not receive individual assistance.

In addition, the investigation found that even though federal fire-suppression costs quadrupled since 1989, damage caused by wildfires has increased fivefold. 

Wildfires over the past decade also have resulted in more than $52 billion in insured losses across the country. Nearly 49,000 structures have burned across the U.S. since 2014, according to the National Interagency Fire Center. That’s more lost structures than in the previous 14 years combined. 

The News21 “State of Emergency” project includes 16 digital stories, portraits of more than 50 survivors, and four half-hour documentaries on hurricanes, wildfires, tornadoes and flooding. The fellows also produced a five-episode podcast following a disaster from the moment a storm hit through the long recovery process.

The project can be found at stateofemergency.news21.com.

“The News21 student journalists produced a well-documented word, audio and visual portrait of the current state emergency in America,” Petchel said. “They traveled thousands of miles, capturing the stories, voices and faces of victims of disasters, first responders and everyday citizens who stepped up and handled whatever nature threw their way.”

News21 student journalists interview a homeowner

Natalie Anderson and Jake Goodrick talk to Morgan “Ted” Mahoney of Lynn Haven, Florida, who is in the midst of legal trouble with his contractor while recovering his home eight months after Hurricane Michael. Photo by Peter Nicieja/News21


The investigation will be published by major media organizations across the country. Previous News21 stories have been published by USA Today, The Washington Post, ProPublica and Center for Public Integrity, in addition to dozens of regional and local news outlets. 

Work on the project started in January 2019 with a seminar on issues surrounding natural disasters taught by Petchel. Students heard from experts on the topic, analyzed data, researched topics and conducted interviews across the country.

Molly Duerig, one of 14 Cronkite students who were part of the project, reported on this year’s historic Midwest floods and then traveled to Puerto Rico for a story about Hurricane Maria’s lasting impact on young people. She also co-wrote an investigative story on the electric power grid in the U.S. and storms that cause power outages. 

“We heard so many stories about people who were able to adapt and rebuild after facing loss and destruction in their communities,” Duerig said. “News21 has been one of the most rewarding experiences of my life.”

(Photos and names of the fellows and their home states are available on the website, or upon request)

Top photo: News21 Fellow Jordan Elder carries camera equipment to a graveyard that's falling into the Chesapeake Bay. Photo by Jordan Laird

Director of communications , Walter Cronkite School of Journalism and Mass Communication and Arizona PBS

 
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Pseudoscience is a danger, says ASU physics prof

August 13, 2019

A quick how-to user guide to debunking scientific myths and rumors

Even though it may seem at first that the internet is an almost infinite source of knowledge, one needs to know how to properly navigate it in order to discern what’s truthful.

The web has generated lots of fake news on both sides of the political spectrum, conspiracy theories and pseudoscience.

Take for example the anti-vaccination movement, which erupted about five years ago thanks to group of celebrity “anti-vaxxers” who expressed concern on social media that certain shots could be harmful.

So how does one distinguish between exciting scientific breakthroughs and just plain baloney?

Arizona State University’s Maxim Sukharev is knowledgeable in debunking various pseudoscientific claims.

ASU Now spoke to Sukharev, a physics professor with the College of Integrative Arts and Sciences, about telling fact from fiction.   

Question: Let’s start off with a good definition of what pseudoscience is.

Answer: Pseudoscience, quackery and junk science is everything but science: claiming things that never happen — telekinesis, ghost haunting, etc., pretending to use scientific language to misguide the public for personal gain, such as that infamous example of Airborne, which turned out to be just a primitive vitamin supplement and settled a $23.3 million class-action lawsuit for false advertisement. Fraud science is when actual scientists purposely misrepresent/fabricate data. Unfortunately, there are quite a few examples of that as well. The scientific community does fight such instances harshly but it takes obviously a significant amount of time to uncover fabrications.

Q: Has pseudoscience always been around?

A: There was time when there was no science at all. There was just pseudoscience all along: astrology, palm reading, etc. Slowly the scientific method emerged from the abyss of ignorance when people began to realize that the objective truth can only be understood through meticulous scientific scrutiny, which cannot be subjective.

Ancient Greeks were arguably the first ones who laid the very foundation of modern science. The scientific revolution brought us cures for many diseases we thought were God-sent and were lethal. Humans learned how to fly when the Wright brothers did something everyone thought was impossible. We now sit comfortably in an airplane moving over 500 mph and complain that the WiFi on board is too slow.

Science brought us deep understanding of very fabric of space-time, we are one step closer to uncovering the mysteries of the Big Bang and may be just a decade away from being able to cure cancer. Yet the pseudoscience is still alive and well. It feeds on our ignorance and natural desire for mystery and miracle. When scientists say that they cannot solve a given problem just yet, many turn to junk science simply because people do not understand that the scientific inquiry is a long and sometimes painful process. It does take time to cure cancer, it does take time to understand how to make a rocket fly. We will get there eventually and the junk science will disappear. Hopefully sooner than later.

Q: Why is pseudoscience so popular and why are people so willing to believe in it?

A: I wish I had an answer to that. Many scientists do. We would have jumped straight at the very cause of it trying to get rid of it once and for all. Personally, I think the best way to fight pseudoscience is to popularize science. Giving free open public lectures on various scientific issues including quantum mechanics and other fascinating subjects is the first step. Getting engaged with our local communities, high schools. Show students how impeccably fascinating real science is. Once exposed to that they will never turn to pseudoscience.

Q: Other than spreading misinformation, what are some other drawbacks about pseudoscience?

A: There are plenty of harmful examples, but this one stands out for me most: As scientists, not only do we have to be able to work on pressing scientific issues but also we must engage in fearless competition between ourselves for funding. The latter usually goes to sponsor PhD students, postdoctoral fellows, equipment for a lab, attending conferences. The success rate for getting funded is quite low. It is thus absolutely appalling when limited resources are spent on funding obvious pseudoscience. There is one infamous incident with one of the federal agencies and its intent to fund physics teleportation studies. The scientific community quickly realized how wasteful and shameful this looked. However, $25,000 was spent on the report. At first, the report looks “scientific-ish.” Two-thirds of it is scientifically sound — some statements in this report appeared to be a copy-paste from textbooks. The real fun however begins right on Page 1: “As for the psychic aspect of teleportation, it became known to Dr. Forward and myself … that anomalous teleportation has been scientifically investigated and separately documented." Mysterious Dr. Forward appears only once in the report and is never mentioned anywhere else. Apart from this excerpt and a few others there is nothing that would make a regular person cringe. This report, minus its copy-paste part, falls into the category of “conspiracy theories.” For fun, try to use Google Street View with the address seen on the title page of the report. Remember this address was used as an official address for the organization called “Warp Drive Metrics.”

Q: What are some tools you can give people for debunking pseudoscientific examples?

A: In my recent essay on pseudoscience, I am trying to provide a possible remedy, i.e. explain the scientific method. If properly followed, these steps most of junk science/quackery/pseudoscientific claims can be exposed.

Step No. 1: Observe 
You observe some phenomenon, say, a UFO, for instance. This very step needs to be repeated multiple times not only by you but by others independently to make this observation objective.

Step No. 2: Question
Here we question our observation, trying to understand what this observation means in the grander picture of what we already know.

Step No. 3: Hypothesis
Come up with a concise, logical hypothesis.

Step No. 4: Predict
Come up with a possible experiment based on No. 3.

Step No. 5: Test prediction

Step No. 6: Draw a conclusion based on outcomes of our experiments
Most importantly, we must remember that extraordinary claims demand extraordinary proof.

Q: What if a real breakthrough in science is taken as a pseudoscience?

A: Indeed, how can we ensure that our skepticism is not filtering out what may be the next scientific revolution? Real scientific discoveries, no matter how insane or amazing they may look, are within the realm of scientific method. Moreover, these discoveries are tirelessly verified and scrutinized by the scientific community over and over and over again. All of this goes through the process of peer review, in which our scientific colleagues check and question every part of your discovery. You may get engaged in a heated discussion, and if for some reason reviewers do not like what they see, they may reject your work. You may appeal and prove them wrong. All of that is solely based on objective science and nothing else. Once your publication passes, your other colleagues may want to repeat your experiments or calculations. If your observations are confirmed, this becomes another solid brick in the wall of science. For example, the revolutionary ideas of Einstein on relativity of time, no matter how controversial they may have sounded, were scrutinized numerous times. These ideas withstood many experimental tests and passed all of them. You may say that science is to make miracles a part of reality. 

Reporter , ASU Now

480-727-5176

ASU and USF investigators collaborate to explain where DNA repairs occur most frequently


August 13, 2019

From hair and eye color to how our biological system is regulated, the blueprint of life is held in the genome.

The gene also is what provides the instructions to the DNA as to what proteins to make and when, but our DNA is under constant attack from our environment — sun exposure, the air we breathe, the foods we eat and the body’s own metabolic processes to sustain life. If the enzymes that repair DNA are not signaled, damaged DNA may affect cell division and may result in the formation of tumors that can lead to cancer. woman and man standing next to each other smiling at the camera ASU researchers Marcia Levitus, associate professor in the School of Molecular Sciences and the Biodesign Institute, and Wade Van Horn, assistant professor in the School of Molecular Sciences and investigator with the Biodesign Institute's Center for Personalized Diagnostics and the Magnetic Resonance Research Center. Download Full Image

For a genome to survive, repairs to the DNA base pair is crucial. But at what rate and where do these repairs occur most frequently?  

Marcia Levitus, associate professor in the School of Molecular Sciences and the Biodesign Institute at Arizona State University, received a National Science Foundation grant to lead a study on the dynamics of DNA sequence and deformability on lesion recognition and excision in the base excision repair pathway, which will help us understand key aspects of DNA repair, DNA mutation rates and molecular evolution.

“Thousands of spontaneous lesions occur to a cell’s DNA on a daily basis, and to maintain the integrity of their genomes, cells have evolved mechanisms to repair damaged DNA," said Levitus. "The mechanism responsible for removing small lesions from the genome is the base excision repair pathway. This pathway is responsible for removing most oxidized, alkylated and deaminated nucleobases from the genome, and is initiated by specialized DNA glycosylases that catalyze the excision of the damaged base.”

Each of us has approximately 3 billion base pairs of DNA, and the instructions for building, repairing or maintaining itself is determined from the base sequence. The average person’s cells are estimated to have 70,000 DNA lesions. It would seem impossible for a cell to maintain the integrity of the DNA or survive if it didn’t evolve or adapt to the surrounding conditions it is continually subjected to.

During a cell cycle, a series of steps or events lead up to DNA replication known as a cell checkpoint, where cells are evaluated for ideal criteria before they can begin the replication process. The mechanisms for a biological system have a critical role in order to assure the genetic material being passed on is correct. Our DNA is constantly undergoing replication and division, and as in any system, errors can happen in the process. The majority of errors in our DNA are able to be detected in the cell cycle through very efficient repair systems, and the human body remains healthy.

The code of instructions in the DNA consists of four chemical bases: adenine (A), guanine (G), cytosine (C) and thymine (T). Nucleic acids are formed from nucleotides. In DNA, there are three parts to a nucleotide: a deoxyribose (a five carbon sugar molecule), a phosphate group and a nitrogenous base. DNA base pairs to form units are made up in the sequence A with T and C with G. 

Role of DNA sequence and deformability on lesion recognition and excision in the base excision repair pathway

Levitus stated recent studies have shown that a number of DNA repair enzymes are more active on particular sequences of DNA than others.

“This sequence specificity results in nonrandom patterns of repair that can lead to nucleotide positions with lower repair efficiencies and exceptionally high mutation frequency,” said Levitus. “Identifying and characterizing factors that determine the rates and spectra of spontaneous mutations is a critical step toward understanding molecular aspects of the evolutionary process.”

Collaborating with Levitus on this research are Wade Van Horn, co-principal investigator and associate professor at ASU's School of Molecular Sciences, investigator at the Biodesign Institute, the Center for Personalized Diagnostics and the Magnetic Resonance Research Center, and Arjan van der Vaart, an associate professor and associate chair at the University of South Florida's Department of Chemistry.

“DNA carries the instructions that govern biology, and there are a variety of ways in which these DNA instructions can be changed (mutated). Consequently, biology has several diverse ways to identify and fix these DNA alterations,” said Van Horn. “Our collaborative studies seek to understand how biology recognizes these changes (lesions), particularly by investigating the relationship between the DNA sequence, its dynamics (i.e., movement) and the efficacy in identifying DNA lesions. Our team will use a mix of cutting edge computational and experimental approaches to investigate how biology protects the genetic instructions carried by DNA.”  

The main goal of this project is to elucidate the molecular basis for sequence effects in lesion repair by DNA glycosylases. Levitus, Van Horn and van der Vaart will test the hypothesis that damage that occurs within a rigid region of DNA is repaired more slowly than damage that occurs within a flexible region. Elucidating the molecular basis for sequence effects in DNA repair requires a multipronged approach that takes advantage of the strengths of a variety of experimental and computational approaches. This collaborative research will capitalize on the expertise in DNA biophysics (Levitus and van der Vaart), fluorescence spectroscopy (Levitus), NMR spectroscopy (Van Horn) and molecular dynamics (MD) simulations (van der Vaart).

Communication specialist, School of Molecular Sciences

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