Category Archives: Genome

In an opinion piece released today in PLOS Genetics, University of Melbourne Dr Ash Porter, evolutionary biologist at the Doherty Institute, along with a team of researchers from the University of Melbourne Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL) at the Doherty Institute, shares their learnings about the COVID-19 pandemic response and recommendations to prepare for the next phase of the COVID-19 pandemic and future pandemics.

Whilst public health and social measures, quarantine restrictions and vaccination have all been utilised in past and current pandemics, the COVID-19 pandemic is the first to employ genomic sequencing on a massive global scale.

It was an incredible achievement to bring public health genomics to the absolute forefront of the COVID-19 response and realising the dream of making day-to-day public health decisions based on pathogen genomic data, reflects University of Melbourne Professor Ben Howden, Director of the MDU-PHL who leads the team that sequenced 75 per cent of the cases in Victoria in the last two years, and co-senior author of this article.

University of Melbourne Dr Sebastian Duchene, infectious disease computational biologist at the Doherty Institute and co-lead author of this article, explained that extensive analyses of the virus genome data have been key to understand the mechanisms under which variants of concern emerge.

What we found through previous research is that SARS-CoV-2 virus has the ability to momentarily accelerate its evolutionary pace, enabling variants to emerge more rapidly than other viruses.

This highlights the importance of continued genome surveillance efforts, Dr Duchene added.

In this piece, Dr Porter et al. argue that as the virus changes, so should our approach.

When were dealing with a pandemic, we cant just keep going with what weve done. Our strategy to manage it has to change along with the virus, explains Dr Porter.

Dr Porter explains that a more strategic approach to manage COVID-19 and future infectious disease outbreaks would be to combine sequence data with surveillance data and other metadata, such as individual travel history or patient treatment data.

Sequencing isnt the only form of data we have here, we have so many other additional streams of data that we can use; and for many infectious disease outbreaks, its not just human data, its animal data as well, Dr Porter says.

Putting some of our resources towards collecting and sharing that data would be more helpful than just focusing on sequencing.

In reconsidering our sequencing strategies and looking forward, we believe that the sequencing strategy could be further optimised from a modelling perspective to utilise our resources effectively.

Dr Porter stresses that a global, coordinated response for data collection and modelling will be essential, both for the ongoing COVID-19 pandemic and future outbreaks.

Much of the long-term COVID-normal future will be informed by our ability to exploit genomic epidemiology through gathering data about SARS-CoV-2 (both at the sequence and metadata level) and sharing it, Dr Porter says.

1 A genome sequence is a list of the molecules that make up the code of our DNA and RNA, known as the nucleotides A (adenine), C (cytosine), G (guanine), and either T (thymine) for DNA genomes or uracil (U) for RNA genomes. Its like a barcode. Genomic sequencing is the process of identifying the barcode.

Through genomic sequencing, we can see how those pathogens, such as viruses, are changing and spreading through mapping even single changes in the genetic code.

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Lessons learnt from COVID-19 shed light on future pandemic preparedness - The Peter Doherty Institute for Infection and Immunity

1. From Neanderthal genome to Nobel prize: meet geneticist Svante Pbo  Nature.com
2. Svante Pbo Awarded Nobel For Examining The Ancient Human Genome  Science Friday
3. Genome Of Ancient Humans Is The Winning Field Of 2022's Nobel Prize in Medicine  IFLScience
4. Nobel awarded to Swedish scientist who deciphered the Neanderthal genome  The Washington Post
5. Nobel Prize Awarded to Scientist Who Sequenced Neanderthal Genome  The New York Times
6. View Full Coverage on Google News

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From Neanderthal genome to Nobel prize: meet geneticist Svante Pbo - Nature.com

From a platypus to a blue whale, all living mammals today are descendants of a single ancestor that existed around 180 million years ago. However, less is known about this animal.

Now, an international team has computationally reconstructed the organization of its genome. The reconstructed ancestral genome could help in understanding mammals Evolution and conservation of modern animals. The reconstructed ancestral genome could help in understanding mammals Evolution and conservation of modern animals.

The earliest mammal ancestor likely looked like the fossil animal Morganucodon, which lived about 200 million years ago.

Harris Lewin, distinguished professor of evolution and ecology at the University of California, Davis, said,Our results have important implications for understanding the evolution of mammals and conservation efforts.

Scientists drew on high-quality genome sequences from 32 living species representing 23 of the 26 known orders of mammals. They included chimpanzees, humans, wombats, domestic cattle, rhinos, bats, pangolins, and manatees. The genomes of the chicken and Chinese alligators were also analyzed as comparison samples. The Earth BioGenome Project and other extensive biodiversity genome sequencing initiatives produce some of these genomes. The Working Group for the Earth BioGenome Project is presided over by Lewin.

Joana Damas, the first author of the study and a postdoctoral scientist at the UC Davis Genome Center, said,The reconstruction shows that the mammal ancestor had 19 autosomal chromosomes, which control the inheritance of an organisms characteristics outside of those controlled by sex-linked chromosomes, (these are paired in most cells, making 38 in total) plus two sex chromosomes. The team identified 1,215 blocks of genes that consistently occur on the same chromosome in the same order across all 32 genomes. These building blocks of all mammal genomes contain genes critical to developing a normal embryo.

The scientists found nine whole chromosomes or chromosome fragments in the mammal ancestor whose gene arrangement is similar to modern birds chromosomes.

Lewin said,This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary timeframe of more than 320 million years. In contrast, regions between these conserved blocks contained more repetitive sequences and were more prone to breakages, rearrangements, and sequence duplications, which are major drivers of genome evolution.

Professor William Murphy, Texas A&M University, who was not an author of the paper, said,Ancestral genome reconstructions are critical to interpreting where and why selective pressures vary across genomes. This study establishes a clear relationship between chromatin architecture, gene regulation, and linkage conservation. This provides the foundation for assessing the role of natural selection in chromosome evolution across the mammalian tree of life.

Scientists could follow the ancestral chromosomes forward in time from the common ancestor. Scientists, in time, could trace ancestral chromosomes from the same ancestor. They discovered that there were variations in chromosomal rearrangement rates among mammal lineages. For instance, when an asteroid strike 66 million years ago wiped out the dinosaurs and gave rise to mammals, the rearrangement process in the ruminant lineagewhich gave rise to contemporary cattle, sheep, and deeraccelerated.

Co-author Dr. Camilla Mazzoni said,The results will help to understand the genetics behind adaptations that have allowed mammals to flourish on a changing planet over the last 180 million years.

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Revealing the genome organization of the earliest common ancestor of all mammals - Tech Explorist

Scientists at the University of Cambridge and Queen Mary University of London have discovered that mitochondrial DNA can make its way into nuclear DNA. The study is published in Nature.

Mitochondria are often referred to as the powerhouses or batteries of a cell, due to their role in energy conversion, among other critical molecular processes. They possess their own circular DNA called mitochondrial DNA (mtDNA), which is particularly interesting to scientists due to its distinct properties, such as a high rate of polymorphisms and mutations.

Another unique feature of mtDNA is that it is inherited by offspring via the maternal line i.e., the DNA is passed down from our mother, not our father. This characteristic of mitochondria was widely accepted until a 2018 paper from researchers at the Cincinnati Childrens Hospital Medical Center proposed it had found evidence of paternal transmission.

Mitochondria are a type of organelle that are found in the cytoplasm of almost all eukaryotic cells. They convert chemical energy obtained via nutrients to a form of energy that can be used by the cell, via a process known as oxidative phosphorylation. In the mitochondria, a reaction called the Krebs cycle produces the chemical NADH, which is then used by enzymes to create adenosine triphosphate (ATP). Dysfunction of the mitochondria resulting in their inefficiency is a hallmark of aging and many chronic diseases.

In 2020, a team led by Professor Patrick Chinnery from the Medical Research Council Mitochondrial Biology Unit utilized data from Genomics Englands 100,000 Genomes Project to study DNA from 11,000 families to explore these claims and hunt for further evidence.

What is the 100,000 Genomes Project?

The 100,000 Genomes Project is a British initiative to sequence 100,000 genomes with the aim of understanding the role our genes play in health and disease.

Essentially, they did discover mtDNA in the nuclear DNA of some children, which they call nuclear-mitochondrial segments (NUMTs). However, these inserts were not present in the parents DNA, meaning they could not have been inherited via the paternal line. Chinnery and colleagues proposed that the earlier work in 2018 had likely discovered these inserts but had reached an incorrect conclusion regarding their origin. We conclude that rare cryptic mega-NUMTs can resemble paternal mtDNA heteroplasmy, but find no evidence of paternal transmission of mtDNA in humans, they wrote in the publication.

The new study published in Nature is an expansion of the 2020 work, adopting an even larger sample size 66,083 people, including 12,509 people with cancer to explore the NUMTs landscape.

They discovered that new inserts of mtDNA into nuclear DNA are happening frequently and offer new insights into the evolution of the human genome. Billions of years ago, a primitive animal cell took in a bacterium that became what we now call mitochondria. These supply energy to the cell to allow it to function normally, while removing oxygen, which is toxic at high levels. Over time, bits of these primitive mitochondria have passed into the cell nucleus, allowing their genomes to talk to each other, Chinnery said. This was all thought to have happened a very long time ago, mostly before we had even formed as a species, but what we've discovered is that thats not true. We can see this happening right now, with bits of our mitochondrial genetic code transferring into the nuclear genome in a measurable way.

The scientists estimate that this DNA transfer occurs once in every 4,000 births. The molecular mechanisms that enable this transfer are not yet clear, but Chinnery hypothesizes that the process occurs within the egg cells of the mother.

Fifty eight percent of the mtDNA insertions were found to occur in protein-coding genome regions. Thus, the transfer of mtDNA will inevitably increase the size of the genome. However, the team found an inverse correlation between NUMT size and the frequency of its occurrence, which they suggest points towards a selective process counter-balancing NUMT insertion, maintaining genome size and removing NUMTs that influence gene expression.

When analyzing the DNA samples from cancer patients, the researchers found a high distribution of NUMTs, arising in around 1 in 1,000 cancers, which they believe reflects genomic instability. In some cases, the insertion of mtDNA contributes to the development of cancer. Our nuclear genetic code is breaking and being repaired all the time, said Chinnery. Mitochondrial DNA appears to act almost like a band-aid, a sticking plaster to help the nuclear genetic code repair itself. And sometimes this works, but on rare occasions if might make things worse or even trigger the development of tumors.

Chinnery and colleagues also questioned whether mtNDA can absorb elements of nuclear DNA, but there was no evidence that this occurs. They attribute this to the large number of mtDNA copies that exist versus the number of copies of nuclear DNA theres a far greater chance that mtDNA will be broken and pass into the nucleus than there is for the reverse to occur. In addition, mtDNA is neatly packaged within two membranes that are not porous, so it would be a challenge for nuclear DNA to work its way in. However, holes in the membrane that protects nuclear DNA can occur, so mtDNA has an easier passageway.

Reference: Wei W, Schon KR, Elgar G, et al. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Nature. 2022. doi:10.1038/s41586-022-05288-7.

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Mitochondrial DNA Is Working Its Way Into the Human Genome - Technology Networks

Explainer: The Different Types of Volcanoes on Earth

Even if you dont live near a volcano, youve been impacted by their activity.

Its estimated that more than 80% of our planets surface has been shaped by volcanic activity. Theyve helped create our mountain ranges, plains, and plateaus, and have even helped fertilize the land that we now use to grow crops.

These critical mounds come in many shapes and sizes. This graphic by Giulia De Amicis provides a brief introduction to volcanoes, explaining their different types of shapes and eruptions.

A volcano starts to form when molten rock rises from a crack in the Earths surface, which often emerge along tectonic plate boundaries.

Magma rises to the Earths surface because its lighter than rock. When it surfaces or erupts, its referred to as lava.

There are various types of volcanic eruptions, depending on the lavas temperature, thickness, and composition. Generally speaking, high gas content and high viscosity lead to explosive eruptions, while low viscosity and gas content lead to an effusive, or steadily flowing, eruption.

Volcanoes vary in size and structure, depending on how theyre formed. Most volcanoes types fall into four main groups:

Shield volcanoes are built slowly, from low-viscosity lava that spreads far and quick. The lava eventually dries to form a thin, wide sheet, and after repeated eruptions, a mount starts to form.

From the top, these types of volcanoes look like a shield, hence the name. While these volcanoes take a while to form, they arent necessarily low. In fact, the worlds tallest active volcano, Mauna Kea in Hawaii, is a shield volcano.

Also known as composite volcanoes, stratovolcanoes are built relatively fast, at least compared to shield volcanoes. This is because, in between lava eruptions, composite volcanoes emit ash and rock, which helps add structure to the mound rather quickly.

Some well-known composite volcanoes are Mount Fuji in Japan, Mount St. Helens in Washington, and Mount Cotopaxi in Ecuador.

Opposite to shield volcanoes, volcanic domes are formed when lava is highly-viscous. Because the thick lava cant travel very far, it starts to pool around the volcanos vent.

This can sometimes create a pressure build-up, meaning dome volcanoes are prone to explosive eruptions.

These types of volcanoes typically dont release lava. Rather, their eruptions typically emit volcanic ash and rocks, known as pyroclastic products.

Cinder cones are characterized by a bowl-shaped crater at the top, and usually dont exceed 400 m (1,312 ft) in height.

Volcanoes have a number of ecological benefits. Once broken down, volcanic materials create exceptionally fertile soil, which can help build prospering new habitats for animals and plants.

Volcanic eruptions can also help cool our climate. When a volcano explodes, ash and sulfur gas from the eruption combine with water droplets and get trapped in the atmosphere for years. This has a cooling effect which is extremely beneficial to us, especially given our current global warming situation.

Dr. Tracy Gregg, associate professor for the University at Buffalos geology department, told Accuweather that volcanoes have actually helped to keep the world about 2 to 3 degrees cooler than it otherwise may be.

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Animated Map: Where to Find Water on Mars - Visual Capitalist

Scientists don't know much about what the very first mammal looked like, but they do know that it lived around 180-250 million years ago and that every mammal on Earth from blue whales to platypuses is descended from it.

But thanks to new research, we now know what its genome looked like.

An international team of scientists has computationally pieced together a likely genome for the common ancestor of mammals by working backward from 32 genomes of living species.

The analysis included a wide range of species from all three types of mammals, including narwhals, bats pangolins, and humans for placental mammals, Tasmanian devils and wombats for marsupials, and the egg-laying platypus.

Chickens and Chinese alligators were used as a non-mammal comparison group.

The researchers reconstructed the complete set of chromosomes at 16 nodes stretching back to the common ancestor of all mammals. (A node represents the last common ancestor between two distinct genetic lines; it is the point where the phylogenetic tree splits into multiple branches.)

Researchers concluded that the species at the very start of the mammal phylogenetic tree likely had 38 chromosomes.

It shared nine of the smallest chromosomes with the common ancestor of mammals, birds, and reptiles, which is a step even further back in the tree.

"This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary timeframe of more than 320 million years," says senior author and evolutionary biologist Harris Lewin.

Many of these highly conserved areas contain genes involved in developmental functions.

The researchers examined how chromosomes were broken apart, combined, deleted, repeated, or translocated over time.

The sections of the chromosomes heavily affected by rearrangements are called 'breakpoints', a rich source of genetic variations that play a role in separating species through evolution.

The highest breakpoint rate was observed when therians marsupial and placental mammals that give birth to live young split from the egg-laying monotremes.

"Our results have important implications for understanding the evolution of mammals and for conservation efforts," says Lewin.

It is likely the earliest mammal looked somewhat like the tiny, rat-like mammal called Morganucodon, which lived around 200 million years ago and laid eggs. Its fossil was discovered in a limestone crevice in 1949 in Wales in the UK.

This genus is related to living mammals, but it isn't considered a common ancestor, making it a sister group to the mammal line.

Another mammalian sister clade is the rodent-like Tritylodont genus. Fossils found in Africa and North America are too specialized to be a common ancestor of all mammals, but they would have lived around the same time as the first mammal species.

This paper was published in the Proceedings of the National Academy of Sciences.

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Reconstruction of The First Mammal's Genome Suggests It Had 38 Chromosomes - ScienceAlert

Since the premier of the wildly popular 1993 dinosaur cloning film Jurassic Park, the sciences featured in the film, genetic engineering and genomics, have advanced at breathtaking rates. When the film was released, the Human Genome Project was already working on sequencing the entire human genome for the first time. They completed the project in 2003 after 13 years and at a cost of $1 billion. Today, the human genome can be sequenced in less than a day and at a cost of less than $1,000.

One leading genomics research organization, The Wellcome Sanger Institute in England, is on a mission to improve the health of all humans by developing a comprehensive understanding of the 23 chromosomes in the human body. Theyre relying on cutting edge technology to operate at incredible speed and scale, including reading and analyzing an average of 40 trillion DNA base pairs a day.

Alongside advances in DNA sequencing techniques and computational biology, high-performance computing (HPC) is at the heart of the advances in genomic research. Powerful HPC helps researchers process large-scale sequencing data to solve complex computing problems and perform intensive computing operations across massive resources.

Genomics at Scale

Genomics is the study of an organisms genes or genome. From curing cancer and combatting COVID-19 to better understanding human, parasite, and microbe evolution and cellular growth, the science of genomics is booming. The global genomics market is projected to grow to $94.65 billion by 2028 from $27.81 billion in 2021, according to Fortune Business Insights. Enabling this growth is a HPC environment that is contributing daily to a greater understanding of our biology, helping to accelerate the production of vaccines and other approaches to health around the world.

Using HPC resources and math techniques known as bioinformatics, genomics researchers analyze enormous amounts of DNA sequence data to find variations and mutations that affect health, disease, and drug response. The ability to search through the approximately 3 billion units of DNA across 23,000 genes in a human genome, for example, requires massive amounts of compute, storage, and networking resources.

After sequencing, billions of data points must be analyzed to look for things like mutations and variations in viruses. Computational biologists use pattern-matching algorithms, mathematical models, image processing, and other techniques to obtain meaning from this genomic data.

A Genomic Powerhouse

At the Sanger Institute, scientific research is happening at the intersection of genomics and HPC informatics. Scientists at the Institute tackle some of the most difficult challenges in genomic research to fuel scientific discoveries and push the boundaries of our understanding of human biology and pathogens. Among many other projects, the Institutes Tree of Life program explores the diversity of complex organisms found in the UK through sequencing and cellular technologies. Scientists are also creating a reference map of the different types of human cells.

Science on the scale of that conducted at the Sanger Institute requires access to massive amounts of data processing power. The Institutes Informatics Support Group (ISG) helps meet this need by providing high performance computing environments for Sangers scientific research teams. The ISG team provides support, architecture design and development services for the Sanger Institutes traditional HPC environment and an expansive OpenStack private cloud compute infrastructure, among other HPC resources.

Responding to a Global Health Crisis

During the COVID-19 pandemic, the Institute started working closely with public health agencies in the UK and academic partners to sequence and analyze the SARS-COV-2 virus as it evolved and spread. The work has been used to inform public health measures and to help save lives.

As of September 2022, over 2.2 million coronavirus genomes have been sequenced at Wellcome Sanger. They are immediately made available to researchers around the world for analysis. Mutations that affect the viruss spike protein, which it uses to bind to and enter human cells, are of particular interest and the target of current vaccines. Genomic data is used by scientists with other information to ascertain which mutations may affect the viruss ability to transmit, cause disease, or evade the immune response.

Societys greater understanding of genomics, and the informatics that goes with it, has accelerated the development of vaccines and our ability to respond to disease in a way thats never been possible before. Along the way, the world is witnessing firsthand the amazing power of genomic science.

Read more about genomics, informatics, and HPC in this white paper and case study of the Wellcome Sanger Institute.

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Genomic Science Breakthroughs Are Happening Faster Than Ever Thanks to HPC - CIO

Swedish geneticist Svante Pbo is the winner of the 2022 Nobel Prize in Physiology or Medicine and he will receive a prize worth 10 million Swedish kronor (896,256.51 US dollars). The prestigious award was given for discoveries concerning the genomes of extinct hominins and human evolution, a field that is now known as paleogenomics.

The work has completely changed the understanding of hominins that co-existed with us for a time. It has also provided new insights into how our body functions and how these ancient genomes are still present in some of us affecting us for better or for worse.

Pbo and his colleagues were able to extract mitochondrial DNA from a Neanderthal bone back in 1997. They showed it was possible to extract genetic material from ancient remains but it took a long while before a full genome could be drafted. The enormous challenge was completed over a decade later, with a draft of the genome published in the journal Science in May 2010.

This was just the beginning of a revolution in how we study the past. Before, it could only be done with paleontological and archeological finds. However, finding fossils alone cant answer all the questions we might have about the past. The work has begun to provide answers on how we are related to extinct humans and how we differ.

The work showed that some of our ancestors and Neanderthals had children together. This species of extinct humans inhabited the Eurasian continent, so between one and two percent of the DNA of people of European or Asian ancestry is Neanderthal. For those whose ancestry is to be found exclusively in sub-Saharan Africa, the value is close (or much closer) to zero.

Together with his team, Pbo discovered a new species of extinct humans: the Denisovans. The discovery was possible by extracting DNA from a single finger bone of a juvenile female. There are very few physical remains of this species, and what we know comes from genomic analysis. This includes the discovery of another young girl whose mother was a Neanderthal and her father a Denisovan.

In 2020, the Nobel Laureate and his team reported that genes link to a higher risk of hospitalization due to COVID-19 were remarkably similar to those of Neanderthals. They suggested that the ancient interbreeding had an effect on the health of their descendants today.

A bit of trivia regarding the winner: hes the son of another Nobel Prize winner Sune Bergstrm, who won the same prize in 1982, and renowned Estonian refugee and food chemist Karin Pbo. He is the 225th winner of the Nobel Prize in Physiology or Medicine, of which 12 are women.

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Genome Of Ancient Humans Is The Winning Field Of 2022's Nobel Prize in Medicine - IFLScience

October 4, 2022

Natalie Diaz loves language.

That love is evidenced by her writing, for which she was awarded the Pulitzer Prize in Poetry in 2021 for her collection Postcolonial Love Poem.

Its also a part of her heritage. Diaz, an associate professor in Arizona State Universitys Department of English, was born in the Fort Mojave Indian Village in Needles, California, and is an enrolled member of the Gila River Indian Community.

The love for her native Mojave language is the backdrop for Diazs appearance on "Habla Loud," the latest installment in the award-winning "Habla" series on HBO. "Habla Loud," which features celebrities and influential Latinos sharing their stories of being Latino in the United States, will premiere at 8 p.m. Arizona time on Friday, Oct. 7, on HBO Latino.

ASU News talked to Diaz about the show and the work shes done to ensure the Mojave language is preserved.

Editor's note: The following interview has been edited for length and clarity.

Question: Tell me about your part in the show.

Answer: Something really generous about the series is the way its looking at whats considered Latina, Latino, Latinx. Because identity is always tense. And something thats been really important for me about his (director Alberto Ferrera's) vision and viewpoint of this is that its really constellating a very large community thats also very nuanced. This often happens with Indigenous people as well, and Im included as a Mexican, Spanish person and a Native person in the United States.

The lens that he opened up for me to talk about the language work that I do with my elders at Fort Mojave is really important because language, especially in the Spanish-speaking community, but also in our Native communities (is being lost). ... How do you recover that? And theres some of the really tough things to talk about, like, "Whos fluent, whos not, how much do you know, am I saying it right?" So, it was really lucky that he invited me, and thats where the conversation went.

Q: Ferreras is quoted as saying youre trying to rescue the Mojave language. Is that the case?

A: So, Im from Fort Mojave, which means the military base was there. In order, it was: Spanish explorers, Mormons, the Ives expedition, the railroad. And then as the railroad came in, they built the military base, once we were kind of quieted and broken down. Then the military was able to leave because we were no longer a threat. They turned the military base into a boarding school, and that boarding school (where English was taught) became one of the final and probably most powerful parts of the process of silencing the Mojave language.

They take the language away from the young people so that when they go home, they dont have their language to speak back to their parents. Their parents quit speaking to them in Mojave because they dont understand.

Q: Did you have a sense growing up there that your language was being lost?

A: I only heard my elders speaking it. When I was growing up as a kid, we had our own street version (of Mojave). We would call each other names, tease each other, maybe even say things we thought were curse words, which Mojave actually doesnt have. Otherwise, I only heard my elders speak it. My great-grandmother, who I would take care of, she and my great-aunt spoke it together, so they would close the door when our elders came to visit and have their private conversation, which wed sometimes overhear. Or I learned command phrases, like behave or go outside.

But, yeah, it was clear to me that it wasnt a language spoken by young people. It was a language that felt like it was a part of us, but I didnt quite understand it.

Q: When did you decide that you wanted to rediscover your language?

A: I was out of graduate school. Id left my reservation for the first time to play basketball at Old Dominion University. I thought I needed to be as far away from home as possible. Then I played basketball overseas, had a career-ending knee injury, went back to graduate school and it was after graduate school that I decided to come home. I originally wanted to just gather stories and oral histories, but my tribe asked if I would engage in this language project. I didnt speak the language, but I was able to come back and just work side by side with my elders.

I spent most of my days with them and, in particular, (an elder named) Hubert almost every day. I knew I wanted to write. I knew I had a gift of writing and that I could express myself. That was what kind of made made me decide that I can go and help tell some of the stories that I heard growing up.

Q: What did your work consist of?

A: One of the things that I did was work with my elders to find pathways for them to share the language, because thats the same way that the boarding school took away the opportunity to teach our children a language. Our current society doesnt give elders a lot of opportunity to share. We were doing a lot of recordings audio and video recordings. I learned small but really important things. I would ask, How do we say, Are you hungry? And what they would tell me is we dont ask if youre hungry. We simply feed you. But heres a way that you might express that. I think we forget sometimes that language is not just about the product that comes at the end or the action, but its all of the values included.

Q: How long did the work take, and what was the final result?

A: We have a pretty large archive. I was working with elders individually and recording their stories and turning them over to their families. There are still some projects that we didnt get to (because Hubert recently passed away). However, I have the previous recordings that he did, and a lot of it is still ongoing.

I think some of it was simply revitalizing peoples interest in it. We have a culture center at Fort Mojave that is carrying on some of that work, but losing (Hubert) is a big blow. It really just shifts your mind and makes you think of all thats lost. But also everything that he gave us by opening up to us. I was working with him almost every day for five years. I have so much of the language he gave me streaming through me and in me.

The more difficult part, of course, is in all the things we gather and collect, how do you turn those into dissemination tools? How do you create things? That was what he and I had been working on the last few years, figuring out ways that we might create materials and put them into archives and places where people can access them. We think about language work as being in the past because were looking back toward something lost or a time when it was spoken, but I think what I learned from him is that its actually very much about preparing for the future in which we might speak it again. I think that was a gift I didnt realize until just the last few days when we lost him.

Q: Is it your hope, then, that this has a generational impact in the sense that the Mojave language lives on?

A: Yes. One of the things that he (Hubert) always talked about, and I think a lot about, is things like dreaming and play. We forget the importance of those in terms of language-making, because language becomes so utilitarian that you just expect it, you assume it. You can teach a language in class to students, but if theyre not speaking it, if theyre not teasing each other in it, if theyre not making jokes Really, for the language to be alive, we need to create opportunities for young people to engage in those ways, to be able to text each other in it, or create new stories of their own or new songs, things like that.

I also realize that it took a long time for that silencing to happen. Its going to take a while for it to be heard, more often, more loudly, with joy. So, I think its about now working with people imagining what that future can look like.

Top photo courtesyScott Baxter photography

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ASU professor to study new genome editing tools with NIH Innovator Award - ASU News Now

A research team led by a University of Massachusetts Amherst scientist has made a significant genetic discovery that sheds light on the use of the drug caspofungin to treat a deadly fungal infection, Aspergillus fumigatus, which kills some 100,000 severely immunocompromised people each year.

Typically, healthy people inhale about 50 to 100 spores of A. fumigatus every day when outdoors. Our body does a great job of identifying them and destroying them, says UMass Amherst associate professor of food science John Gibbons, whose microbial genomics lab studies the fungus.

But in people with compromised immune systems from cancer treatment, organ transplants, HIV, COVID-19 and other conditions, A. fumigatus can cause a really nasty infection, invasive pulmonary aspergillosis, with a 50% mortality rate, Gibbons says. And theres a limited way to treat these infections.

To complicate matters, when given in high concentrations as a treatment for an A. fumigatus infection, the anti-fungal drug sometimes creates a caspofungin paradoxical effect [CPE], which increases the fungal growth rather than eradicating it.

In research published in the journal Microbiology Spectrum, senior author Gibbons, Shu Zhao, a former graduate student in the Gibbons lab, and colleagues describe a first important step in the effort to understand when and why treatment with caspofungin could be more harmful than beneficial. The team, including scientists from Vanderbilt University, the University of Tennessee Science Health Center and the University of So Paolo in Brazil, completed the first genomic and molecular identification of two genes that contribute to the paradoxical effect in A. fumigatus.

This is one of the first studies to apply genome-wide association (GWA) analysis to identify genes involved in an Aspergillus fumigatus phenotype, the paper states.

The team sequenced the genome of 67 clinical samples, about half of which had CPE, spotting genetic differences between the groups and then using GWA, a statistical method, to determine how these genetic variants are associated with growth patterns at high concentrations of caspofungin. We identified a few candidate genes that we thought might contribute to this paradoxical effect, Gibbons says.

The scientists then used the genetic engineering technology, CRISPR, to delete those candidate genes from the genome, creating gene-deletion mutants and enabling the researchers to determine that two of the genes were involved in the paradoxical effect.

It looks like there are many genes and many genetic variants that contribute to this phenotype, Gibbons says. We arent done yet. One idea is that we could potentially generate new drug targets if we find the full collection of genes. We dont understand the mechanisms yet.

Ultimately the team hopes they can use DNA sequencing to understand the genetic basis of different phenotypes in general and to predict for clinical benefits if a patient sample of A. fumigatus has a genotype that is associated with the paradoxical effect.

That would be an important tool that could really improve treatment, Gibbons says.

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Genomic Research Aids in the Effort to Understand How Best to Treat Deadly Infections Caused by a Fungus - UMass News and Media Relations