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Kansas City, Kansas, United States

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News Article | November 28, 2016
Site: www.eurekalert.org

What if humans could regrow an amputated arm or leg, or completely restore nervous system function after a spinal cord injury? A new study of one of our closest invertebrate relatives, the acorn worm, reveals that this feat might one day be possible. Acorn worms burrow in the sand around coral reefs, but their ancestral relationship to chordates means they have a genetic makeup and body plan surprisingly similar to ours. A study led by the University of Washington and published in the December issue of the journal Developmental Dynamics has shown that acorn worms can regrow every major body part -- including the head, nervous system and internal organs -- from nothing after being sliced in half. If scientists can unlock the genetic network responsible for this feat, they might be able to regrow limbs in humans through manipulating our own similar genetic heritage. "We share thousands of genes with these animals, and we have many, if not all, of the same genes they are using to regenerate their body structures," said lead author Shawn Luttrell, a UW biology doctoral student based at Friday Harbor Laboratories. "This could have implications for central nervous system regeneration in humans if we can figure out the mechanism the worms use to regenerate." The new study finds that when an acorn worm -- one of the few living species of hemichordates -- is cut in half, it regrows head or tail parts on each opposite end in perfect proportion to the existing half. Imagine if you cut a person in half at the waist, the bottom half would grow a new head and the top half would grow new legs. After three or four days, the worms start growing a proboscis and mouth, and five to 10 days after being cut the heart and kidneys reappear. By day 15, the worms had regrown a completely new neural tube, the researchers showed. In humans, this corresponds to the spinal cord and brain. After being cut, each half of the worm continues to thrive, and subsequent severings also produce vital, healthy worms once all of the body parts regrow. "Regeneration gives animals or populations immortality," said senior author Billie Swalla, director of Friday Harbor Laboratories and a UW biology professor. "Not only are the tissues regrown, but they are regrown exactly the same way and with the same proportions so that at the end of the process, you can't tell a regenerated animal from one that has never been cut." The researchers also analyzed the gene expression patterns of acorn worms as they regrew body parts, which is an important first step in understanding the mechanisms driving regeneration. They suspect that a "master control" gene or set of genes is responsible for activating a pattern of genetic activity that promotes regrowth, because once regeneration begins, the same pattern unfolds in every worm. It's as if the cells are independently reading road signs that tell them how far the mouth should be from the gill slits, and in what proportion to other body parts and the original worm's size. When these gene patterns are known, eventually tissue from a person with an amputation could be collected and the genes in those cells activated to go down a regeneration pathway. Then, a tissue graft could be placed on the end of a severed limb and the arm or leg could regrow to the right size, Swalla explained. "I really think we as humans have the potential to regenerate, but something isn't allowing that to happen," Swalla said. "I believe humans have these same genes, and if we can figure out how to turn on these genes, we can regenerate." Regeneration is common in many animal lineages, though among the vertebrates (which includes humans) it is most robust in amphibians and fish. Humans can regrow parts of organs and skin cells to some degree, but we have lost the ability to regenerate complete body parts. Scientists suspect several reasons for this: Our immune systems -- in a frenzy to staunch bleeding or prevent infection -- might inhibit regeneration by creating impenetrable scar tissue over wounds, or perhaps our relatively large size compared with other animals might make regeneration too energy intensive. Replacing a limb might not be cost-effective, from an energy perspective, if we can adapt to using nine fingers instead of 10 or one arm instead of two. The researchers are now trying to decipher which type of cells the worms are using to regenerate. They might be using stem cells to promote regrowth, or they could be reassigning cells to take on the task of regrowing tissue. They also hope to activate genes to stimulate complete regeneration in animals that currently aren't able to regrow all tissues, such as zebrafish. Co-authors are Kirsten Gotting of Stowers Institute for Medical Research, and Eric Ross and Alejandro Sánchez Alvarado of both the Stowers Institute and the Howard Hughes Medical Institute. This research was funded by the National Institutes of Health, Howard Hughes Medical Institute, the Seeley Fund for Ocean Research on Tetiaroa and a National Science Foundation graduate fellowship. For more information, contact Luttrell at shawnl2@uw.edu or 206-543-1484 and Swalla at bjswalla@uw.edu or 206-616-0764.


News Article | February 15, 2017
Site: phys.org

The work, published online in eLife, is the first to discover that adult stem cells called neoblasts, key to planaria regeneration, arise during a specific stage of embryonic development. Ordinarily, embryonic cells do not persist beyond embryogenesis. However, neoblasts made in early planarian embryos persist beyond embryonic development and are present throughout the animal's lifetime. Neoblasts seemingly retain the ability to access embryonic developmental programs during adulthood to drive the regeneration of body parts lost to traumatic injury. "While a large body of research focuses on regeneration in adult planaria, much less is known about planarian embryogenesis - the process of growing from a single fertilized egg into a properly formed organism," says Erin Davies, Ph.D., the study's first author and a postdoctoral research associate in the laboratory of Howard Hughes Medical Institute and Stowers Institute Investigator Alejandro Sánchez Alvarado, Ph.D. Wanting to know more, Davies and colleagues generated a staging series, or a set of unique molecular fingerprints, for Schmidtea mediterranea embryos, as well as a gene expression atlas describing embryonic tissues and the formation of major organ systems during embryogenesis. These resources are available online at https://planosphere.stowers.org. Together, these tools lay the foundation for scientists to begin comparing the processes of embryogenesis and regeneration in planaria. "In planaria, we have a really great system for studying regeneration during adulthood," Davies says. "It offers us the opportunity to start to compare and contrast what is similar and what is different about developmental processes during embryogenesis and regeneration in an adult animal." Planaria have an ability to regenerate that is unparalleled among other organisms. If an adult worm is cut apart, nearly any piece can form a new, fully-functional animal complete with a brain and nervous system, eyes, kidneys, gut, muscle, and skin - within just two weeks. Adult stem cells called neoblasts power the planaria's extraordinary talent for regeneration. These cells both replace themselves and make every type of cell needed to create an adult worm. But their origin has been unclear. "Because neoblasts have only been studied in adults, we did not know how they were made in the first place during embryonic development," says Sánchez Alvarado. "Our work has uncovered both the precise embryonic time when neoblasts are formed, and the gene expression profile that precedes their formation." The researchers observed a large-scale shift in the types of genes being expressed at about one week into development, explains Davies. "The genes that we think of as being required to make different types of tissues in the body - brain, muscle, gut, kidneys - all these genes start to turn on during this time window," she says. The researchers found that when planarian embryonic cells start to form major organ systems, adult neoblasts arise as well. When transplanted into adult planaria depleted of stem cells, these embryonic cells took hold and proliferated. The embryonic cells replenished the adult planarian stem cell population and extended its life. However, transplanted embryonic cells from earlier time periods did not take, and the adult planarian hosts died. During embryogenesis, neoblast offspring help build the worm. Once established, neoblasts are maintained throughout the worm's life, allowing the animal continued access to embryonic development programs during adulthood. Understanding this unique planarian flatworm attribute may provide further insight into their incredible regenerative abilities. "Planarian embryogenesis has remained obscure for many decades, and the embryogenesis of Schmidtea mediterranea particularly so. It is to Erin Davies' great credit that this is no longer the case and that we, as a community interested in regeneration and stem cell biology, can now peer into a world of biological activity we could not access previously," adds Sánchez Alvarado. The finding lays the foundation for future research on how stem cells are specified, maintained, and regulated, and will facilitate direct comparisons of gene function during embryogenesis and regeneration. Many of the genes required to build and maintain organs in planaria appear to work in both developmental contexts. "I think that there are likely to be many similarities, but also critical differences," Davies adds. "We understand very little about how regeneration cues are transmitted to stem cells in the adult. In planaria, we'll have the opportunity to investigate embryonic and regenerative processes both at the level of single genes, and globally at the level of what happens to all genes expressed in a particular tissue over time." Knowledge of the developmental pathways responsible for regeneration could also guide future therapeutic advances for patients suffering from degenerative diseases or traumatic injuries. The work was funded by the Stowers Institute for Medical Research, the Howard Hughes Medical Institute, and the National Institute of General Medical Sciences of the National Institutes of Health (R37GM057260-17). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Planarian flatworms have an ability to regenerate that is unparalleled among other organisms. If an adult worm is cut apart, almost any piece can form a new, fully-functional animal complete with a brain and nervous system, eyes, kidneys, gut, muscle, and skin - within just two weeks. That's why scientists consider them an ideal organism in which to study regeneration. But this phenomenon is still poorly understood. A new report from researchers in the Sánchez Alvarado Lab at the Stowers Institute for Medical Research chronicles stage-by-stage how the planarian flatworm develops as an embryo and provides new insight into the animal's remarkable regenerative abilities. The work is the first to show that stem cells key to planarian regeneration, called neoblasts, form during a specific stage of embryonic development. Neoblasts are present throughout the worm's life, and can replenish themselves and make every type of cell in the body. This feature is unique to planarian flatworms, and may underlie their incredible regenerative abilities. The findings could guide future therapeutic advances for patients suffering from degenerative diseases or traumatic injuries. Explore further: Key molecular signal that shapes regeneration in planarian stem cells discovered


Martens L.,Vlaams Institute for Biotechnology | Martens L.,Ghent University | Chambers M.,Vanderbilt University | Sturm M.,University of Tübingen | And 16 more authors.
Molecular and Cellular Proteomics | Year: 2011

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.


Yu Y.,State University of New York at Stony Brook | Srinivasan M.,State University of New York at Stony Brook | Nakanishi S.,Stowers Institute | Leatherwood J.,State University of New York at Stony Brook | And 2 more authors.
Molecular and Cellular Biology | Year: 2011

A screen of Saccharomyces cerevisiae histone alanine substitution mutants revealed that mutations in any of three adjacent residues, L97, Y98, or G99, near the C terminus of H4 led to a unique phenotype. The mutants grew slowly, became polyploid or aneuploid rapidly, and also lost chromosomes at a high rate, most likely because their kinetochores were not assembled properly. There was lower histone occupancy, not only in the centromeric region, but also throughout the genome for the H4 mutants. The mutants displayed genetic interactions with the genes encoding two different histone chaperones, Rtt106 and CAF-I. Affinity purification of Rtt106 and CAF-I from yeast showed that much more H4 and H3 were bound to these histone chaperones in the case of the H4 mutants than in the wild type. However, in vitro binding experiments showed that the H4 mutant proteins bound somewhat more weakly to Rtt106 than did wild-type H4. These data suggest that the H4 mutant proteins, along with H3, accumulate on Rtt106 and CAF-I in vivo because they cannot be deposited efficiently on DNA or passed on to the next step in the histone deposition pathway, and this contributes to the observed genome instability and growth defects. © 2011, American Society for Microbiology. All Rights Reserved.


Zhang D.,University of Kansas Medical Center | O'Neil M.F.,University of Kansas Medical Center | Cunningham M.T.,University of Kansas Medical Center | Fan F.,University of Kansas Medical Center | And 2 more authors.
Leukemia and Lymphoma | Year: 2010

The variable natural history of mucosa-associated lymphoid tissue (MALT) lymphoma poses a challenge in predicting clinical outcome. Since Wnt signaling, as indicated by nuclear localization of β-catenin, is believed to be key in stem cell activation and stem cell self-renewal, we explored the possibility that it might have a predictive value in marginal zone lymphoma. We chose to analyze pβ-catenin-S552 because its nuclear localization by immunohistochemistry appears to coincide with Wnt signaling-initiated tumorigenesis in intestinal and hematopoietic tissues. Wnt signaling and activation was studied in 22 tissue samples of extranodal marginal zone lymphoma, atypical lymphoid hyperplasia, reactive lymphoid hyperplasia, and normal lymphoid tissue to determine whether Wnt signaling could help distinguish MALT lymphoma from benign lesions. Compared to normal or reactive lymphoid tissue, we found increased nuclear expression of localized pβ-catenin-S552 in atypical lymphoid hyperplasia and extranodal marginal zone lymphoma. We show that the anti-pβ-catenin-S552 antibody may be useful in diagnosing and monitoring the progression of or response to therapy of MALT lymphoma. © 2010 Informa Healthcare USA, Inc.


Oelz D.B.,Courant Institute of Mathematical Sciences | Rubinstein B.Y.,Stowers Institute | Mogilner A.,Courant Institute of Mathematical Sciences | Mogilner A.,New York University
Biophysical Journal | Year: 2015

We investigate computationally the self-organization and contraction of an initially random actomyosin ring. In the framework of a detailed physical model for a ring of cross-linked actin filaments and myosin-II clusters, we derive the force balance equations and solve them numerically. We find that to contract, actin filaments have to treadmill and to be sufficiently cross linked, and myosin has to be processive. The simulations reveal how contraction scales with mechanochemical parameters. For example, they show that the ring made of longer filaments generates greater force but contracts slower. The model predicts that the ring contracts with a constant rate proportional to the initial ring radius if either myosin is released from the ring during contraction and actin filaments shorten, or if myosin is retained in the ring, while the actin filament number decreases. We demonstrate that a balance of actin nucleation and compression-dependent disassembly can also sustain contraction. Finally, the model demonstrates that with time pattern formation takes place in the ring, worsening the contractile process. The more random the actin dynamics are, the higher the contractility will be. © 2015 Biophysical Society.


PubMed | Stowers Institute and Courant Institute of Mathematical Sciences
Type: Journal Article | Journal: Biophysical journal | Year: 2015

We investigate computationally the self-organization and contraction of an initially random actomyosin ring. In the framework of a detailed physical model for a ring of cross-linked actin filaments and myosin-II clusters, we derive the force balance equations and solve them numerically. We find that to contract, actin filaments have to treadmill and to be sufficiently cross linked, and myosin has to be processive. The simulations reveal how contraction scales with mechanochemical parameters. For example, they show that the ring made of longer filaments generates greater force but contracts slower. The model predicts that the ring contracts with a constant rate proportional to the initial ring radius if either myosin is released from the ring during contraction and actin filaments shorten, or if myosin is retained in the ring, while the actin filament number decreases. We demonstrate that a balance of actin nucleation and compression-dependent disassembly can also sustain contraction. Finally, the model demonstrates that with time pattern formation takes place in the ring, worsening the contractile process. The more random the actin dynamics are, the higher the contractility will be.


News Article | August 29, 2016
Site: www.chromatographytechniques.com

Researchers at the Stowers Institute have established a definitive link between the makeup of the microbiome, the host immune response and an organism's ability to heal itself. They showed that a dramatic shift in the microbial community of planaria robs the freshwater flatworm of its superior regenerative abilities. This same shift has been observed in human inflammatory disorders, though previous attempts to mimic it in lower organisms like fruit flies or zebrafish have proved unsuccessful. The study, published in the journal eLife, provides a valuable model for uncovering the basic molecular mechanisms governing the interplay of immunity and regeneration, and could point the way toward new therapies to combat serious human ailments like chronic non-healing wounds. "This is the first animal model to link pathological shifts in endogenous bacteria with the inhibition of regeneration," says Alejandro Sánchez Alvarado, Ph.D., an investigator at the Stowers Institute and the Howard Hughes Medical Institute, and senior author of the study. "We know that some kinds of bacteria are critical to our health, and that other kinds of bacteria can make it very difficult for us to recover from illness. Now we can study how the changing nature of the microbiome - and the way the immune system responds to those changes - impacts the natural execution of regenerative processes." For a long time, researchers believed that the immune response primarily posed a barrier to effective tissue regeneration and repair. However, recent studies in a variety of different organisms have shown that it can play a central role in promoting this process as well. Still, the molecular mechanisms driving these diametrically opposed outcomes remain unclear. A sudden dilemma in the Sánchez Alvarado Laboratory presented an opportunity to dissect the perplexing duality of the immune system. An infection struck part of the lab's planaria population. The infected animals developed lesions around their eyes, and those lesions grew larger and larger until their entire head degenerated. Normally, the worms could simply regrow a new head, but the infection somehow thwarted their regenerative powers. Sánchez Alvarado's team and the Stowers aquatics facility developed a modified tank system that was capable of circulating and sanitizing the culture media so they could rear healthy worms, but they found that when they took the worms out of that system, they quickly got sick again. Although most of the lab members viewed this development with frustration, Chris Arnold, Ph.D., a new postdoctoral research associate at the time, took a different perspective. "I saw this as the perfect inducible model system. It was making lemonade out of lemons," Arnold said. "We could take worms that were healthy, remove them from the tank system when desired, and place them in other conditions where they would then become ill. Amazingly, we found that when we withdrew the worms from the tank system and they developed problems, we could successfully treat their tissue degeneration with antibiotics. That suggested bacteria might be involved." Arnold decided to determine what kind of bacteria were living with the worms. He conducted a bacterial census and found that the microbiome of the worms was surprisingly similar to that of humans. When the worms were healthy, they housed a large population of Bacteroides - a group of helpful, supportive, symbiotic bacteria - and a smaller population of Proteobacteria - a group that contains a number of dangerous human pathogens. But when the worms developed lesions, they experienced a huge surge in Proteobacteria, some members of which have been shown to cause peptic ulcers and stomach cancer in humans. The researchers wondered if it was not the bacteria itself, but rather the immune system's response to the bacteria that was impairing the worm's ability to regenerate. To test this hypothesis, Arnold used an advanced molecular technique called RNA interference to silence core components of the immune system. Then, he looked to see how each one affected the ability of the worms to repair their lesions and regenerate their heads during infection. The researchers discovered that when they blocked a gene called TAK1 kinase, the worms were able to recover from the damage incurred from infection. They looked at other genes that interacted with TAK1 kinase including activators and inhibitors of the TAK1 pathway and found that most of them also affected regeneration, but only when worms were infected. "Our findings suggest that there is something special about regeneration during infection that's different than normal regeneration. There are genes that prompt degeneration in one case, and regeneration in another. It is topsy-turvy, completely different from what we would expect. We think this pathway might act to get rid of infected cells, clearing them out so the infection cannot spread to healthy tissue. Only when we block the pathway, can we allow regeneration to occur even in the presence of infection," said Sánchez Alvarado. Sánchez Alvarado says that in the future, it may be possible to develop small molecules that suppress this immune pathway in order to bump up tissue repair and regeneration not just in a simple organism like planaria, but also in higher organisms like humans. However, first they will need to understand more about the activators and inhibitors in the pathway, and how they interact. "Our healthcare system is struggling to deal with conditions of impaired wound healing. We know that bacteria are impediments to healing in patients, and that antibiotics aren't always effective, especially with the rise of antibiotic-resistant bacteria. By understanding the genes and pathways involved in the immune response, we may be able to interpret the signals that determine whether an organism decides it is beyond repair or tries to regenerate. Perhaps then could we develop more effective therapies," said Arnold.


News Article | August 26, 2016
Site: phys.org

They showed that a dramatic shift in the microbial community of planaria robs the freshwater flatworm of its superior regenerative abilities. This same shift has been observed in human inflammatory disorders, though previous attempts to mimic it in lower organisms like fruit flies or zebrafish have proved unsuccessful. The study, published in the journal eLife, provides a valuable model for uncovering the basic molecular mechanisms governing the interplay of immunity and regeneration, and could point the way toward new therapies to combat serious human ailments like chronic non-healing wounds. "This is the first animal model to link pathological shifts in endogenous bacteria with the inhibition of regeneration," says Alejandro Sánchez Alvarado, Ph.D., an investigator at the Stowers Institute and the Howard Hughes Medical Institute, and senior author of the study. "We know that some kinds of bacteria are critical to our health, and that other kinds of bacteria can make it very difficult for us to recover from illness. Now we can study how the changing nature of the microbiome - and the way the immune system responds to those changes - impacts the natural execution of regenerative processes." For a long time, researchers believed that the immune response primarily posed a barrier to effective tissue regeneration and repair. However, recent studies in a variety of different organisms have shown that it can play a central role in promoting this process as well. Still, the molecular mechanisms driving these diametrically opposed outcomes remain unclear. A sudden dilemma in the Sánchez Alvarado Laboratory presented an opportunity to dissect the perplexing duality of the immune system. An infection struck part of the lab's planaria population. The infected animals developed lesions around their eyes, and those lesions grew larger and larger until their entire head degenerated. Normally, the worms could simply regrow a new head, but the infection somehow thwarted their regenerative powers. Sánchez Alvarado's team and the Stowers aquatics facility developed a modified tank system that was capable of circulating and sanitizing the culture media so they could rear healthy worms, but they found that when they took the worms out of that system, they quickly got sick again. Although most of the lab members viewed this development with frustration, Chris Arnold, Ph.D., a new postdoctoral research associate at the time, took a different perspective. "I saw this as the perfect inducible model system. It was making lemonade out of lemons," Arnold said. "We could take worms that were healthy, remove them from the tank system when desired, and place them in other conditions where they would then become ill. Amazingly, we found that when we withdrew the worms from the tank system and they developed problems, we could successfully treat their tissue degeneration with antibiotics. That suggested bacteria might be involved." Arnold decided to determine what kind of bacteria were living with the worms. He conducted a bacterial census and found that the microbiome of the worms was surprisingly similar to that of humans. When the worms were healthy, they housed a large population of Bacteroides - a group of helpful, supportive, symbiotic bacteria - and a smaller population of Proteobacteria - a group that contains a number of dangerous human pathogens. But when the worms developed lesions, they experienced a huge surge in Proteobacteria, some members of which have been shown to cause peptic ulcers and stomach cancer in humans. The researchers wondered if it was not the bacteria itself, but rather the immune system's response to the bacteria that was impairing the worm's ability to regenerate. To test this hypothesis, Arnold used an advanced molecular technique called RNA interference to silence core components of the immune system. Then, he looked to see how each one affected the ability of the worms to repair their lesions and regenerate their heads during infection. The researchers discovered that when they blocked a gene called TAK1 kinase, the worms were able to recover from the damage incurred from infection. They looked at other genes that interacted with TAK1 kinase including activators and inhibitors of the TAK1 pathway and found that most of them also affected regeneration, but only when worms were infected. "Our findings suggest that there is something special about regeneration during infection that's different than normal regeneration. There are genes that prompt degeneration in one case, and regeneration in another. It is topsy-turvy, completely different from what we would expect. We think this pathway might act to get rid of infected cells, clearing them out so the infection cannot spread to healthy tissue. Only when we block the pathway, can we allow regeneration to occur even in the presence of infection," said Sánchez Alvarado. Sánchez Alvarado says that in the future, it may be possible to develop small molecules that suppress this immune pathway in order to bump up tissue repair and regeneration not just in a simple organism like planaria, but also in higher organisms like humans. However, first they will need to understand more about the activators and inhibitors in the pathway, and how they interact. "Our healthcare system is struggling to deal with conditions of impaired wound healing. We know that bacteria are impediments to healing in patients, and that antibiotics aren't always effective, especially with the rise of antibiotic-resistant bacteria. By understanding the genes and pathways involved in the immune response, we may be able to interpret the signals that determine whether an organism decides it is beyond repair or tries to regenerate. Perhaps then could we develop more effective therapies," said Arnold. Explore further: Planaria deploy an ancient gene expression program in the course of organ regeneration


For the first time, researchers at the Stowers Institute have mapped where recombination occurs across the whole genome of the fruit fly Drosophila melanogaster after a single round of meiosis. Their results indicate that separate mechanisms position the two main kinds of recombination events, crossovers and non-crossovers. The findings, which are reported online ahead of print in the journal Genetics, give important insights into the understanding of chromosomes and the mechanisms of inheritance. "It is amazing to me that more than 100 years after the discovery of genetic recombination in flies, we are only starting to understand just how these events are distributed," says R. Scott Hawley, Ph.D., an investigator at the Stowers Institute and senior author of the study. This genetic recombination takes place during a specialized form of cell division called meiosis. During meiosis, the cell copies all its chromosomes, pairs them up, and shuffles sections of genetic material between the arms of the paired or homologous chromosomes. This shuffling can occur one of two ways. In crossover events, large tracts of DNA are exchanged, like two people swapping playing cards. In non-crossover events, smaller pieces of DNA are copied from one arm and pasted onto another, like the crown from the King of Hearts in one player's hand suddenly appearing atop another player's King of Spades. Once the deck is sufficiently shuffled, the cell divides, and then divides again to create four cells, each carrying only one copy of the organism's genome. Recombination ensures that each gamete ends up with a unique copy of every chromosome, but when the process goes awry, it can result in chromosomal abnormalities. For example, improperly placed crossovers or the complete lack of crossovers on chromosome 21 are a major cause of trisomy 21 or Down Syndrome in humans. With one exception, all previous genetic studies of recombination in Drosophila have focused either on a single chromosome arm or on groups of flies pooled together. In this study, the Stowers researchers wanted to determine how both crossovers and non-crossovers are distributed across all five major chromosomal arms of fruit flies. Crossovers are relatively easy to identify because they involve entire chromosomal arms or parts of arms encompassing thousands of base pairs, the A's, C's, T's, and G's that make up DNA. But non-crossovers are tougher to spot, because they only involve a few hundred of those letters. Therefore, Danny Miller, an MD-PhD student at the University of Kansas Medical Center who is conducting his doctoral research in the Hawley lab, had to rely on whole genome sequencing and new computer algorithms to pinpoint the locations of both kinds of events. Miller, lead author of the study, says the project gave him the opportunity to delve into the genetic principles that underlie human health and disease. "I would like to keep doing research as a physician-scientist when I graduate," says Miller, who plans to pursue a specialty in pediatric oncology or pediatric medical genetics. "I want to have a good foundational understanding of genetics. Some people may gloss over these basic questions, instead of looking at the data and trying to answer them." In this study alone, Miller generated a vast amount of data. First, he mated two genetically distinct varieties of fruit flies, known to differ at roughly 500,000 different spots in their genetic code. Miller then sequenced the entire genomes of the resulting 196 progeny and wrote a custom computer program that could scan the 160 million bases of each fruit fly genome for evidence of recombination. The approach identified a total of 541 crossovers and 291 non-crossovers. Unlike crossovers, which are generally distributed over the distal two-thirds of the chromosome arms, the non-crossovers were spread uniformly among the five major chromosome arms. Non-crossovers formed in places where crossovers rarely do, such as near the knotty centromere that ties the arms of chromosomes together. And they popped up close together, in contrast to crossovers that respond to a phenomenon known as interference when they try to form near other crossovers. The researchers discovered that the number of crossovers varied widely not just according to their position along the chromosome arm, but also from chromosome to chromosome. For example, they identified five double crossovers on one arm of chromosome 2—fewer than expected. "The finding gives credence to a certain kind of lore that has circulated in the field—the idea that each of the chromosomal arms was behaving a little differently—but nobody really knew for sure because nobody had looked at each of the arms in the same experiment," says Hawley. "What we found was that each chromosome has its own rules for making sure it gets its crossovers exactly where it wants them." In addition to crossovers and non-crossovers, the researchers also noticed evidence of duplications and deletions caused by the presence of transposons, a special class of genetic elements that can jump from one area in the genome to another. These transposable elements are a serious problem for the meiotic machinery because they can skew the pairing of homologous chromosomes, triggering duplications or deletions of genetic material that affect the viability of an organism. The study identified transposable elements in 1-2 percent of the genome, in line with previous reports.

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