Sara Sawyer

BioFrontiers scientists developing COVID-19 test that knows you’re sick before you do

Anonymous — Mon, 13 Apr 2020 15:02:49 +0000

BioFrontiers scientists developing COVID-19 test that knows you’re sick before you do Anonymous (not verified) Mon, 04/13/2020 - 09:02

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Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease

Anonymous — Mon, 13 Jan 2020 15:05:33 +0000

Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease Anonymous (not verified) Mon, 01/13/2020 - 08:05

Flaviviruses such as dengue encode a protease that is essential for viral replication. The protease functions by cleaving well-conserved positions in the viral polyprotein. In addition to the viral polyprotein, the dengue protease cleaves at least one host protein involved in immune response. This raises the question, what other host proteins are targeted and cleaved? Here we present a new computational method for identifying putative host protein targets of the dengue virus protease. Our method relies on biochemical and secondary structure features at the known cleavage sites in the viral polyprotein in a two-stage classification process to identify putative cleavage targets. The accuracy of our predictions scaled inversely with evolutionary distance when we applied it to the known cleavage sites of several other flaviviruses—a good indication of the validity of our predictions. Ultimately, our classifier identified 257 human protein sites possessing both a similar target motif and accessible local structure. These proteins are promising candidates for further investigation. As the number of viral sequences expands, our method could be adopted to predict host targets of other flaviviruses.

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A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Anonymous — Wed, 30 Oct 2019 17:01:26 +0000

A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species Anonymous (not verified) Wed, 10/30/2019 - 11:01

Historically, the evolution of bats has been analyzed using a small number of genetic loci for many species or many genetic loci for a few species. Here we present a phylogeny of 18 bat species, each of which is represented in 1,107 orthologous gene alignments used to build the tree. We generated a transcriptome sequence of Hypsignathus monstrosus, the African hammer-headed bat, and additional transcriptome sequence for Rousettus aegyptiacus, the Egyptian fruit bat. We then combined these data with existing genomic and transcriptomic data from 16 other bat species. In the analysis of such datasets, there is no clear consensus on the most reliable computational methods for the curation of quality multiple sequence alignments since these public datasets represent multiple investigators and methods, including different source materials (chromosomal DNA or expressed RNA). Here we lay out a systematic analysis of parameters and produce an advanced pipeline for curating orthologous gene alignments from combined transcriptomic and genomic data, including a software package: the Mismatching Isoform eXon Remover (MIXR). Using this method, we created alignments of 11,677 bat genes, 1,107 of which contain orthologs from all 18 species. Using the orthologous gene alignments created, we assessed bat phylogeny and also performed a holistic analysis of positive selection acting in bat genomes. We found that 181 genes have been subject to positive natural selection. This list is dominated by genes involved in immune responses and genes involved in the production of collagens.

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A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV)

Anonymous — Wed, 30 Oct 2019 16:54:39 +0000

A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV) Anonymous (not verified) Wed, 10/30/2019 - 10:54

Pandemic HIV-1 (group M) emerged following the cross-species transmission of a simian immunodeficiency virus from chimpanzees (SIVcpz) to humans. Primate lentiviruses (HIV/SIV) require the T cell receptor CD4 to enter into target cells. By surveying the sequence and function of CD4 in 50 chimpanzee individuals, we find that all chimpanzee CD4 alleles encode a fixed, chimpanzee-specific substitution (34T) that creates a glycosylation site on the virus binding surface of the CD4 receptor. Additionally, a single nucleotide polymorphism (SNP) has arisen in chimpanzee CD4 (68T) that creates a second glycosylation site on the same virus-binding interface. This substitution is not yet fixed, but instead alleles containing this SNP are still circulating within chimpanzee populations. Thus, all allelic versions of chimpanzee CD4 are singly glycosylated at the virus binding surface, and some allelic versions are doubly glycosylated. Doubly glycosylated forms of chimpanzee CD4 reduce HIV-1 and SIVcpz infection by as much as two orders of magnitude. Full restoration of virus infection in cells bearing chimpanzee CD4 requires reversion of both threonines at sites 34 and 68, destroying both of the glycosylation sites, suggesting that the effects of the glycans are additive. Differentially glycosylated CD4 receptors were biochemically purified and used in neutralization assays and microscale thermophoresis to show that the glycans on chimpanzee CD4 reduce binding affinity with the lentiviral surface glycoprotein, Env. These glycans create a shield that protects CD4 from being engaged by viruses, demonstrating a powerful form of host resistance against deadly primate lentiviruses.

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dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA

Anonymous — Wed, 30 Oct 2019 16:48:08 +0000

dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA Anonymous (not verified) Wed, 10/30/2019 - 10:48

RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that RNA viruses produce double-stranded RNA (dsRNA) while replicating. Purifying and sequencing dsRNA from the total RNA isolated from infected tissue allowed us to recover dsRNA virus sequences and replicated sequences from single-stranded RNA (ssRNA) viruses. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length or partial RNA viral genomes of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here, we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don’t have sequenced genomes and/or commercially available rRNA depletion reagents. In addition, a significant advantage of this method is the ability to identify replicated viral sequences of ssRNA viruses, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants.

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Researchers describe new viral mechanism for balancing alternate host species

Anonymous — Thu, 19 Apr 2018 15:48:53 +0000

Researchers describe new viral mechanism for balancing alternate host species Anonymous (not verified) Thu, 04/19/2018 - 09:48

BioFrontiers

Sawyer Lab, BioFrontiers Institute, University of Colorado Boulder

University of Colorado Boulder researchers studying virus spillover have uncovered a clue explaining why dengue viruses reach high concentrations in humans, but not in primates, their presumed natural source. The work was performed by the lab of Dr. Sara Sawyer at the BioFrontiers Institute, and published recently in the journal eLIFE.

Dengue viruses cause disease in approximately 100 million individuals each year. As of yet, no vaccine exists to protect against all human dengue viruses. Dengue is related to yellow fever virus, Zika virus, and West Nile virus, all of which spread via mosquitoes in highly populated areas. Human dengue viruses emerged from primates, yet dengue does not reach high titers in primate populations.

“This paper characterizes one way dengue virus avoids detection by the human immune system. Despite being genetically very similar, small changes that exist between humans and their primate relatives affect the ability of dengue virus to replicate,” said Alex Stabell, a graduate student in Dr. Sara Sawyer’s lab and lead author of the study.

The research shows dengue virus cleaves human STING protein, impairing the body’s immune response. In other primates, dengue does not cleave STING, lessening the pathogenicity of the disease. The authors trace this disparity to residues 78 and 79 in the STING protein, which read ‘RG’ in humans. Monkeys and other mammals have different residues in these locations, causing STING to evade detection by viral proteases. Conversion of these residues to the human-encoded ‘RG’ renders all primate STINGs susceptible to viral cleavage.

“Dengue viruses have evolved to suppress innate immunity in humans in order to increase viral titers and spread,” the authors note. “What we have uncovered is a brilliant method for balancing alternate host species.”

In dense human populations, the cost of severe disease is outweighed by excellent spread. But in smaller animal populations, decreased disease impact allows the virus to use these animals as a long-term reservoir. Thus, dengue viruses have evolved to achieve ideal pathogenesis in both humans and nonhuman primates.

“Hopefully, the species-specific differences we discovered in this paper will help guide further studies, and help us better understand dengue virus replication,” said Stabell. These results will help researchers identify better laboratory animals for studying dengue virus pathogenesis, a crucial step in the development of drugs and vaccines.

Co-authors of the study include Rebekah Gulberg and Rushika Perera of Colorado State University.

The research was supported by the National Institutes of Health, the National Science Foundation, and the Burroughs Wellcome fund.

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Sara Sawyer selected for the 2018 Avant-Garde Award for HIV/AIDS Research from the National Institute on Drug Abuse (NIDA)

Anonymous — Tue, 13 Mar 2018 14:34:19 +0000

Sara Sawyer selected for the 2018 Avant-Garde Award for HIV/AIDS Research from the National Institute on Drug Abuse (NIDA) Anonymous (not verified) Tue, 03/13/2018 - 08:34

NIH’s awards support groundbreaking approaches to HIV prevention and treatment

With diverse proposals focused on everything from natural killer cells to therapeutic vaccines to treat HIV, three recipients have been selected for the 2018 Avant-Garde Award for HIV/AIDS Research from the National Institute on Drug Abuse (NIDA), part of the National Institutes of Health. The awards will each provide $500,000 per year for up to five years (subject to the availability of funds) to support the research of three scientists, Drs. Catherine Blish, Nathaniel Landau, and Sara Sawyer. NIDA’s annual Avant-Garde Award competition, now in its 11th year, is intended to stimulate high-impact research that may lead to groundbreaking opportunities for the prevention and treatment of HIV/AIDS in drug users.

“We are thrilled to see the innovative approaches being stimulated by our Avant-Garde program,” said NIDA Director Nora D. Volkow, M.D. “The scientists at these institutions are looking at complex nuances that could reshape how we manage HIV/AIDS treatment – a unique issue with people who use drugs – bringing continued energy to the science of HIV and AIDS.”

The principal investigators funded by the awards are listed below:

Catherine A. Blish, Ph.D., M.D.	Stanford University, Palo Alto, California	Targeting Natural Killer Cells to HIV in Intravenous Drug Users	Dr. Catherine Blish proposes a novel approach to fight HIV by using natural killer cells to optimally target HIV strains transmitted through injection drug use. Current approaches focus on targeting HIV strains transmitted through sexual contact, which could differ in immune response properties unique to injection drug users. This approach could be valuable in the development of vaccines and therapeutics for HIV prevention and cure strategies.
Nathaniel R. Landau, Ph.D.	New York University School of Medicine, New York City	Therapeutic Dendritic Cell Vaccine for HIV	Dr. Nathaniel Landau proposes to develop a therapeutic vaccine that enhances the immune response against HIV so that patients can discontinue or reduce antiretroviral drug regimens. The long-term misuse of drugs including alcohol, methamphetamine and opioids is associated with suppressed immune responses. For such individuals, stimulation of an immune response via a vaccine could slow disease progression. Moreover, minimizing the need for treatment would be beneficial for those who may be less able to adhere to complex antiretroviral drug regimens.
Sara L. Sawyer, Ph.D.	University of Colorado Boulder	Hunting the HIV-1 Unicorn	Dr. Sara Sawyer proposes to open an exciting new platform for vaccine development. Currently, most HIV infections are HIV-1. A hindrance to HIV-1 vaccine development has been the lack of an effective animal model system in which to study transmission and develop vaccines. Dr. Sawyer proposes to harness mammalian genetics to identify an improved model, which could open up a whole new avenue of HIV/AIDS research.

The Avant-Garde Awards are modeled after the NIH Pioneer Awards and are granted to fund scientists of exceptional creativity who propose high-impact research that could open new avenues for prevention and treatment of HIV/AIDS among people with substance use disorders. For information about NIDA’s AIDS Research Program, including the Avant-Garde Award Program for HIV/AIDS Research, go to www.drugabuse.gov/AIDS. Read about selected highlights of past Avant-Garde awardees. Drs. Blish, Landau and Sawyer are funded under grant numbers DA046089-01, DA046100-01 and DA046108-01, respectively.

https://www.drugabuse.gov/news-events/news-releases/2018/03/nidas-2018-avant-garde-awards-highlight-immune-response-killer-cells

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New clue in how simian immunodeficiency virus emerged from monkeys to start the HIV-1 pandemic in humans

Anonymous — Fri, 09 Mar 2018 20:30:21 +0000

New clue in how simian immunodeficiency virus emerged from monkeys to start the HIV-1 pandemic in humans Anonymous (not verified) Fri, 03/09/2018 - 13:30

Lindsay Diamond

Sawyer Lab, BioFrontiers Institute, University of Colorado Boulder

University of Colorado Boulder researchers studying the emergence of viruses from wildlife populations provide a key clue to how simian immunodeficiency virus emerged from monkeys, ultimately starting the HIV-1 pandemic in humans.

“These new observations show that differences in the RanBP2 gene between closely related species (Human-Chimp-Gorilla) affect the ability of human immunodeficiency virus (HIV-1) and related viruses in apes to infect cells. This suggests that this gene played an important role in the evolutionary processes that lead to the emergence of HIV-1 in humans,” said Nick Meyerson, a postdoctoral researcher in CU Boulder’s BioFrontiers Institute and lead author of the new research.

HIV-1 entered the human population after a series of spillover events where the simian immunodeficiency viruses (SIVs) successfully made the jump from African monkeys to great apes (chimpanzees and gorillas) and, finally, to humans. During spillover events, the virus must adapt to the new host species to gain access to critical cellular machinery. Once inside a cell, the virus requires entry to the nucleus to replicate. However, there are myriad gatekeepers designed to prevent such access.

The new research, which was recently published in the journal PLOS Pathogens, found that the transmission of SIVs from monkeys to chimpanzees, and then from chimpanzees to gorillas, both coincided with changes in the virus that enabled interaction with the cofactor RanBP2 of the new host species. RanBP2 is a component of the nuclear pore complex known to facilitate nuclear entry of HIV-1. Interestingly, human RanBP2 did not act as a barrier to transmission from great apes to human. This indicates that the transmission events of SIV from monkeys to apes paved the way for ultimately infecting humans.

“Now that we know how these monkey viruses adapted to humans, we may be able to look for similar types of changes in related viruses in nature,” said Sara Sawyer, an associate professor in the BioFrontiers Institute and senior author of the new study.

The findings could also provide new avenues of inquiry for better understanding individual levels of infectivity. “In the current study I looked at variation in RanBP2 between species whereas I am now investigating how RanBP2 variation within a species might affect an individual's susceptibility to viruses like HIV-1,” said Meyerson.

Co-authors of the study include Daniel A. S. A. Vieira and Felipe Diaz-Griferro of the Albert Einstein College of Medicine.

The research was supported by the National Institutes of Health, National Science Foundation, and the Burroughs Wellcome Fund.

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Sara Sawyer Receives Richard M. Elliott Memorial Award in Glasgow, Scotland

Anonymous — Tue, 23 Jan 2018 07:00:00 +0000

Sara Sawyer Receives Richard M. Elliott Memorial Award in Glasgow, Scotland Anonymous (not verified) Tue, 01/23/2018 - 00:00

BioFrontiers Institute

For billions of years, the battle between cells and viruses has been a primary driver of evolution. University of Colorado Boulder researcher Dr. Sara Sawyer has dedicated her career to this relationship, combining methods from virology and molecular evolution to investigate emerging human and animal viruses. Sawyer, an Associate Professor in the Department of Molecular, Cellular, and Developmental Biology and core faculty member of the BioFrontiers Institute, is receiving the Richd M. Elliott Memorial Award from the University of Glasgow Centre for Virus Research. This award is in honor of Richard M. Elliott, the former Chair of Infectious Diseases at the University of Glasgow, and a pioneer in the field of emerging viruses.

Richard M. Elliott was a pioneer in the field of bunyaviruses, which are RNA viruses transmitted by arthropod carriers such as mosquitoes. His work was pivotal in understanding the structure and function of viral genomes.

“I came to virology through the backdoor, entering this field originally so that I could test ideas in evolutionary theory,” Sawyer commented. “I am really honored to receive this recognition by the virology community.”

Sawyer frequently turns to genomics to trace the evolutionary history of antiviral genes in humans and primates, as well as viral proteins that can evade the immune system. Using tools from molecular evolution, Sawyer sheds light on why humans are resistant to animal viruses and how viruses evolve the ability to infect new species. Her work in virology will be recognized at the 23rd Glasgow Virology Workshop on February 10th.

“The prize really belongs to my whole lab, past and present,” Sawyer said. “Many people have worked together to mold the new field we are helping to pioneer, which is to combine evolutionary theory and experimentation to understand how viruses jump from animals to humans.”

Sawyer is implementing innovative approaches to continue the work of pioneering virologists such as Richard M. Elliott. Her achievements have already been recognized by the Omenn Prize for the best Evolutionary Medicine paper of 2013, and a Presidential Early Career Award for Scientists and Engineers, given to her in 2011 by President Barack Obama in a ceremony held at the White House. By merging disciplines, Sara Sawyer is beginning to answer longstanding questions about how new viral diseases emerge from nature.

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Flu researchers discover new mechanism for battling influenza

Anonymous — Thu, 02 Nov 2017 06:00:00 +0000

Flu researchers discover new mechanism for battling influenza Anonymous (not verified) Thu, 11/02/2017 - 00:00

Lisa Marshall

Just as flu season swings into full gear, researchers from the University of Colorado Boulder and University of Texas at Austin have uncovered a previously unknown mechanism by which the human immune system tries to battle the influenza A virus. The discovery sheds new light on how the virus — which kills 12,000 to 56,000 people in the United States annually — often wins, and it could ultimately lead to new treatments.

“We’ve solved a mystery, revealing a new aspect of our innate immune system and what flu has to do to get around it,” says Nicholas Meyerson, a postdoctoral researcher in the BioFr ontiers Institute and lead author of a paper published in the Nov. 8 issue of Cell Host and Microbe.

The findings, several years in the making, could lead to a better understanding of how the seasonal flu virus, which typically originates in birds, makes its way to humans. They could also inform development of next-generation antivirals able to combat a broad spectrum of influenza strains, says co-senior author Robert Krug, a leading influenza researcher and professor at the University of Texas at Austin.

The paper focuses on two key molecular players in the story of influenza infection: a human protein called TRIM25, which was recently discovered to play an important role in the human immune response to flu infection; and a protein called NS1 present in all strains of the influenza A virus and shown to bind TRIM25 to keep it from doing its job.

“We were basically trying to find out what TRIM25 was doing that flu did not want it to be doing and the role NS1 was playing in blocking that function,” Krug said.

Through a series of laboratory tests, the team revealed two main findings:

TRIM25 acts earlier than previously believed, latching on to a critical and unique flu virus structure like a “molecular clamp” to keep the virus from replicating as soon as TRIM25 detects this unique structure.

NS1 produced by the flu virus can block this function of TRIM25, enabling flu to circumvent the immune response and cause infection.

Previous research had suggested that TRIM25 fought off flu by switching on what is known as the “interferon response” — a complex signaling pathway that arms cells through the body to fight off pathogens. But not all strains of influenza block this interferon signaling pathway, which led Meyerson to suspect another mechanism was at play in helping TRIM25 fight flu.

The paper reveals that TRIM25 is also a “restriction factor,” a special protein present in the fastest-acting arm of the immune system, before spreading infection occurs.

“Restriction factors lie in wait, and should a virus be detected in one of your cells, they have immediate destructive ability,” explains co-senior author Sara Sawyer, an associate professor of Molecular, Cellular and Developmental Biology (MCDB) at CU Boulder.

Flu uses its NS1 protein to evade TRIM25’s early flu-fighting response, the researchers found.

To do the study, the researchers first infected transgenic cell lines loaded with nonhuman primate versions of TRIM25 with the human influenza A virus. They found that the cells fought off the virus far better than human versions of the TRIM25 protein.

“This told us that TRIM25 has the capacity to crush influenza, but that its human form was less active,” Meyerson said.

To find out how it crushes influenza, the researchers combined purified TRIM25 with purified viral ribonucleoproteins (vRNPs) — eight-piece protein chains that house the influenza genome — and used state-of-the-art electron microscopy to take pictures of what happened.They found that TRIM25 appears to swiftly recognize the unique structure of vRNPs and clamps down on them to keep them from replicating inside the cell.Other experiments confirmed that the NS1 protein in flu virus inhibits this function.

They also found that TRIM25 (previously believed to be present only in the cell cytoplasm) is also present in the cell nucleus, which is the same cellular location where flu replication occurs.

Sawyer and Meyerson are now looking to further investigate the role TRIM25 plays in cross-species transmission of influenza.

More studies are needed, but Krug believes new therapeutics could be designed to block the NS1 protein produced by the flu virus, hobbling its ability to evade the human immune system.

“If you could somehow block NS1 from acting, you could block all strains of the virus,” he says.

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