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Genetic Similarities in ACE2 Receptor Likely Made Zoo Gorillas Vulnerable to SARS-CoV-2

Egghead Blog - January 13, 2021 - 3:16pm

By Lisa Howard

On Jan. 11, the San Diego Zoo announced members of its gorilla troop had tested positive for SARS-CoV-2, the first known instance of natural transmission to great apes. Two gorillas had begun coughing Jan. 6. The presence of virus in the troop was confirmed by testing fecal samples.

The Gorilla Doctors program, affiliated with the UC Davis School of Veterinary Medicine, monitors the health of wild mountain gorillas in central Africa. Gorillas are susceptible to other human respiratory diseases and may be at risk from COVID-19.

Gorillas, of course, are among our closest relatives and share many genetic similarities with humans. One particular similarity has likely made them vulnerable to COVID-19: the gene coding for angiotensin-converting enzyme-2, or ACE2.

ACE2 is the main receptor site for SARS-CoV-2, the novel coronavirus that causes COVID-19. It is found on epithelial cells that line the nose, mouth and lungs, among other locations. The virus engages with ACE2 through its surface “spike protein,” allowing it to attach to and enter cells. A sequence of 25 amino acids within the human ACE2 protein are crucial for this binding to occur.

Survey of species ACE2 proteins

Last year, an international team of researchers led by Joana Damas, postdoctoral researcher at UC Davis and Harris Lewin, distinguished professor of evolution and ecology at UC Davis, published a survey of the ACE2 protein sequences of 410 species of animals including birds, fish, amphibians and reptiles. They discovered that many animals, including gorillas, share the same amino acids on their ACE2 receptors as humans, likely leaving them potentially vulnerable to the SARS-CoV-2 virus.

In their work, published in August 2020 in Proceedings of the National Academy of Sciences, the researchers predicted that the risk of infection with the novel coronavirus would decrease the more each species’ ACE2 amino acids differ from those of humans. They noted, though, that the virus may utilize a different receptor in other species. The San Diego Zoo was one of the many institutions that contributed genomic material for the study.

Monitoring wild gorillas

Wild gorillas are susceptible to human respiratory diseases, according to Gorilla Doctors, a program affiliated with the Karen C. Drayer Wildlife Health Center at the UC Davis School of Veterinary Medicine. So far, however, there is no evidence of wild gorillas contracting SARS-CoV-2, according to a Jan. 12 blog post from Gorilla Doctors. The organization has added the novel coronavirus to their regular monitoring of the animals’ health, mostly by fecal sampling.

In addition to Western Lowland gorillas, a number of other endangered and critically-endangered primates are predicted to be at high risk of contracting COVID-19 based on their ACE2 protein sequence including bonobos, chimpanzees, and orangutans.

The risk of contracting COVID-19 is not limited to primates, however. A few other animals flagged as high risk in the survey include marine mammals such as gray whales and bottlenose dolphins. Domestic animals such as cats, cattle and sheep were found to have medium risk, and dogs, horses and pigs were found to have a low risk based on ACE2 binding.

In practice, there have been sporadic reports from around the world of cats and dogs (including big cats in zoos) being infected with SARS-CoV-2, as well as some cases in mink farms. There is no evidence of cats, dogs or other domestic animals transmitting the virus to humans, according to the UC Davis School of Veterinary Medicine.

More information

Genomic Analysis Reveals Many Animal Species May Be Vulnerable to SARS-CoV-2 Infection (UC Davis News)

Gorilla Troop at San Diego Zoo Safari Park Test Positive for COVID-19 (San Diego Zoo news release)

Captive Western Lowland Gorillas Proven Susceptible to COVID-19 (Gorilla Doctors)

FAQs for Pet Owners during the COVID-19 Pandemic (UC Davis School of Veterinary Medicine)

Lisa Howard is a writer with the UC Davis Office of Research. 

The post Genetic Similarities in ACE2 Receptor Likely Made Zoo Gorillas Vulnerable to SARS-CoV-2 appeared first on Egghead.

Genetic Similarities in ACE2 Receptor Likely Made Zoo Gorillas Vulnerable to SARS-CoV-2

Egghead - January 13, 2021 - 3:16pm

By Lisa Howard

On Jan. 11, the San Diego Zoo announced members of its gorilla troop had tested positive for SARS-CoV-2, the first known instance of natural transmission to great apes. Two gorillas had begun coughing Jan. 6. The presence of virus in the troop was confirmed by testing fecal samples.

The Gorilla Doctors program, affiliated with the UC Davis School of Veterinary Medicine, monitors the health of wild mountain gorillas in central Africa. Gorillas are susceptible to other human respiratory diseases and may be at risk from COVID-19.

Gorillas, of course, are among our closest relatives and share many genetic similarities with humans. One particular similarity has likely made them vulnerable to COVID-19: the gene coding for angiotensin-converting enzyme-2, or ACE2.

ACE2 is the main receptor site for SARS-CoV-2, the novel coronavirus that causes COVID-19. It is found on epithelial cells that line the nose, mouth and lungs, among other locations. The virus engages with ACE2 through its surface “spike protein,” allowing it to attach to and enter cells. A sequence of 25 amino acids within the human ACE2 protein are crucial for this binding to occur.

Survey of species ACE2 proteins

Last year, an international team of researchers led by Joana Damas, postdoctoral researcher at UC Davis and Harris Lewin, distinguished professor of evolution and ecology at UC Davis, published a survey of the ACE2 protein sequences of 410 species of animals including birds, fish, amphibians and reptiles. They discovered that many animals, including gorillas, share the same amino acids on their ACE2 receptors as humans, likely leaving them potentially vulnerable to the SARS-CoV-2 virus.

In their work, published in August 2020 in Proceedings of the National Academy of Sciences, the researchers predicted that the risk of infection with the novel coronavirus would decrease the more each species’ ACE2 amino acids differ from those of humans. They noted, though, that the virus may utilize a different receptor in other species. The San Diego Zoo was one of the many institutions that contributed genomic material for the study.

Monitoring wild gorillas

Wild gorillas are susceptible to human respiratory diseases, according to Gorilla Doctors, a program affiliated with the Karen C. Drayer Wildlife Health Center at the UC Davis School of Veterinary Medicine. So far, however, there is no evidence of wild gorillas contracting SARS-CoV-2, according to a Jan. 12 blog post from Gorilla Doctors. The organization has added the novel coronavirus to their regular monitoring of the animals’ health, mostly by fecal sampling.

In addition to Western Lowland gorillas, a number of other endangered and critically-endangered primates are predicted to be at high risk of contracting COVID-19 based on their ACE2 protein sequence including bonobos, chimpanzees, and orangutans.

The risk of contracting COVID-19 is not limited to primates, however. A few other animals flagged as high risk in the survey include marine mammals such as gray whales and bottlenose dolphins. Domestic animals such as cats, cattle and sheep were found to have medium risk, and dogs, horses and pigs were found to have a low risk based on ACE2 binding.

In practice, there have been sporadic reports from around the world of cats and dogs (including big cats in zoos) being infected with SARS-CoV-2, as well as some cases in mink farms. There is no evidence of cats, dogs or other domestic animals transmitting the virus to humans, according to the UC Davis School of Veterinary Medicine.

More information

Genomic Analysis Reveals Many Animal Species May Be Vulnerable to SARS-CoV-2 Infection (UC Davis News)

Gorilla Troop at San Diego Zoo Safari Park Test Positive for COVID-19 (San Diego Zoo news release)

Captive Western Lowland Gorillas Proven Susceptible to COVID-19 (Gorilla Doctors)

FAQs for Pet Owners during the COVID-19 Pandemic (UC Davis School of Veterinary Medicine)

Lisa Howard is a writer with the UC Davis Office of Research. 

The post Genetic Similarities in ACE2 Receptor Likely Made Zoo Gorillas Vulnerable to SARS-CoV-2 appeared first on Egghead.

Uncovering How Plants See Blue Light

Egghead Blog - January 4, 2021 - 10:53am

Plants can perceive and react to light across a wide spectrum. New research from Prof. Nitzan Shabek’s laboratory in the Department of Plant Biology, College of Biological Sciences shows how plants can respond to blue light in particular.

“Plants can see much better than we can,” Shabek said.

Plants don’t have dedicated light-detecting organs, like our eyes. They do have a variety of dedicated receptors that can sense almost every single wavelength. One such are the blue light photoreceptors called cryptochromes. When the cryptochrome detects an incoming photon, it reacts in a way that triggers a unique physiological response.

Cryptochrome-2 allows plants to detect and react to blue light. (Shabek lab)

Cryptochromes probably appeared billions of years ago with the first living bacteria and they are very similar across bacteria, plants and animals. We have cryptochromes in our own eyes, where they are involved in maintaining our circadian clock. In plants, cryptochromes govern a variety of critical processes including seed germination, flowering time and entrainment of the circadian clock. However, the photochemistry, regulation, and light-induced structural changes remain unclear.

In a new study, published Jan. 4 in Nature Communications Biology, Shabek’s lab determined the crystal structure of part of the blue-light receptor, cryptochrome-2, in the model plant Arabidopsis thaliana. They found that the light-detecting part of the molecule changes its structure when it reacts with light particles, going from a single unit to a structure made of four units linked together, or tetramer.

Rearrangement leads to gene activation

“This rearrangement process, called photo-induced oligomerization, is also very intriguing because certain elements within the protein undergo changes when exposed to blue light. Our molecular structure suggests that these light-induced changes release transcriptional regulators that control expression of specific genes in plants,” Shabek said.

Shabek in his lab at UC Davis

The researchers were able to work out the structure of cryptochrome-2 with the aid of the Advanced Light Source X-ray facility at the Lawrence Berkeley National Laboratory.

The Shabek lab broadly studies how plants sense their environment from the molecular to the organismal levels.

“This work is part of our long-term goals to understand sensing mechanisms in plants. We are interested in hormone perceptions as well as light signaling pathways,” Shabek said.

The team first solved the crystal structure of the blue light receptor two years ago, using X-ray crystallography and biochemical approaches. With recent advances in plant sciences and structural biology, they were able to update the model and reveal the missing piece of the puzzle.

Coauthors on the work are Malathy Palayam, Jagadeesan Ganapathy, Angelica Guercio, Lior Tal and Samuel Deck. The Advanced Light Source is a U.S. Department of Energy Office of Science User Facility.

More information

Structural insights into photoactivation of plant Cryptochrome-2 (Nature Communications Biology)

Innovation Award to Find Disease-Fighting Plant Compounds (UC Davis News)

The post Uncovering How Plants See Blue Light appeared first on Egghead.

Uncovering How Plants See Blue Light

Egghead - January 4, 2021 - 10:53am

Plants can perceive and react to light across a wide spectrum. New research from Prof. Nitzan Shabek’s laboratory in the Department of Plant Biology, College of Biological Sciences shows how plants can respond to blue light in particular.

“Plants can see much better than we can,” Shabek said.

Plants don’t have dedicated light-detecting organs, like our eyes. They do have a variety of dedicated receptors that can sense almost every single wavelength. One such are the blue light photoreceptors called cryptochromes. When the cryptochrome detects an incoming photon, it reacts in a way that triggers a unique physiological response.

Cryptochrome-2 allows plants to detect and react to blue light. (Shabek lab)

Cryptochromes probably appeared billions of years ago with the first living bacteria and they are very similar across bacteria, plants and animals. We have cryptochromes in our own eyes, where they are involved in maintaining our circadian clock. In plants, cryptochromes govern a variety of critical processes including seed germination, flowering time and entrainment of the circadian clock. However, the photochemistry, regulation, and light-induced structural changes remain unclear.

In a new study, published Jan. 4 in Nature Communications Biology, Shabek’s lab determined the crystal structure of part of the blue-light receptor, cryptochrome-2, in the model plant Arabidopsis thaliana. They found that the light-detecting part of the molecule changes its structure when it reacts with light particles, going from a single unit to a structure made of four units linked together, or tetramer.

Rearrangement leads to gene activation

“This rearrangement process, called photo-induced oligomerization, is also very intriguing because certain elements within the protein undergo changes when exposed to blue light. Our molecular structure suggests that these light-induced changes release transcriptional regulators that control expression of specific genes in plants,” Shabek said.

Shabek in his lab at UC Davis

The researchers were able to work out the structure of cryptochrome-2 with the aid of the Advanced Light Source X-ray facility at the Lawrence Berkeley National Laboratory.

The Shabek lab broadly studies how plants sense their environment from the molecular to the organismal levels.

“This work is part of our long-term goals to understand sensing mechanisms in plants. We are interested in hormone perceptions as well as light signaling pathways,” Shabek said.

The team first solved the crystal structure of the blue light receptor two years ago, using X-ray crystallography and biochemical approaches. With recent advances in plant sciences and structural biology, they were able to update the model and reveal the missing piece of the puzzle.

Coauthors on the work are Malathy Palayam, Jagadeesan Ganapathy, Angelica Guercio, Lior Tal and Samuel Deck. The Advanced Light Source is a U.S. Department of Energy Office of Science User Facility.

More information

Structural insights into photoactivation of plant Cryptochrome-2 (Nature Communications Biology)

Innovation Award to Find Disease-Fighting Plant Compounds (UC Davis News)

The post Uncovering How Plants See Blue Light appeared first on Egghead.

Behind the UC Davis Saliva Test for COVID-19

Egghead Blog - December 18, 2020 - 2:48pm

Since Sept. 14, UC Davis has been offering weekly free COVID-19 testing, initially for students living on campus and employees regularly visiting campus. Testing has since been expanded to all employees and students and in December was rolled out to residents of the City of Davis through the Healthy Davis Together Initiative.

Taking the test involves no more than spitting in a tube and results are typically returned in two to three days. The spit test is for people who do not have COVID-19 symptoms: those who are sick should go to their healthcare provider.

Chancellor Gary May goes through UC Davis’ new saliva test for COVID-19 on Sept. 16.

The UC Davis testing program has attracted national attention. What’s behind the test, and how was it put together?

Applying agricultural genetic technology

The tests are run in the DNA Technology Core facility at the UC Davis Genome Center. Richard Michelmore, director of the Genome Center and professor of plant sciences, and his team developed a proposal for a testing program which was funded by the campus on Aug. 4 with a goal of beginning test in mid-September as students moved into dorms for Fall quarter.

“This triggered a tremendous mobilization across campus,” Michelmore said.

The key to the testing program are two IntelliQube high-throughput quantitative PCR machines, manufactured by LGC Biosearch. These machines use “array tape” technology. Instead of sample tubes or plates with wells, the machines use a tape printed with thousands of tiny wells, each of which can carry out a PCR reaction. Originally developed for use in agricultural genetics, array-tape machines can run thousands of PCR tests a day, far more than machines built specifically for medical diagnostics.

Collecting spit samples

Samples are collected at the testing kiosk, set up initially in a parking structure and now in the basketball courts of the campus Activities and Recreation Center. You sign up for a test online and get a barcode, which is matched to the barcode on a small sample tube. Take a sip of water, drip it back into the tube, cap it and you are done.

The de-identified barcoded tubes are taken to the Genome Center, where the samples are heat-treated to inactivate any virus. SARS-CoV2 virus particles survive well in saliva, Michelmore noted.

The samples are then treated with papain protease (a.k.a. meat tenderizer) to reduce the viscosity of the saliva and transferred into 384-well plastic plates. Two plates at a time go into an IntelliQube machine. The reaction takes about an hour and a half, meaning that each machine can run about 6,000 tests in a 12-hour day. The results are analyzed with Cloud-based UgenTech FastFinder software.

The PCR test is adapted from protocols approved by the FDA. The laboratory is CLIA-approved as an extension of the UC Davis Student Health Center’s laboratory.

The test can detect as little as fifteen copies of the virus in a microliter of saliva, below the threshold of what is likely to be an infectious individual. Initially, the saliva tests were compared to nasal swabs taken at the same time and processed at a commercial laboratory, but this was discontinued once the accuracy of the saliva test was confirmed.

Two teams of staff

Two separate teams of technical staff, led by DNA Core manager Lutz Froenicke, work to run the tests on different days with a reserve team as backup.

Since Sept. 14, the program has run more than 68,000 tests with 142 positive results. In the week of Dec. 6-12, they ran almost 14,000 tests.

Michelmore credited a “massive effort across campus” with getting the testing program up and running, including Dr. Ralph Greene at the UC Davis Department of Pathology and Laboratory Medicine, Dr. Cindy Schorzmann, medical director of the Student Health and Counseling Services and Dr. Sheri Belafsky, UC Davis Medical Surveillance program and many, many others who have worked to stand up and run the testing kiosk, acquire machines and equipment, run tests and analyze and report out results.

While Michelmore has received many inquiries from other universities and businesses, he noted they are not currently planning to expand testing beyond UC Davis, Davis, other locations in Yolo County, and UC Merced due to finite capacity. However, he noted that none of the protocols and workflows are patented and could be replicated by others.

More information

GenomeWeb webinar on Deployment of High-Throughput SARS-CoV-2 Testing at UC Davis (free registration required)

UC Davis Campus Ready: COVID-19 Testing

UC Davis COVID-19 Dashboard (with testing data)

Healthy Davis Together

The post Behind the UC Davis Saliva Test for COVID-19 appeared first on Egghead.

Behind the UC Davis Saliva Test for COVID-19

Egghead - December 18, 2020 - 2:48pm

Since Sept. 14, UC Davis has been offering weekly free COVID-19 testing, initially for students living on campus and employees regularly visiting campus. Testing has since been expanded to all employees and students and in December was rolled out to residents of the City of Davis through the Healthy Davis Together Initiative.

Taking the test involves no more than spitting in a tube and results are typically returned in two to three days. The spit test is for people who do not have COVID-19 symptoms: those who are sick should go to their healthcare provider.

Chancellor Gary May goes through UC Davis’ new saliva test for COVID-19 on Sept. 16.

The UC Davis testing program has attracted national attention. What’s behind the test, and how was it put together?

Applying agricultural genetic technology

The tests are run in the DNA Technology Core facility at the UC Davis Genome Center. Richard Michelmore, director of the Genome Center and professor of plant sciences, and his team developed a proposal for a testing program which was funded by the campus on Aug. 4 with a goal of beginning test in mid-September as students moved into dorms for Fall quarter.

“This triggered a tremendous mobilization across campus,” Michelmore said.

The key to the testing program are two IntelliQube high-throughput quantitative PCR machines, manufactured by LGC Biosearch. These machines use “array tape” technology. Instead of sample tubes or plates with wells, the machines use a tape printed with thousands of tiny wells, each of which can carry out a PCR reaction. Originally developed for use in agricultural genetics, array-tape machines can run thousands of PCR tests a day, far more than machines built specifically for medical diagnostics.

Collecting spit samples

Samples are collected at the testing kiosk, set up initially in a parking structure and now in the basketball courts of the campus Activities and Recreation Center. You sign up for a test online and get a barcode, which is matched to the barcode on a small sample tube. Take a sip of water, drip it back into the tube, cap it and you are done.

The de-identified barcoded tubes are taken to the Genome Center, where the samples are heat-treated to inactivate any virus. SARS-CoV2 virus particles survive well in saliva, Michelmore noted.

The samples are then treated with papain protease (a.k.a. meat tenderizer) to reduce the viscosity of the saliva and transferred into 384-well plastic plates. Two plates at a time go into an IntelliQube machine. The reaction takes about an hour and a half, meaning that each machine can run about 6,000 tests in a 12-hour day. The results are analyzed with Cloud-based UgenTech FastFinder software.

The PCR test is adapted from protocols approved by the FDA. The laboratory is CLIA-approved as an extension of the UC Davis Student Health Center’s laboratory.

The test can detect as little as fifteen copies of the virus in a microliter of saliva, below the threshold of what is likely to be an infectious individual. Initially, the saliva tests were compared to nasal swabs taken at the same time and processed at a commercial laboratory, but this was discontinued once the accuracy of the saliva test was confirmed.

Two teams of staff

Two separate teams of technical staff, led by DNA Core manager Lutz Froenicke, work to run the tests on different days with a reserve team as backup.

Since Sept. 14, the program has run more than 68,000 tests with 142 positive results. In the week of Dec. 6-12, they ran almost 14,000 tests.

Michelmore credited a “massive effort across campus” with getting the testing program up and running, including Dr. Ralph Greene at the UC Davis Department of Pathology and Laboratory Medicine, Dr. Cindy Schorzmann, medical director of the Student Health and Counseling Services and Dr. Sheri Belafsky, UC Davis Medical Surveillance program and many, many others who have worked to stand up and run the testing kiosk, acquire machines and equipment, run tests and analyze and report out results.

While Michelmore has received many inquiries from other universities and businesses, he noted they are not currently planning to expand testing beyond UC Davis, Davis, other locations in Yolo County, and UC Merced due to finite capacity. However, he noted that none of the protocols and workflows are patented and could be replicated by others.

More information

GenomeWeb webinar on Deployment of High-Throughput SARS-CoV-2 Testing at UC Davis (free registration required)

UC Davis Campus Ready: COVID-19 Testing

UC Davis COVID-19 Dashboard (with testing data)

Healthy Davis Together

The post Behind the UC Davis Saliva Test for COVID-19 appeared first on Egghead.

Zika Virus Affects Eye Development Before But Not After Birth

Egghead - December 18, 2020 - 10:48am

By Lisa Howard

While the SARS-CoV-2 virus has dominated the news this past year, researchers continue to study the health effects of the Zika virus, which has been reported in 86 countries globally.

Zika infections are primarily spread through the bite of an Aedes mosquito. Infection during pregnancy can cause ocular anomalies in the developing fetus, but a new study reveals the virus does not appear to affect ocular growth postnatally. (iStock photo)

The Zika virus is primarily transmitted by the bite of an infected mosquito from the Aedes genus. However, it can also be passed through sexual contact, blood transfusions, organ transplants, and between mother and baby during pregnancy. The virus has been documented to cause a range of birth defects, including microcephaly and various neurological, musculoskeletal, and eye abnormalities.

A new study from Glenn Yiu, associate professor in the Department of Ophthalmology, and Koen Van Rompay, a core scientist at the California National Primate Research Center, found that Zika infection during the first trimester of pregnancy can impact fetal retinal development and cause congenital ocular anomalies. The virus does not appear to affect ocular growth postnatally, however.

”It has been known that congenital infection with the Zika virus can lead to eye defects, but it was unclear if the virus continues to replicate or affect eye development after birth,” Yiu said. “Our study in rhesus monkeys suggest that the virus primarily affects fetal development during pregnancy, but not the growth of eye after birth.”

In this collaboration between the UC Davis Eye Center and the California National Primate Research Center, two pregnant rhesus monkeys were infected with Zika virus late in the first trimester. The ocular development of the Zika-exposed infants was then studied for two years following their birth.

Ocular birth defects

The Zika-exposed infant monkeys did not display microcephaly or apparent neurological or behavioral deficits. The infants did exhibit several ocular birth defects, however. The defects included large colobomas, a missing gap in the eye due to abnormal development. The Zika-exposed infant monkeys also exhibited a loss of photoreceptors — the light-sensing cells of the retina — and retinal ganglion neuron, which helps transmit visual information to the brain.

Cross-section of an infant rhesus monkey eye showing an oval-shaped defect in the retina.

Despite congenital ocular malformations at birth, their eyes appeared to follow normal development during their first two years.

The findings suggest that ocular defects due to Zika infection primarily occur in utero and likely do not have a continued impact on ocular development after birth.

Rhesus macaques are natural hosts of the virus and share similar immune and ocular characteristics to humans, including blood–retinal barrier characteristics and the unique presence of a macula, making them superior animal models of the infection than typical laboratory animals like mice and rats. The findings were published in JCI Insight, an open-access peer-reviewed journal dedicated to biomedical research.

Other authors on the study are Sara M. Thomasy, M. Isabel Casanova, Alexander Rusakevich, Rebekah I. Keesler, Jennifer Watanabe, Jodie Usachenko, Anil Singapuri, Erin E. Ball, Eliza Bliss-Moreau, Wendi Guo, Helen Webster, Tulika Singh, Sallie Permar, Amir Ardeshir, and Lark L. Coffey.

The study received support from the Office of Research Infrastructure Program, National Institutes of Health, National Eye Institute, BrightFocus Foundation and the Macula Society. Histological studies of the eyes were conducted at the Comparative Ocular Pathology Laboratory of Wisconsin.

More information

Evolution of ocular defects in infant macaques following in utero Zika virus infection (JCI Insight)

Lisa Howard is a writer with the UC Davis Office of Research

The post Zika Virus Affects Eye Development Before But Not After Birth appeared first on Egghead.

Zika Virus Affects Eye Development Before But Not After Birth

Egghead Blog - December 18, 2020 - 10:48am

By Lisa Howard

While the SARS-CoV-2 virus has dominated the news this past year, researchers continue to study the health effects of the Zika virus, which has been reported in 86 countries globally.

Zika infections are primarily spread through the bite of an Aedes mosquito. Infection during pregnancy can cause ocular anomalies in the developing fetus, but a new study reveals the virus does not appear to affect ocular growth postnatally. (iStock photo)

The Zika virus is primarily transmitted by the bite of an infected mosquito from the Aedes genus. However, it can also be passed through sexual contact, blood transfusions, organ transplants, and between mother and baby during pregnancy. The virus has been documented to cause a range of birth defects, including microcephaly and various neurological, musculoskeletal, and eye abnormalities.

A new study from Glenn Yiu, associate professor in the Department of Ophthalmology, and Koen Van Rompay, a core scientist at the California National Primate Research Center, found that Zika infection during the first trimester of pregnancy can impact fetal retinal development and cause congenital ocular anomalies. The virus does not appear to affect ocular growth postnatally, however.

”It has been known that congenital infection with the Zika virus can lead to eye defects, but it was unclear if the virus continues to replicate or affect eye development after birth,” Yiu said. “Our study in rhesus monkeys suggest that the virus primarily affects fetal development during pregnancy, but not the growth of eye after birth.”

In this collaboration between the UC Davis Eye Center and the California National Primate Research Center, two pregnant rhesus monkeys were infected with Zika virus late in the first trimester. The ocular development of the Zika-exposed infants was then studied for two years following their birth.

Ocular birth defects

The Zika-exposed infant monkeys did not display microcephaly or apparent neurological or behavioral deficits. The infants did exhibit several ocular birth defects, however. The defects included large colobomas, a missing gap in the eye due to abnormal development. The Zika-exposed infant monkeys also exhibited a loss of photoreceptors — the light-sensing cells of the retina — and retinal ganglion neuron, which helps transmit visual information to the brain.

Cross-section of an infant rhesus monkey eye showing an oval-shaped defect in the retina.

Despite congenital ocular malformations at birth, their eyes appeared to follow normal development during their first two years.

The findings suggest that ocular defects due to Zika infection primarily occur in utero and likely do not have a continued impact on ocular development after birth.

Rhesus macaques are natural hosts of the virus and share similar immune and ocular characteristics to humans, including blood–retinal barrier characteristics and the unique presence of a macula, making them superior animal models of the infection than typical laboratory animals like mice and rats. The findings were published in JCI Insight, an open-access peer-reviewed journal dedicated to biomedical research.

Other authors on the study are Sara M. Thomasy, M. Isabel Casanova, Alexander Rusakevich, Rebekah I. Keesler, Jennifer Watanabe, Jodie Usachenko, Anil Singapuri, Erin E. Ball, Eliza Bliss-Moreau, Wendi Guo, Helen Webster, Tulika Singh, Sallie Permar, Amir Ardeshir, and Lark L. Coffey.

The study received support from the Office of Research Infrastructure Program, National Institutes of Health, National Eye Institute, BrightFocus Foundation and the Macula Society. Histological studies of the eyes were conducted at the Comparative Ocular Pathology Laboratory of Wisconsin.

More information

Evolution of ocular defects in infant macaques following in utero Zika virus infection (JCI Insight)

Lisa Howard is a writer with the UC Davis Office of Research

The post Zika Virus Affects Eye Development Before But Not After Birth appeared first on Egghead.

Artificial Intelligence Makes Big Leap in Predicting Protein Folding

Egghead Blog - December 8, 2020 - 8:01am

Scientists last week announced a big step forward in predicting the three-dimensional structure of proteins based only on their amino acid sequence. The results of the biennial CASP (Critical Assessment of Structure Prediction) challenge showed AlphaFold, a program developed by DeepMind, an offshoot of Google carrying out research in artificial intelligence, could predict protein structures with an average error of about the width of an atom.

A protein structure models obtained by DeepMind’s AlphaFold program. A model of the SARS-CoV-2 protein ORF8 is shown in green and the corresponding crystal structure in cyan. Of note is the extraordinary accuracy obtained in the modeling of side chains.

“We’re on the verge of a breakthrough in protein structure prediction,” said Krzysztof Fidelis, director of the Protein Structure Prediction Center at the UC Davis Genome Center. “It’s a bit of a revolution, definitely.”

Proteins are made up of chains of amino acids. But the properties of a protein depend very much on how those chains arrange themselves into a three-dimensional structure: to become tough scales or hair, to move as muscle, to accelerate chemical reactions as enzymes.

Almost 50 years ago, Nobel laureate Christian Anfinsen postulated that a protein’s structure could in theory be predicted from its amino acid sequence. But this has proved a difficult problem to crack, because the number of different ways in which any given protein could fold is very, very large.

There are other ways to figure out protein structure. Proteins can be imaged directly by X-ray crystallography or cryoelectron microscopy, and scientists can build models to see what works. All of these techniques have their advantages and weaknesses, and in fact are best used in combination. Being able to accurately predict protein structure directly from the primary, amino acid sequence would be a powerful tool. As less than one percent of sequenced proteins have had their structure solved, there is plenty to do.

The CASP challenge was founded in 1994 by Fidelis and John Moult, professor at the University of Maryland. The original organizing center for CASP was at the Lawrence Livermore National Laboratory and later moved to UC Davis with Fidelis in 2005.

Machine learning leads to big advance

CASP works by choosing newly sequenced proteins whose structures have not been published and sending them out to modeling and prediction centers. These teams submit their structure predictions to CASP, which compares them to experimental results as they become available. Every two years, they hold a conference to review the results.

Over the decades, the results have shown slow but steady improvement. In 2018 (CASP-13), DeepMind entered the challenge and results showed some movement. In 2020, CASP-14 showed the biggest gains yet, with DeepMind’s AlphaFold program well ahead of other centers.

AlphaFold is an example of machine learning, meaning that the program “learns” a task by studying examples. According to DeepMind, AlphaFold was trained on about 170,000 protein structures from the open source Protein Data Bank.

So far, AlphaFold can only successfully predict structures of single subunit proteins, said project scientist Andriy Krysthafovych, who works with Fidelis. Many functional proteins are made up of complexes of smaller units. Nonetheless, it is an exciting period, he said.

“The last ten to 15 years have seen a clear path forward, and now we can see even very minute details, not just the backbone but sidechains,” Fidelis said. “It’s the right moment to think of grand scale programs to put these insights together.”

More information

AlphaFold: a solution to a 50-year-old grand challenge in biology (DeepMind blog)

Protein Structure Prediction Center (UC Davis Genome Center)

 

 

 

 

The post Artificial Intelligence Makes Big Leap in Predicting Protein Folding appeared first on Egghead.

Artificial Intelligence Makes Big Leap in Predicting Protein Folding

Egghead - December 8, 2020 - 8:01am

Scientists last week announced a big step forward in predicting the three-dimensional structure of proteins based only on their amino acid sequence. The results of the biennial CASP (Critical Assessment of Structure Prediction) challenge showed AlphaFold, a program developed by DeepMind, an offshoot of Google carrying out research in artificial intelligence, could predict protein structures with an average error of about the width of an atom.

A protein structure models obtained by DeepMind’s AlphaFold program. A model of the SARS-CoV-2 protein ORF8 is shown in green and the corresponding crystal structure in cyan. Of note is the extraordinary accuracy obtained in the modeling of side chains.

“We’re on the verge of a breakthrough in protein structure prediction,” said Krzysztof Fidelis, director of the Protein Structure Prediction Center at the UC Davis Genome Center. “It’s a bit of a revolution, definitely.”

Proteins are made up of chains of amino acids. But the properties of a protein depend very much on how those chains arrange themselves into a three-dimensional structure: to become tough scales or hair, to move as muscle, to accelerate chemical reactions as enzymes.

Almost 50 years ago, Nobel laureate Christian Anfinsen postulated that a protein’s structure could in theory be predicted from its amino acid sequence. But this has proved a difficult problem to crack, because the number of different ways in which any given protein could fold is very, very large.

There are other ways to figure out protein structure. Proteins can be imaged directly by X-ray crystallography or cryoelectron microscopy, and scientists can build models to see what works. All of these techniques have their advantages and weaknesses, and in fact are best used in combination. Being able to accurately predict protein structure directly from the primary, amino acid sequence would be a powerful tool. As less than one percent of sequenced proteins have had their structure solved, there is plenty to do.

The CASP challenge was founded in 1994 by Fidelis and John Moult, professor at the University of Maryland. The original organizing center for CASP was at the Lawrence Livermore National Laboratory and later moved to UC Davis with Fidelis in 2005.

Machine learning leads to big advance

CASP works by choosing newly sequenced proteins whose structures have not been published and sending them out to modeling and prediction centers. These teams submit their structure predictions to CASP, which compares them to experimental results as they become available. Every two years, they hold a conference to review the results.

Over the decades, the results have shown slow but steady improvement. In 2018 (CASP-13), DeepMind entered the challenge and results showed some movement. In 2020, CASP-14 showed the biggest gains yet, with DeepMind’s AlphaFold program well ahead of other centers.

AlphaFold is an example of machine learning, meaning that the program “learns” a task by studying examples. According to DeepMind, AlphaFold was trained on about 170,000 protein structures from the open source Protein Data Bank.

So far, AlphaFold can only successfully predict structures of single subunit proteins, said project scientist Andriy Krysthafovych, who works with Fidelis. Many functional proteins are made up of complexes of smaller units. Nonetheless, it is an exciting period, he said.

“The last ten to 15 years have seen a clear path forward, and now we can see even very minute details, not just the backbone but sidechains,” Fidelis said. “It’s the right moment to think of grand scale programs to put these insights together.”

More information

AlphaFold: a solution to a 50-year-old grand challenge in biology (DeepMind blog)

Protein Structure Prediction Center (UC Davis Genome Center)

 

 

 

 

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Warning Labels Reduce Sugary Drink Consumption in University Setting, Researchers Found

Egghead Blog - December 7, 2020 - 9:54am

College Students Reported Cutting Back Consumption

By Karen Nikos-Rose

As municipalities have taxed sugar-sweetened beverages and schools and worksites have banned their sales, university researchers have found that simple warning labels on such beverages in a college cafeteria helped students reduce their reported consumption of drinks by 14.5 percent. The results signal that such labels could reduce sugar consumption in larger settings.

“Sugar-sweetened beverages are a major driver of chronic disease. Health warning labels may reduce the intake of sugar-sweetened beverages, but the effectiveness of such labels in real-world settings is only beginning to be established,” said Jennifer Falbe, assistant professor of Nutrition and Human Development at UC Davis, who is a senior author of the study and designed the warning label used.  “This experiment takes the evidence a step further by looking at young adult behavior in a setting that they frequent each day,” she said. The study was conducted by the University of Michigan School of Public Health and UC Davis. 

Taking a cue from tobacco control efforts, researchers placed warning labels on beverage dispensers at a University of Michigan cafeteria for one semester in 2019. In language based on previous proposed California legislation, the bright yellow labels with a large triangle and exclamation mark state:

“Warning: Drinking beverages with added sugar(s) contributes to type 2 diabetes, heart disease, and tooth decay.” Two other cafeterias on campus — located geographically distant from the cafeteria with the labels — served as control sites, and displayed no warning labels.

Nearly 1,000 college students were contacted by email before and after the warning labels were implemented to ask them to participate in surveys with no specific mention of sugar-sweetened beverages. Participants were given a $10 gift card after completing each survey.

In total, 840 students across all cafeterias were included in the study. At the intervention site, consumption of sugar-sweetened drinks that had the warning label declined by 18.5 percent compared to a decline of 4.7 percent at the control sites at which no label was used. Students exposed to the warning labels also reduced their consumption of 100-percent juice drinks by 21 percent even though, in the experiment, juices had not been labeled as sugar-sweetened beverages.

A tool to reduce sugar consumption

“The results of this study indicate that warning labels may be effective tools for reducing consumption of sugar-sweetened beverages, particularly beverages such as sweetened teas, pink lemonade and chocolate milk for which the sugar content is not immediately obvious or well known,” said Cindy Leung, assistant professor of Nutritional Sciences at the University of Michigan School of Public Health and lead author of the study.

“Sugar-sweetened beverages remain ubiquitous in retail and cafeteria settings. As we explore avenues to promote healthy food and beverage choices, warning labels are a potential tool to reduce their consumption that should be tested in other populations and other settings.” said Julia Wolfson, assistant professor of Health Management and Policy at the U-M School of Public Health and co-author of the study.

The study, “Warning Labels Reduce Sugar-Sweetened Beverage Intake among College Students,” was published last month in the Journal of Nutrition. Additional co-authors are Robert Hsu, Keith Soster and Steve Mangan, all of University of Michigan, Ann Arbor. Falbe teaches in the UC Davis Department of Human Ecology.

“These results provide evidence to inform future institutional strategies… and legislative efforts to use warning labels as a promising approach to SSB consumption,” the researchers concluded.

For instance, nine jurisdictions, including California, have introduced, at various times, sugar-sweetened beverage warning label legislation. “These laws could ensure that consumers have the necessary information to make informed choices,” Falbe said.

The research was funded by a grant from Poverty Solutions at the University of Michigan, the McNerney Award from the Department of Health Management and Policy at the University of Michigan School of Public Health, and the National Institutes of Health.

More information

Warning Labels Reduce Sugar-Sweetened Beverage Intake among College Students (Journal of Nutrition)

Sugar-sweetened Beverages are Harmful and May Be Addictive (UC Davis News)

Some Calories More Harmful than Others (UC Davis News)

Improving Water Quality in Rural Immigrant Communities (UC Davis Center for Poverty and Inequality Research)

 

The post Warning Labels Reduce Sugary Drink Consumption in University Setting, Researchers Found appeared first on Egghead.

Warning Labels Reduce Sugary Drink Consumption in University Setting, Researchers Found

Egghead - December 7, 2020 - 9:54am

College Students Reported Cutting Back Consumption

By Karen Nikos-Rose

As municipalities have taxed sugar-sweetened beverages and schools and worksites have banned their sales, university researchers have found that simple warning labels on such beverages in a college cafeteria helped students reduce their reported consumption of drinks by 14.5 percent. The results signal that such labels could reduce sugar consumption in larger settings.

“Sugar-sweetened beverages are a major driver of chronic disease. Health warning labels may reduce the intake of sugar-sweetened beverages, but the effectiveness of such labels in real-world settings is only beginning to be established,” said Jennifer Falbe, assistant professor of Nutrition and Human Development at UC Davis, who is a senior author of the study and designed the warning label used.  “This experiment takes the evidence a step further by looking at young adult behavior in a setting that they frequent each day,” she said. The study was conducted by the University of Michigan School of Public Health and UC Davis. 

Taking a cue from tobacco control efforts, researchers placed warning labels on beverage dispensers at a University of Michigan cafeteria for one semester in 2019. In language based on previous proposed California legislation, the bright yellow labels with a large triangle and exclamation mark state:

“Warning: Drinking beverages with added sugar(s) contributes to type 2 diabetes, heart disease, and tooth decay.” Two other cafeterias on campus — located geographically distant from the cafeteria with the labels — served as control sites, and displayed no warning labels.

Nearly 1,000 college students were contacted by email before and after the warning labels were implemented to ask them to participate in surveys with no specific mention of sugar-sweetened beverages. Participants were given a $10 gift card after completing each survey.

In total, 840 students across all cafeterias were included in the study. At the intervention site, consumption of sugar-sweetened drinks that had the warning label declined by 18.5 percent compared to a decline of 4.7 percent at the control sites at which no label was used. Students exposed to the warning labels also reduced their consumption of 100-percent juice drinks by 21 percent even though, in the experiment, juices had not been labeled as sugar-sweetened beverages.

A tool to reduce sugar consumption

“The results of this study indicate that warning labels may be effective tools for reducing consumption of sugar-sweetened beverages, particularly beverages such as sweetened teas, pink lemonade and chocolate milk for which the sugar content is not immediately obvious or well known,” said Cindy Leung, assistant professor of Nutritional Sciences at the University of Michigan School of Public Health and lead author of the study.

“Sugar-sweetened beverages remain ubiquitous in retail and cafeteria settings. As we explore avenues to promote healthy food and beverage choices, warning labels are a potential tool to reduce their consumption that should be tested in other populations and other settings.” said Julia Wolfson, assistant professor of Health Management and Policy at the U-M School of Public Health and co-author of the study.

The study, “Warning Labels Reduce Sugar-Sweetened Beverage Intake among College Students,” was published last month in the Journal of Nutrition. Additional co-authors are Robert Hsu, Keith Soster and Steve Mangan, all of University of Michigan, Ann Arbor. Falbe teaches in the UC Davis Department of Human Ecology.

“These results provide evidence to inform future institutional strategies… and legislative efforts to use warning labels as a promising approach to SSB consumption,” the researchers concluded.

For instance, nine jurisdictions, including California, have introduced, at various times, sugar-sweetened beverage warning label legislation. “These laws could ensure that consumers have the necessary information to make informed choices,” Falbe said.

The research was funded by a grant from Poverty Solutions at the University of Michigan, the McNerney Award from the Department of Health Management and Policy at the University of Michigan School of Public Health, and the National Institutes of Health.

More information

Warning Labels Reduce Sugar-Sweetened Beverage Intake among College Students (Journal of Nutrition)

Sugar-sweetened Beverages are Harmful and May Be Addictive (UC Davis News)

Some Calories More Harmful than Others (UC Davis News)

Improving Water Quality in Rural Immigrant Communities (UC Davis Center for Poverty and Inequality Research)

 

The post Warning Labels Reduce Sugary Drink Consumption in University Setting, Researchers Found appeared first on Egghead.

Gotta Catch ‘Em All: Pokémon Paper Pokes Predatory Journals

Egghead Blog - December 4, 2020 - 3:29pm

By Kathy Keatley Garvey

In the era of #fakenews, add #predatoryjournals.

What are “predatory journals?” Entomologist Matan Shelomi defines them as those that “appear legitimate, but practice no peer review, no editing, not even a reality check.”

Predatory journals are especially dangerous during the COVID-19 pandemic, says Shelomi, a Harvard graduate and UC Davis-trained entomologist who is now an assistant professor of entomology at the National Taiwan University, Taipei, Taiwan. And what he recently did showed why.

Here’s what occurred.

Being an avid Pokémon scholar and fan — and a foe of fake news — Shelomi wrote a fictitious research paper about how eating a bat-like Pokémon sparked the spread of COVID-19. A journal editor accepted it for publication (without peer-review) and it appeared online, for a time, as open access.

Contrary to (briefly) published research, you cannot catch a virus by eating this animal.

As Shelomi recounted in his Nov. 1 opinion piece, “Using Pokémon to Detect Scientific Misinformation,” in The Scientist: “On March 18, 2020, the American Journal of Biomedical Science & Research published my paper claiming that eating a bat-like Pokémon sparked the spread of COVID-19. This paper, ‘Cyllage City COVID-19 outbreak linked to Zubat consumption,’ blames a fictional creature for an outbreak in a fictional city, cites fictional references (including one from author Bruce Wayne in Gotham Forensics Quarterly on using bats to fight crime), and is cowritten by fictional authors such as Pokémon’s Nurse Joy and House, MD. Nonetheless, four days after submission, editor Catherine Nichols was ‘cheerful to inform’ me via email that it had “received positive review comments” and was accepted for publication.”

The fake research article no longer appears online; staff removed it for nonpayment of fees.

Shelomi offers this advice: “How, then, to catch a predator, besides checking Beall’s List? First, assume all journals or conferences that email you unsolicited submission invitations are predatory, especially if they are outside your field, cover overly broad subjects, promise rapid review, or flatter you with compliments such as ’eminent researcher.’ Any journal with multiple email domains is predatory, as are absolutely all journals that list the worthless “Index Copernicus” number on their website.”

“There are no shortcuts in science,” he pointed out in The Scientist. “If you want to be taken seriously as an academic, do not give predatory journals your business, especially as institutes wise up to the problem and stop accepting such articles on CVs or applications. Although, if any institute wants to grant me an honorary degree in Pokémon Studies for my eminence in the field, I would cheerfully accept.”

Reactions

Did Shelomi get much reaction from his Pokémon project?

“I haven’t had much reaction, honestly, though what little I had has all been very favorable,” he told us. “I’m disappointed this doesn’t get much traction among the Pokémon community, at least. I wrote the tell-all for The Scientist as a way to get more attention to the original articles. The predatory journals, of course, do not know or care about any negative press.”

Shelomi noted that a legitimate, peer-reviewed journal had accepted (and eventually retracted) a paper saying COVID-19 is caused by earth’s magnetic field, and that jade amulets can prevent it.

“Why do I bother sending fake papers to fraudulent journals when real journals are publishing such nonsense? And we should never forget that the modern anti-vaxxer movement started from a paper in The Lancet, then the top medical journal on earth.”

“I suspect most scientists are unaware of what predatory journals are, especially in the developing world where quantity matters over quality regarding publish or perish,” Shelomi said. “I suspect most researchers worldwide go from undergrad to tenure without ever learning about the difference between garbage journal and fake ones. If my Pokémon papers can be used to educate, then they are doing their jobs.”

In an ironic twist, some pseudoscience and conspiracy theory blogs are now using Shelomi’s paper to argue that science is not to be trusted, despite the fact that he explicitly calls out anti-vaxxers and other anti-science people.

“I will be the first to say that not everything written in IMRaD format (Introduction, Methods, Results and Discussion) is trustworthy, but it’s still going to be far more reliable than a 140-character tweet. People, including scientists, need to learn how to identify good sources and how to identify garbage, and 2020 being what it is I am not optimistic that we can teach them. I will certainly do my part in trying!”

While at UC Davis, Shelomi co-authored “A Phylogeny and Evolutionary History of the Pokémon,” a paper published in the Annals of Improbable Research (August 2012), a tongue-in-cheek journal meant to make people laugh and then think. (See feature story). Basically, it was “a very real phylogeny of the very fake Pokémon creatures,” as he described it.

And, as Matan Shelomi acknowledged in The Scientist, he writes “fake articles under the pseudonym Mattan Schlomi.”

More information

Using Pokémon to Detect Scientific Misinformation (The Scientist)

Taking at Poke at Pokemon (UCANR Entomology news blog)

Kathy Keatley Garvey writes for the UC Davis Department of Entomology and Nematology and UC Division of Ag and Natural Resources. For more news, follow her Bug Squad blog. 

The post Gotta Catch ‘Em All: Pokémon Paper Pokes Predatory Journals appeared first on Egghead.

Gotta Catch ‘Em All: Pokémon Paper Pokes Predatory Journals

Egghead - December 4, 2020 - 3:29pm

By Kathy Keatley Garvey

In the era of #fakenews, add #predatoryjournals.

What are “predatory journals?” Entomologist Matan Shelomi defines them as those that “appear legitimate, but practice no peer review, no editing, not even a reality check.”

Predatory journals are especially dangerous during the COVID-19 pandemic, says Shelomi, a Harvard graduate and UC Davis-trained entomologist who is now an assistant professor of entomology at the National Taiwan University, Taipei, Taiwan. And what he recently did showed why.

Here’s what occurred.

Being an avid Pokémon scholar and fan — and a foe of fake news — Shelomi wrote a fictitious research paper about how eating a bat-like Pokémon sparked the spread of COVID-19. A journal editor accepted it for publication (without peer-review) and it appeared online, for a time, as open access.

Contrary to (briefly) published research, you cannot catch a virus by eating this animal.

As Shelomi recounted in his Nov. 1 opinion piece, “Using Pokémon to Detect Scientific Misinformation,” in The Scientist: “On March 18, 2020, the American Journal of Biomedical Science & Research published my paper claiming that eating a bat-like Pokémon sparked the spread of COVID-19. This paper, ‘Cyllage City COVID-19 outbreak linked to Zubat consumption,’ blames a fictional creature for an outbreak in a fictional city, cites fictional references (including one from author Bruce Wayne in Gotham Forensics Quarterly on using bats to fight crime), and is cowritten by fictional authors such as Pokémon’s Nurse Joy and House, MD. Nonetheless, four days after submission, editor Catherine Nichols was ‘cheerful to inform’ me via email that it had “received positive review comments” and was accepted for publication.”

The fake research article no longer appears online; staff removed it for nonpayment of fees.

Shelomi offers this advice: “How, then, to catch a predator, besides checking Beall’s List? First, assume all journals or conferences that email you unsolicited submission invitations are predatory, especially if they are outside your field, cover overly broad subjects, promise rapid review, or flatter you with compliments such as ’eminent researcher.’ Any journal with multiple email domains is predatory, as are absolutely all journals that list the worthless “Index Copernicus” number on their website.”

“There are no shortcuts in science,” he pointed out in The Scientist. “If you want to be taken seriously as an academic, do not give predatory journals your business, especially as institutes wise up to the problem and stop accepting such articles on CVs or applications. Although, if any institute wants to grant me an honorary degree in Pokémon Studies for my eminence in the field, I would cheerfully accept.”

Reactions

Did Shelomi get much reaction from his Pokémon project?

“I haven’t had much reaction, honestly, though what little I had has all been very favorable,” he told us. “I’m disappointed this doesn’t get much traction among the Pokémon community, at least. I wrote the tell-all for The Scientist as a way to get more attention to the original articles. The predatory journals, of course, do not know or care about any negative press.”

Shelomi noted that a legitimate, peer-reviewed journal had accepted (and eventually retracted) a paper saying COVID-19 is caused by earth’s magnetic field, and that jade amulets can prevent it.

“Why do I bother sending fake papers to fraudulent journals when real journals are publishing such nonsense? And we should never forget that the modern anti-vaxxer movement started from a paper in The Lancet, then the top medical journal on earth.”

“I suspect most scientists are unaware of what predatory journals are, especially in the developing world where quantity matters over quality regarding publish or perish,” Shelomi said. “I suspect most researchers worldwide go from undergrad to tenure without ever learning about the difference between garbage journal and fake ones. If my Pokémon papers can be used to educate, then they are doing their jobs.”

In an ironic twist, some pseudoscience and conspiracy theory blogs are now using Shelomi’s paper to argue that science is not to be trusted, despite the fact that he explicitly calls out anti-vaxxers and other anti-science people.

“I will be the first to say that not everything written in IMRaD format (Introduction, Methods, Results and Discussion) is trustworthy, but it’s still going to be far more reliable than a 140-character tweet. People, including scientists, need to learn how to identify good sources and how to identify garbage, and 2020 being what it is I am not optimistic that we can teach them. I will certainly do my part in trying!”

While at UC Davis, Shelomi co-authored “A Phylogeny and Evolutionary History of the Pokémon,” a paper published in the Annals of Improbable Research (August 2012), a tongue-in-cheek journal meant to make people laugh and then think. (See feature story). Basically, it was “a very real phylogeny of the very fake Pokémon creatures,” as he described it.

And, as Matan Shelomi acknowledged in The Scientist, he writes “fake articles under the pseudonym Mattan Schlomi.”

More information

Using Pokémon to Detect Scientific Misinformation (The Scientist)

Taking at Poke at Pokemon (UCANR Entomology news blog)

Kathy Keatley Garvey writes for the UC Davis Department of Entomology and Nematology and UC Division of Ag and Natural Resources. For more news, follow her Bug Squad blog. 

The post Gotta Catch ‘Em All: Pokémon Paper Pokes Predatory Journals appeared first on Egghead.

Eleven UC Davis Researchers Are Highly Cited

Egghead Blog - November 20, 2020 - 8:58am

Eleven UC Davis researchers have been named in the annual Highly Cited Researchers 2020 list released by the Web of Science Group, which compiles statistics on scientific publishing. The list identifies scientists and social scientists who have published multiple papers ranking in the top 1 percent by citations in a particular field and year, over a 10-year period.

Citation counts represent how often a particular paper has been cited in other scientific publications.

UC Davis researchers included in this year’s list are:

  • Andreas Bäumler, Microbiology and Immunology, School of Medicine
  • Eduardo Blumwald, Plant Sciences, College of Agricultural and Environmental Sciences
  • Alan Crozier, Nutrition, College of Agricultural and Environmental Sciences
  • Jorge Dubcovsky, Plant Sciences, College of Agricultural and Environmental Sciences
  • Oliver Fiehn, Genome Center
  • Carlito Lebrilla, Chemistry, College of Letters and Science
  • David A. Mills, Food Science and Technology, College of Agricultural and Environmental Sciences
  • Thomas W. Scott, Entolomology and Nematology, College of Agricultural and Environmental Sciences
  • Andrew Sih, Environmental Science and Policy, College of Agricultural and Environmental Sciences
  • James S. Trimmer, Physiology and Membrane Biology, School of Medicine
  • Heike Wulff, Pharmacology, School of Medicine

The Web of Science Group is a Clarivate Analytics company, formerly a division of Thomson Reuters.

More information

Highly Cited Researchers 2020

Clarivate identifies global scientific pioneers on annual Highly Cited Researchers list

 

 

 

The post Eleven UC Davis Researchers Are Highly Cited appeared first on Egghead.

Eleven UC Davis Researchers Are Highly Cited

Egghead - November 20, 2020 - 8:58am

Eleven UC Davis researchers have been named in the annual Highly Cited Researchers 2020 list released by the Web of Science Group, which compiles statistics on scientific publishing. The list identifies scientists and social scientists who have published multiple papers ranking in the top 1 percent by citations in a particular field and year, over a 10-year period.

Citation counts represent how often a particular paper has been cited in other scientific publications.

UC Davis researchers included in this year’s list are:

  • Andreas Bäumler, Microbiology and Immunology, School of Medicine
  • Eduardo Blumwald, Plant Sciences, College of Agricultural and Environmental Sciences
  • Alan Crozier, Nutrition, College of Agricultural and Environmental Sciences
  • Jorge Dubcovsky, Plant Sciences, College of Agricultural and Environmental Sciences
  • Oliver Fiehn, Genome Center
  • Carlito Lebrilla, Chemistry, College of Letters and Science
  • David A. Mills, Food Science and Technology, College of Agricultural and Environmental Sciences
  • Thomas W. Scott, Entolomology and Nematology, College of Agricultural and Environmental Sciences
  • Andrew Sih, Environmental Science and Policy, College of Agricultural and Environmental Sciences
  • James S. Trimmer, Physiology and Membrane Biology, School of Medicine
  • Heike Wulff, Pharmacology, School of Medicine

The Web of Science Group is a Clarivate Analytics company, formerly a division of Thomson Reuters.

More information

Highly Cited Researchers 2020

Clarivate identifies global scientific pioneers on annual Highly Cited Researchers list

 

 

 

The post Eleven UC Davis Researchers Are Highly Cited appeared first on Egghead.

Black Carbon Soot Not as Important as CO2 in Climate Impacts

Egghead Blog - November 17, 2020 - 10:20am

Burning carbon-based fuels releases carbon dioxide and other heat-trapping greenhouse gases into the atmosphere. It also produces tiny particles of sooty black carbon within the broader category often referred to as PM2.5 (for particulate matter below a certain size). These black carbon particles cause ground-level air pollution and also contribute to warming the atmosphere.

Greenhouse gases like carbon dioxide will stay in the atmosphere for decades, but black carbon particles only persist for days to weeks. So as California cuts back on use of carbon fuels, levels of black carbon should fall quite quickly, possibly yielding an early effect on climate. But just how big an effect could this be?

Temperature changes in the atmosphere over California from reducing airborne black carbon particles. The viewer is facing west, with southern California to the left of the figure. Credit Kumar et al, 2020.

The state of California has a stated goal of reducing greenhouse gas emissions to 80 percent of 1990 levels. Researchers at UC Davis led by Michael Kleeman, Department of Civil and Environmental Engineering, used models to study the effect of this policy on long-lived and short-lived carbon pollutants. The models include weather and air quality effects of carbon emissions. The work was published recently in the Journal of Geophysical Research: Atmospheres.

They found that adopting low-carbon fuels in California reduces black carbon particles at ground level leading to improved air quality. But the changes to the concentrations of black carbon particles above the surface were minor, and so the particles did not have a significant impact on climate. The corresponding reduction in greenhouse gases has a much larger climate effect, lowering the surface temperature in California by 0.76 Kelvin in the year 2054.

The authors note that the changes caused by long-lived greenhouse gases are orders of magnitude larger than those caused by reducing short-lived black carbon particles.

“Adoption of low‐carbon energy will mostly affect climate in California through changes to long-lived as opposed to short-lived carbon pollutants,” they wrote.

Other authors on the paper are: Anikender Kumar, Christina Zapata, Chris Yang, Joan Ogden, Hsiang‐He Lee and Shu‐Hua Chen, all at UC Davis and Sonia Yeh, Chalmers University, Gothenburg, Sweden. The work was funded by the U.S. Environmental Protection Agency.

More information

Effects of Low‐Carbon Energy Adoption on Airborne Particulate Matter Concentrations With Feedbacks to Future Climate Over California (JGR Atmospheres)

Comparing Impacts of CO2 and Particle Emission Reductions (Eos Editor’s Highlights)

 

 

 

The post Black Carbon Soot Not as Important as CO2 in Climate Impacts appeared first on Egghead.

Black Carbon Soot Not as Important as CO2 in Climate Impacts

Egghead - November 17, 2020 - 10:20am

Burning carbon-based fuels releases carbon dioxide and other heat-trapping greenhouse gases into the atmosphere. It also produces tiny particles of sooty black carbon within the broader category often referred to as PM2.5 (for particulate matter below a certain size). These black carbon particles cause ground-level air pollution and also contribute to warming the atmosphere.

Greenhouse gases like carbon dioxide will stay in the atmosphere for decades, but black carbon particles only persist for days to weeks. So as California cuts back on use of carbon fuels, levels of black carbon should fall quite quickly, possibly yielding an early effect on climate. But just how big an effect could this be?

Temperature changes in the atmosphere over California from reducing airborne black carbon particles. The viewer is facing west, with southern California to the left of the figure. Credit Kumar et al, 2020.

The state of California has a stated goal of reducing greenhouse gas emissions to 80 percent of 1990 levels. Researchers at UC Davis led by Michael Kleeman, Department of Civil and Environmental Engineering, used models to study the effect of this policy on long-lived and short-lived carbon pollutants. The models include weather and air quality effects of carbon emissions. The work was published recently in the Journal of Geophysical Research: Atmospheres.

They found that adopting low-carbon fuels in California reduces black carbon particles at ground level leading to improved air quality. But the changes to the concentrations of black carbon particles above the surface were minor, and so the particles did not have a significant impact on climate. The corresponding reduction in greenhouse gases has a much larger climate effect, lowering the surface temperature in California by 0.76 Kelvin in the year 2054.

The authors note that the changes caused by long-lived greenhouse gases are orders of magnitude larger than those caused by reducing short-lived black carbon particles.

“Adoption of low‐carbon energy will mostly affect climate in California through changes to long-lived as opposed to short-lived carbon pollutants,” they wrote.

Other authors on the paper are: Anikender Kumar, Christina Zapata, Chris Yang, Joan Ogden, Hsiang‐He Lee and Shu‐Hua Chen, all at UC Davis and Sonia Yeh, Chalmers University, Gothenburg, Sweden. The work was funded by the U.S. Environmental Protection Agency.

More information

Effects of Low‐Carbon Energy Adoption on Airborne Particulate Matter Concentrations With Feedbacks to Future Climate Over California (JGR Atmospheres)

Comparing Impacts of CO2 and Particle Emission Reductions (Eos Editor’s Highlights)

 

 

 

The post Black Carbon Soot Not as Important as CO2 in Climate Impacts appeared first on Egghead.

Deep Past is Key to Predicting Future Climate, Scientists Say

Egghead Blog - November 5, 2020 - 1:21pm

By Daniel Stolte

An international team of climate scientists, including Professor Isabel Montañez at the UC Davis Department of Earth and Planetary Sciences, suggests that researchers using numerical models to predict future climate change should include simulations of past climates in their evaluation and statement of their model performance. The report is published this week in the journal Science.

“We urge the climate model developer community to pay attention to the past and actively involve it in predicting the future,” said Jessica Tierney, the paper’s lead author and an associate professor in the University of Arizona’s Department of Geosciences. “If your model can simulate past climates accurately, it likely will do a much better job at getting future scenarios right.”

As more and better information becomes available, Earth’s past climates are increasingly relevant for improving our understanding of how key elements of the climate system are affected by greenhouse gas levels, according to the study’s authors. Unlike historic climate records, which typically only go back a century or two – a mere blink of an eye in the planet’s climate history – paleoclimates cover a vastly broader range of climatic conditions millions of years before humans existed. These periods in Earth’s past span a large range of temperatures, precipitation patterns and ice sheet distribution.

Past carbon dioxide concentrations (left) compared to possible future emissions scenarios (right). Jessica Tierney/University of Arizona

“Past climates should be used to evaluate and fine-tune climate models,” Tierney said. “Looking to the past to inform the future could help narrow uncertainties surrounding projections of changes in temperature, ice sheets, and the water cycle.”

“The geologic record of past climate change, in particular periods of global warming, makes a unique and necessary contribution to climate change discussions as it is our only repository for insight into how the Earth system will function in the evolving and high CO2 environment that we anticipate for the not too distant future,” Montañez said.

Evaluating models against historic and prehistoric climates

Typically, climate scientists evaluate their models with data from historical weather records, such as satellite measurements, sea surface temperatures, wind speeds, cloud cover and other parameters. The model’s algorithms are then adjusted until their predictions mesh with the observed climate records. Thus, if a computer simulation produces a historically accurate climate based on the observations made during that time, it is considered fit to predict future climate with reasonable accuracy.

“We find that many models perform very well with historic climates, but not so well with climates from the Earth’s geological past,” Tierney said.

One reason for the discrepancies are differences in how the models compute the effects of clouds, which is one of the great challenges in climate modeling, Tierney said. Such differences cause different models to diverge from each other in terms of what climate scientists refer to as climate sensitivity: a measure of how strongly the Earth’s climate responds to a doubling of greenhouse gas emissions.

Several of the latest generation models that are being used for the next report by the Intergovernmental Panel on Climate Change, or IPCC, have a higher climate sensitivity than previous iterations, Tierney said.

“This means that if you double carbon dioxide emissions, they produce more global warming than their previous counterparts, so the question is: How much confidence do we have in these very sensitive new models?”

In between IPCC reports, which typically are released every eight years, climate models are being updated based on the latest research data.

“Models become more complex, and in theory, they get better, but what does that mean?” Tierney said. “You want to know what happens in the future, so you want to be able to trust the model with regard to what happens in response to higher levels of carbon dioxide.”

While there is no debate in the climate science community about human fossil fuel consumption pushing the Earth toward a warmer state for which there is no historical precedent, different models generate varying predictions. Some forecast an increase as large as 6 degrees Celsius by the end of the century.

High CO2 and warm climates

Tierney said while Earth’s atmosphere has experienced carbon dioxide concentrations much higher than today’s level of about 400 parts per million, there is no time in the geological record that matches the speed at which humans are contributing to greenhouse gas emissions.

In the paper, the authors applied climate models to several known past climate extremes from the geological record. The most recent warm climate offering a glimpse into the future occurred about 50 million years ago during the Eocene epoch, Tierney said. Global carbon dioxide was at 1,000 parts per million at that time and there were no large ice sheets.

“If we don’t cut back emissions, we are headed for Eocene-like CO2 levels by 2100,” Tierney said.

The authors discuss climate changes all the way to the Cretaceous period, about 90 million years ago, when dinosaurs still ruled the Earth. That period shows that the climate can get even warmer, a scenario that Tierney described as “even scarier,” with carbon dioxide levels up to 2,000 parts per million and the oceans as warm as a bathtub.

“The key is CO2,” Tierney said. “Whenever we see evidence of warm climate in the geologic record, CO2 is high as well.”

Some models are much better than others at producing the climates seen in the geologic record, which underscores the need to test climate models against paleoclimates, the authors said. In particular, past warm climates such as the Eocene highlight the role that clouds play in contributing to warmer temperatures under increased carbon dioxide levels.

“We urge the climate community to test models on paleoclimates early on, while the models are being developed, rather than afterwards, which tends to be the current practice,” Tierney said. “Seemingly small things like clouds affect the Earth’s energy balance in major ways and can affect the temperatures your model produces for the year 2100.”

The paper is the outcome of an Aspen Global Change Institute workshop organized by Tierney, Montañez and Chris Poulsen of the University of Michigan, Ann Arbor. The workshop was funded by NASA and the Heising-Simons Foundation.

More information

Past climates inform our future (Science)

Daniel Stolte is a science writer at the University of Arizona. Adapted from a University of Arizona news release

 

The post Deep Past is Key to Predicting Future Climate, Scientists Say appeared first on Egghead.

Deep Past is Key to Predicting Future Climate, Scientists Say

Egghead - November 5, 2020 - 1:21pm

By Daniel Stolte

An international team of climate scientists, including Professor Isabel Montañez at the UC Davis Department of Earth and Planetary Sciences, suggests that researchers using numerical models to predict future climate change should include simulations of past climates in their evaluation and statement of their model performance. The report is published this week in the journal Science.

“We urge the climate model developer community to pay attention to the past and actively involve it in predicting the future,” said Jessica Tierney, the paper’s lead author and an associate professor in the University of Arizona’s Department of Geosciences. “If your model can simulate past climates accurately, it likely will do a much better job at getting future scenarios right.”

As more and better information becomes available, Earth’s past climates are increasingly relevant for improving our understanding of how key elements of the climate system are affected by greenhouse gas levels, according to the study’s authors. Unlike historic climate records, which typically only go back a century or two – a mere blink of an eye in the planet’s climate history – paleoclimates cover a vastly broader range of climatic conditions millions of years before humans existed. These periods in Earth’s past span a large range of temperatures, precipitation patterns and ice sheet distribution.

Past carbon dioxide concentrations (left) compared to possible future emissions scenarios (right). Jessica Tierney/University of Arizona

“Past climates should be used to evaluate and fine-tune climate models,” Tierney said. “Looking to the past to inform the future could help narrow uncertainties surrounding projections of changes in temperature, ice sheets, and the water cycle.”

“The geologic record of past climate change, in particular periods of global warming, makes a unique and necessary contribution to climate change discussions as it is our only repository for insight into how the Earth system will function in the evolving and high CO2 environment that we anticipate for the not too distant future,” Montañez said.

Evaluating models against historic and prehistoric climates

Typically, climate scientists evaluate their models with data from historical weather records, such as satellite measurements, sea surface temperatures, wind speeds, cloud cover and other parameters. The model’s algorithms are then adjusted until their predictions mesh with the observed climate records. Thus, if a computer simulation produces a historically accurate climate based on the observations made during that time, it is considered fit to predict future climate with reasonable accuracy.

“We find that many models perform very well with historic climates, but not so well with climates from the Earth’s geological past,” Tierney said.

One reason for the discrepancies are differences in how the models compute the effects of clouds, which is one of the great challenges in climate modeling, Tierney said. Such differences cause different models to diverge from each other in terms of what climate scientists refer to as climate sensitivity: a measure of how strongly the Earth’s climate responds to a doubling of greenhouse gas emissions.

Several of the latest generation models that are being used for the next report by the Intergovernmental Panel on Climate Change, or IPCC, have a higher climate sensitivity than previous iterations, Tierney said.

“This means that if you double carbon dioxide emissions, they produce more global warming than their previous counterparts, so the question is: How much confidence do we have in these very sensitive new models?”

In between IPCC reports, which typically are released every eight years, climate models are being updated based on the latest research data.

“Models become more complex, and in theory, they get better, but what does that mean?” Tierney said. “You want to know what happens in the future, so you want to be able to trust the model with regard to what happens in response to higher levels of carbon dioxide.”

While there is no debate in the climate science community about human fossil fuel consumption pushing the Earth toward a warmer state for which there is no historical precedent, different models generate varying predictions. Some forecast an increase as large as 6 degrees Celsius by the end of the century.

High CO2 and warm climates

Tierney said while Earth’s atmosphere has experienced carbon dioxide concentrations much higher than today’s level of about 400 parts per million, there is no time in the geological record that matches the speed at which humans are contributing to greenhouse gas emissions.

In the paper, the authors applied climate models to several known past climate extremes from the geological record. The most recent warm climate offering a glimpse into the future occurred about 50 million years ago during the Eocene epoch, Tierney said. Global carbon dioxide was at 1,000 parts per million at that time and there were no large ice sheets.

“If we don’t cut back emissions, we are headed for Eocene-like CO2 levels by 2100,” Tierney said.

The authors discuss climate changes all the way to the Cretaceous period, about 90 million years ago, when dinosaurs still ruled the Earth. That period shows that the climate can get even warmer, a scenario that Tierney described as “even scarier,” with carbon dioxide levels up to 2,000 parts per million and the oceans as warm as a bathtub.

“The key is CO2,” Tierney said. “Whenever we see evidence of warm climate in the geologic record, CO2 is high as well.”

Some models are much better than others at producing the climates seen in the geologic record, which underscores the need to test climate models against paleoclimates, the authors said. In particular, past warm climates such as the Eocene highlight the role that clouds play in contributing to warmer temperatures under increased carbon dioxide levels.

“We urge the climate community to test models on paleoclimates early on, while the models are being developed, rather than afterwards, which tends to be the current practice,” Tierney said. “Seemingly small things like clouds affect the Earth’s energy balance in major ways and can affect the temperatures your model produces for the year 2100.”

The paper is the outcome of an Aspen Global Change Institute workshop organized by Tierney, Montañez and Chris Poulsen of the University of Michigan, Ann Arbor. The workshop was funded by NASA and the Heising-Simons Foundation.

More information

Past climates inform our future (Science)

Daniel Stolte is a science writer at the University of Arizona. Adapted from a University of Arizona news release

 

The post Deep Past is Key to Predicting Future Climate, Scientists Say appeared first on Egghead.

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