thescientist--2020-12-18--Top Technical Advances of 2020

Top Technical Advances of 2020

Much of the world became aware of the disease now known as COVID-19 in January , and impressively , a diagnostic PCR test became available the same month .
We ’ ve since seen an explosion in potential variations on that assay , including saliva tests , which bypass the need for scarce swabs , and a slew of techniques that could be considerably faster and cheaper than PCR , including breath tests , at-home antigen tests , a diagnostic that combines loop-mediated isothermal amplification ( LAMP ) and CRISPR , and even an AI model that detects telltale signs @ @ @ @ @ @ @ diagnostics gave us hard numbers on SARS-CoV-2 ’ s devastating sweep , the rapid development of vaccines against it allowed us to imagine the pandemic coming under control .
mRNA vaccines from Pfizer and Moderna were among the early leaders of the vaccine race , training the spotlight on a newer technique that had been attempted for other diseases but had not yet made it to the market before 2020 .
The principle is to deliver a stretch of viral mRNA to recipients ’ cells , which go on to manufacture viral proteins @ @ @ @ @ @ @ response .
The year also saw researchers experimenting with other innovative ways of producing vaccines .
In one example—which , unlike with mRNA vaccines , would avoid the need for cold temperatures during transport and storage—researchers showed that a flu vaccine delivered orally as a thin film induced an immune response in mice .
The pandemic ’ s effects on science were far-reaching , and necessitated adaptation as many researchers were shut out of their labs in a bid to prevent infection .
Among the creative means scientists devised to continue their work @ @ @ @ @ @ @ a protocol for profiling chromosome components that Steven Henikoff of the Fred Hutchinson Cancer Research Center devised in his laundry room .
Induced pluripotent stem cells ( iPSCs ) have proved a boon to research , but most labs grow the cells in expensive commercial media that require frequent tending to replenish the stock .
In a paper at the start of this year , researchers described a DIY recipe for a medium with ingredients that cost a fraction of what commercial alternatives do , and that only needs to be changed every @ @ @ @ @ @ @ weekends off .
Collecting data on humans ’ brain activity typically requires researchers to put their subjects into expensive MRI or PET scanners , or to affix wires to their skulls for a traditional EEG setup .
But advances in brain-computer interface ( BCI ) technology—much of it made with an eye toward the consumer market for devices that could be used for applications such as gaming—hold the potential for neuroscientists to gather a wealth of brain activity information as subjects go about their daily activities .
The field continued to advance this @ @ @ @ @ @ @ BCI headsets , NextMind , which decodes visual attention , and the Neurosity Notion 2 , an upgraded iteration of a product that , while designed for coders , can also be used to collect research data .

COVID-19 diagnostics
A mockup of an at-home test MAMMOTH BIOSCIENCES
Much of the world became aware of the disease now known as COVID-19 in January, and impressively, a diagnostic PCR test became available the same month. We’ve since seen an explosion in potential variations on that assay, including saliva tests, which bypass the need for scarce swabs, and a slew of techniques that could be considerably faster and cheaper than PCR, including breath tests, at-home antigen tests, a diagnostic that combines loop-mediated isothermal amplification (LAMP) and CRISPR, and even an AI model that detects telltale signs of COVID-19 from CT scans.
New paths in vaccine development
While diagnostics gave us hard numbers on SARS-CoV-2’s devastating sweep, the rapid development of vaccines against it allowed us to imagine the pandemic coming under control. mRNA vaccines from Pfizer and Moderna were among the early leaders of the vaccine race, training the spotlight on a newer technique that had been attempted for other diseases but had not yet made it to the market before 2020. The principle is to deliver a stretch of viral mRNA to recipients’ cells, which go on to manufacture viral proteins from the transcripts, provoking an immune response.
The year also saw researchers experimenting with other innovative ways of producing vaccines. In one example—which, unlike with mRNA vaccines, would avoid the need for cold temperatures during transport and storage—researchers showed that a flu vaccine delivered orally as a thin film induced an immune response in mice.
Bringing the lab home
A colony of spotted wing Drosophila flies entomologist Hannah Burrack maintained at home COURTESY HANNAH BURRACK
The pandemic’s effects on science were far-reaching, and necessitated adaptation as many researchers were shut out of their labs in a bid to prevent infection. Among the creative means scientists devised to continue their work was Cut&Tag@home, a protocol for profiling chromosome components that Steven Henikoff of the Fred Hutchinson Cancer Research Center devised in his laundry room.
Stem cells for less
Induced pluripotent stem cells (iPSCs) have proved a boon to research, but most labs grow the cells in expensive commercial media that require frequent tending to replenish the stock. In a paper at the start of this year, researchers described a DIY recipe for a medium with ingredients that cost a fraction of what commercial alternatives do, and that only needs to be changed every 3.5 days, enabling caretakers to have weekends off.
Wiring the brain
Neurosity’s Notion headset, released in 2019, is one of a handful of consumer brain-computer interface devices that scientists are adapting for their EEG research. STEVE GONG
Collecting data on humans’ brain activity typically requires researchers to put their subjects into expensive MRI or PET scanners, or to affix wires to their skulls for a traditional EEG setup. But advances in brain-computer interface (BCI) technology—much of it made with an eye toward the consumer market for devices that could be used for applications such as gaming—hold the potential for neuroscientists to gather a wealth of brain activity information as subjects go about their daily activities. The field continued to advance this year with the release of two new BCI headsets, NextMind, which decodes visual attention, and the Neurosity Notion 2, an upgraded iteration of a product that, while designed for coders, can also be used to collect research data.


thescientist--2020-12-18--Those We Lost in 2020

Those We Lost in 2020

For a complete list of our obituaries , see here .
Jeff McKnight , a molecular biologist at the University of Oregon , died in October at the age of 36 .
McKnight ’ s research focused on chromatin , a complex of DNA and proteins that controls when and how DNA can be accessed for replication and gene expression .
He was one of the earliest researchers in the world capable of directly manipulating its structure , stemming back to his postdoctoral work at the Fred Hutchinson Cancer Research Center using the model organism Saccharomyces cerevisiae .
When he @ @ @ @ @ @ @ , McKnight said at the time that his “ real dream ” was to apply his work to the dozens of human diseases that involve some level of chromatin disruption , including Parkinson ’ s , Alzheimer ’ s , and Huntington ’ s .
Prior to his death from lymphoma , McKnight had spent months chronicling his diagnosis and treatment on social media , prompting an outpouring of support from fellow scientists .
“ He had this humility and vulnerability about him that was really endearing , ” David Garcia , a @ @ @ @ @ @ @ , told The Scientist .
Biologist Lynika Strozier , a researcher at the Field Museum and an instructor at Malcom X College , died June 7 at age 35 due to complications associated with COVID-19 .
After being introduced to molecular biology as an undergraduate at Truman College , Strozier developed a passion for using DNA to identify new and sometimes cryptic species .
For her thesis work as a master ’ s student at Loyola University , Strozier sequenced DNA from 200 individual birds in Madagascar thought to belong to three species @ @ @ @ @ @ @ species that were indistinguishable based only on the birds ’ appearance .
Her steady hand and aptitude in extracting usable genetic material from old samples earned the admiration of her colleagues .
“ Our entire team entrusted Lynika with extracting DNA from old dried plant material of over 15 years and only very little material from which to do so , ” Matt Von Konrat , the head of botanical collections at the Field Museum , told The Scientist .
Nobel laureate and biochemist Stanley Cohen , who led pioneering studies of cell @ @ @ @ @ @ @ He was 97 .
“ Stan ’ s work not only provided key insights into how cells grow , but it led to the development of many drugs that are used to treat cancer , ” Lawrence Marnett , the dean of basic sciences at Vanderbilt University , where Cohen taught for 40 years , said to The Tennessean .
Cohen ’ s work on different types of growth factors alongside biochemist Rita Levi-Montalcini earned them the 1986 Nobel Prize in Physiology or Medicine .
Cohen was honored for his discovery of epidermal @ @ @ @ @ @ @ and differentiation and plays an important role in tumor development—while Levi-Montalcini was acknowledged for first isolating nerve growth factor .
Growth factor receptors have since become the target of numerous drugs , such as gefitinib and cetuximab , that slow or prevent the progression of certain cancers .
Angelika Amon , a cell biologist at MIT , died on October 29 from ovarian cancer at the age of 53 .
Amon dedicated her career to researching the cell cycle and how disruptions to its normal function can lead to cancer .
During her @ @ @ @ @ @ @ her subsequent postdoc at MIT ’ s Koch Institute for Integrative Cancer Research , Amon used model organisms such as yeast and fruit flies to study how certain proteins and enzymes direct cells through mitosis .
Later , Amon turned her focus to the study of aneuploidy , an abnormal number of chromosomes , and chromosome segregation .
She found that extra chromosomes disrupt protein folding and cell metabolism , leading to errors in those processes that can drive cancer .
“ More than anyone else I ’ ve ever met , she @ @ @ @ @ @ @ ” Matthew Vander Heiden , an MIT biologist and close friend of Amon , told The Scientist .
“ She just has this larger than life personality—there ’ s no other way to put it.
” Computational biologist James Taylor , who developed a widely used bioinformatics platform , died in April .
He was 40 .
“ James made huge contributions to open-source , accessibility , and reproducibility , ” genomicist Andrew Carroll tweeted following his death .
“ Anyone who runs a bioinformatics tool on the cloud does so thanks to @ @ @ @ @ @ @ PhD at Penn State University , Taylor helped develop the Galaxy Project , a platform that allows researchers to share genomic data without needing to know how to program .
He continued refining the platform as he moved from teaching at Emory University to Johns Hopkins University , and since then Galaxy has been used in more than 10,000 publications across disciplines .
Prior to his death , Taylor spoke on Twitter of the need “ to make transparent , reusable and reproducible analysis pipelines ” to address the current pandemic , by @ @ @ @ @ @ @ and analyzing data .
Sleep scientist William Dement , who described a number of sleep disorders and opened one of the world ’ s first sleep disorder clinics , died in June .
He was 91 .
During his graduate studies at the University of Chicago in the 1950 ’ s , Dement studied the physiology of REM sleep and its relationship to dreaming .
He later joined the faculty at Stanford University , where he taught for 50 years .
There , his focus became the study of sleep apnea and the @ @ @ @ @ @ @ , he launched the Stanford Sleep Medicine Center and is credited with prompting Congress to establish the National Center on Sleep Disorders Research .
“ There are not a lot of people who can say they saved the lives of hundreds of thousands of people , ” Emmanuel Mignot , a professor of psychiatry and behavioral sciences at Stanford University , said in an obituary .
“ But just by pushing this field forward , making sleep apnea recognized , as well as sleep disorders and sleep deprivation , Bill did that.
” @ @ @ @ @ @ @ Scripps Research Institute who studied the role of gamma-delta T cells in wound healing , died January 20 at the age of 64 .
Havran first became interested in immunology after meeting John Cambier , an immunologist at Duke University , where she completed her undergraduate degree .
While she had intended to study medicine , she became enamored of doing research .
“ It just clicked , and there was no going back , ” she told The Scientist in a 2019 profile .
“ I wanted to understand how the immune @ @ @ @ @ @ @ at the University of Chicago , Havran used monoclonal antibodies to study CD4 and CD8 surface markers on T cells .
Later , as a postdoc at the University of California , Berkeley , Havran began focusing specifically on gamma-delta T cells , which had only just been described .
She was able to map their abundance throughout the body , showing for the first time that they were common in the skin and intestines .
In her own lab at Scripps , Havran went on to demonstrate the cells ’ ability to @ @ @ @ @ @ @ Immunologist and microbiologist Noel Rose , whose early experiments established the concept of autoimmunity , died of a stroke on July 30 at the age of 92 .
Before his pioneering work , it was believed that the body was incapable of launching an immune response against itself .
But as a young medical student at the University of Buffalo , Rose showed that rabbits injected with their own thyroid-derived antigens mounted an immune response that damaged or destroyed the animals ’ thyroid .
Over the next several decades , he would further @ @ @ @ @ @ @ diseases , publishing more than 880 articles and book chapters .
“ In every aspect , [ Rose ] is the father of autoimmunity , ” George Tsokos , a professor of rheumatology at Harvard Medical School , told The Scientist in a profile of Rose .
“ The man opened a whole chapter in the book of medicine.
” Phillip Leder , a molecular geneticist at Harvard Medical School whose research furthered the fields of molecular biology , immunology , and cancer genetics , died in February .
He was 85 .
@ @ @ @ @ @ @ a postdoc in the 1960s , Leder developed a technique that confirmed , for the first time , that amino acids were encoded by three nucleotides .
Speaking in a 2012 interview , he recalled the excitement of those early experiments .
“ I would go to bed thinking about the next day ’ s experiments and then jump out of bed in the morning and rush to the laboratory .
It was a lot of work , but the intellectual excitement was enormous.
” Having revealed the genetic basis of protein coding @ @ @ @ @ @ @ the first complete sequence of a mammalian gene , develop the first recombinant DNA vector system , and discover a cancer-causing gene that led to the development of the first mouse model of cancer , among other achievements .
He established the genetics department at Harvard Medical School in 1981 only a year after joining the faculty and served as chair for 25 years .
“ Phil Leder was special .
Among great scientists , he was special , and among scientists , he was an icon , ” David Livingston , a @ @ @ @ @ @ @ .
Molecular virologist Flossie Wong-Staal , a researcher at the University of California , San Diego ( UCSD ) , who first cloned the human immunodeficiency virus ( HIV ) , died in July at age 73 due to complications from pneumonia .
When Wong-Staal first entered the laboratory of fellow virologist Robert Gallo as a postdoc in 1973 , scientists were skeptical that retroviruses could cause cancer in humans .
Wong-Staal ’ s work helped to overturn this dogma after she and her team identified the first human retrovirus ( HTLV-1 ) @ @ @ @ @ @ @ to cancer .
Together , she and Gallo published more than 100 papers in 20 years , making Wong-Staal the most-cited woman in science during the 1980s .
As AIDS cases began to spike in the 1980s , Wong-Staal became the first person to clone HIV— the retrovirus that causes the disease—and began studying the functions of its genes , a necessary step towards developing eventual treatments .
She left Gallo ’ s lab at the National Cancer Institute in 1990 to launch the Center for AIDS Research at UCSD , where she @ @ @ @ @ @ @ virus and developing treatments , many of which are still in use today .

For a complete list of our obituaries, see here.
Laura McKnight
Jeff McKnight, a molecular biologist at the University of Oregon, died in October at the age of 36.
McKnight’s research focused on chromatin, a complex of DNA and proteins that controls when and how DNA can be accessed for replication and gene expression. He was one of the earliest researchers in the world capable of directly manipulating its structure, stemming back to his postdoctoral work at the Fred Hutchinson Cancer Research Center using the model organism Saccharomyces cerevisiae. When he had started his own lab in 2016, McKnight said at the time that his “real dream” was to apply his work to the dozens of human diseases that involve some level of chromatin disruption, including Parkinson’s, Alzheimer’s, and Huntington’s.
Prior to his death from lymphoma, McKnight had spent months chronicling his diagnosis and treatment on social media, prompting an outpouring of support from fellow scientists. “He had this humility and vulnerability about him that was really endearing,” David Garcia, a molecular biologist at the University of Oregon, told The Scientist.
KYLE FLUBACKER
Biologist Lynika Strozier, a researcher at the Field Museum and an instructor at Malcom X College, died June 7 at age 35 due to complications associated with COVID-19.
After being introduced to molecular biology as an undergraduate at Truman College, Strozier developed a passion for using DNA to identify new and sometimes cryptic species. For her thesis work as a master’s student at Loyola University, Strozier sequenced DNA from 200 individual birds in Madagascar thought to belong to three species. Instead, she identified several new species that were indistinguishable based only on the birds’ appearance.
Her steady hand and aptitude in extracting usable genetic material from old samples earned the admiration of her colleagues. “Our entire team entrusted Lynika with extracting DNA from old dried plant material of over 15 years and only very little material from which to do so,” Matt Von Konrat, the head of botanical collections at the Field Museum, told The Scientist.
VANDERBILT UNIVERSITY MEDICAL CENTER
Nobel laureate and biochemist Stanley Cohen, who led pioneering studies of cell growth factors, died in February. He was 97.
“Stan’s work not only provided key insights into how cells grow, but it led to the development of many drugs that are used to treat cancer,” Lawrence Marnett, the dean of basic sciences at Vanderbilt University, where Cohen taught for 40 years, said to The Tennessean.
Cohen’s work on different types of growth factors alongside biochemist Rita Levi-Montalcini earned them the 1986 Nobel Prize in Physiology or Medicine. Cohen was honored for his discovery of epidermal growth factor—a protein that stimulates cell growth and differentiation and plays an important role in tumor development—while Levi-Montalcini was acknowledged for first isolating nerve growth factor. Growth factor receptors have since become the target of numerous drugs, such as gefitinib and cetuximab, that slow or prevent the progression of certain cancers.
SAMARA VISE, KOCH INSTITUTE AT MIT
Angelika Amon, a cell biologist at MIT, died on October 29 from ovarian cancer at the age of 53.
Amon dedicated her career to researching the cell cycle and how disruptions to its normal function can lead to cancer.
During her PhD at the University of Vienna and her subsequent postdoc at MIT’s Koch Institute for Integrative Cancer Research, Amon used model organisms such as yeast and fruit flies to study how certain proteins and enzymes direct cells through mitosis.
Later, Amon turned her focus to the study of aneuploidy, an abnormal number of chromosomes, and chromosome segregation. She found that extra chromosomes disrupt protein folding and cell metabolism, leading to errors in those processes that can drive cancer.
“More than anyone else I’ve ever met, she was an absolute force of nature,” Matthew Vander Heiden, an MIT biologist and close friend of Amon, told The Scientist. “She just has this larger than life personality—there’s no other way to put it.”
WILL KIRK/JOHNS HOPKINS UNIVERSITY
Computational biologist James Taylor, who developed a widely used bioinformatics platform, died in April. He was 40.
“James made huge contributions to open-source, accessibility, and reproducibility,” genomicist Andrew Carroll tweeted following his death. “Anyone who runs a bioinformatics tool on the cloud does so thanks to James’s work.”
During his PhD at Penn State University, Taylor helped develop the Galaxy Project, a platform that allows researchers to share genomic data without needing to know how to program. He continued refining the platform as he moved from teaching at Emory University to Johns Hopkins University, and since then Galaxy has been used in more than 10,000 publications across disciplines. Prior to his death, Taylor spoke on Twitter of the need “to make transparent, reusable and reproducible analysis pipelines” to address the current pandemic, by developing resources for best practices in sharing and analyzing data.
ED SOUZA/STANFORD NEWS SERVICE
Sleep scientist William Dement, who described a number of sleep disorders and opened one of the world’s first sleep disorder clinics, died in June. He was 91.
During his graduate studies at the University of Chicago in the 1950’s, Dement studied the physiology of REM sleep and its relationship to dreaming. He later joined the faculty at Stanford University, where he taught for 50 years. There, his focus became the study of sleep apnea and the effects of sleep deprivation. In 1970, he launched the Stanford Sleep Medicine Center and is credited with prompting Congress to establish the National Center on Sleep Disorders Research.
“There are not a lot of people who can say they saved the lives of hundreds of thousands of people,” Emmanuel Mignot, a professor of psychiatry and behavioral sciences at Stanford University, said in an obituary. “But just by pushing this field forward, making sleep apnea recognized, as well as sleep disorders and sleep deprivation, Bill did that.”
wendy havran
Wendy Havran, an immunologist at the Scripps Research Institute who studied the role of gamma-delta T cells in wound healing, died January 20 at the age of 64.
Havran first became interested in immunology after meeting John Cambier, an immunologist at Duke University, where she completed her undergraduate degree. While she had intended to study medicine, she became enamored of doing research. “It just clicked, and there was no going back,” she told The Scientist in a 2019 profile. “I wanted to understand how the immune system worked.”
During her doctorate research at the University of Chicago, Havran used monoclonal antibodies to study CD4 and CD8 surface markers on T cells. Later, as a postdoc at the University of California, Berkeley, Havran began focusing specifically on gamma-delta T cells, which had only just been described. She was able to map their abundance throughout the body, showing for the first time that they were common in the skin and intestines. In her own lab at Scripps, Havran went on to demonstrate the cells’ ability to heal wounds and suppress tumor growth.
JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH
Immunologist and microbiologist Noel Rose, whose early experiments established the concept of autoimmunity, died of a stroke on July 30 at the age of 92.
Before his pioneering work, it was believed that the body was incapable of launching an immune response against itself. But as a young medical student at the University of Buffalo, Rose showed that rabbits injected with their own thyroid-derived antigens mounted an immune response that damaged or destroyed the animals’ thyroid. Over the next several decades, he would further unravel the causes and mechanisms of autoimmune diseases, publishing more than 880 articles and book chapters.
“In every aspect, [Rose] is the father of autoimmunity,” George Tsokos, a professor of rheumatology at Harvard Medical School, told The Scientist in a profile of Rose. “The man opened a whole chapter in the book of medicine.”
LIZA GREEN, HARVARD MEDICAL SCHOOL
Phillip Leder, a molecular geneticist at Harvard Medical School whose research furthered the fields of molecular biology, immunology, and cancer genetics, died in February. He was 85.
Working alongside NIH geneticist Marshall Nirenberg as a postdoc in the 1960s, Leder developed a technique that confirmed, for the first time, that amino acids were encoded by three nucleotides. Speaking in a 2012 interview, he recalled the excitement of those early experiments. “I would go to bed thinking about the next day’s experiments and then jump out of bed in the morning and rush to the laboratory. It was a lot of work, but the intellectual excitement was enormous.”
Having revealed the genetic basis of protein coding, Leder next went on to map the first complete sequence of a mammalian gene, develop the first recombinant DNA vector system, and discover a cancer-causing gene that led to the development of the first mouse model of cancer, among other achievements. He established the genetics department at Harvard Medical School in 1981 only a year after joining the faculty and served as chair for 25 years.
“Phil Leder was special. Among great scientists, he was special, and among scientists, he was an icon,” David Livingston, a geneticist at Harvard, told The Scientist.
University of california, san diego
Molecular virologist Flossie Wong-Staal, a researcher at the University of California, San Diego (UCSD), who first cloned the human immunodeficiency virus (HIV), died in July at age 73 due to complications from pneumonia.
When Wong-Staal first entered the laboratory of fellow virologist Robert Gallo as a postdoc in 1973, scientists were skeptical that retroviruses could cause cancer in humans. Wong-Staal’s work helped to overturn this dogma after she and her team identified the first human retrovirus (HTLV-1) and showed that it could indeed lead to cancer. Together, she and Gallo published more than 100 papers in 20 years, making Wong-Staal the most-cited woman in science during the 1980s.
As AIDS cases began to spike in the 1980s, Wong-Staal became the first person to clone HIV— the retrovirus that causes the disease—and began studying the functions of its genes, a necessary step towards developing eventual treatments. She left Gallo’s lab at the National Cancer Institute in 1990 to launch the Center for AIDS Research at UCSD, where she spent the next several decades studying the virus and developing treatments, many of which are still in use today.


thescientist--2020-12-21--Liver Dysfunction: Causes and Mechanisms

An estimated 4.5 million adults in the United States were diagnosed with liver disease in 2018 .
The prevalence of @ @ @ @ @ grow with the increased prevalence of comorbidities .
Several factors , including environment , dietary @ @ @ @ @ , and genetic predispositions may contribute to liver dysfunction .
Download this poster from The @ @ @ @ @ to learn about • The underlying causes and mechanisms of liver dysfunction • Common diseases @ @ @ @ @ problems

An estimated 4.5 million adults in the United States were diagnosed with liver disease in 2018. The prevalence of chronic liver disease continues to grow with the increased prevalence of comorbidities. Several factors, including environment, dietary habits, comorbidities, toxins, and genetic predispositions may contribute to liver dysfunction.
Download this poster from The Scientist's Creative Services team to learn about
The underlying causes and mechanisms of liver dysfunction
Common diseases and conditions that cause liver problems
The stages of liver disease
How scientists identify liver disease
Current treatments for liver dysfunction
New omics-based drug discovery and therapeutic research


thescientist--2020-12-21--The Brain on COVID-19

The Brain on COVID-19

Patients with COVID-19 present a host of neurological impairments , including reduced ability to smell or taste , altered mental @ @ @ @ @ , and even delirium .
Yet , brain autopsy results from those who have passed @ @ @ @ @ vexing ; only a few virus particles and small pockets of inflammation appear .
Instead @ @ @ @ @ of oxygen deprivation in the brain , possibly caused by systemic clotting , which is @ @ @ @ @ this poster from The Scientist 's Creative Services team to explore how SARS-CoV-2 infection affects @ @ @ @ @ mechanisms for these manifestations .

Patients with COVID-19 present a host of neurological impairments, including reduced ability to smell or taste, altered mental status, stroke, seizure, and even delirium. Yet, brain autopsy results from those who have passed away from the disease are vexing; only a few virus particles and small pockets of inflammation appear. Instead, researchers find widespread evidence of oxygen deprivation in the brain, possibly caused by systemic clotting, which is characteristic of COVID-19.
Download this poster from The Scientist's Creative Services team to explore how SARS-CoV-2 infection affects neurological function and the underlying mechanisms for these manifestations.


thescientist--2020-12-21--The Ultimate Guide to Flow Imaging Microscopy

Researchers often turn to basic microscopy or volumetric analysis techniques to determine the shape , count , concentration , and @ @ @ @ @ a sample .
However , manual microscopy is time-consuming and subject to human error , @ @ @ @ @ for samples composed of heterogeneous particle shapes .
Flow imaging microscopy ( FIM ) for @ @ @ @ @ of microscopy and volumetric analysis to rapidly measure particles from digital images , producing statistically @ @ @ @ @ ebook from Yokogawa Fluid Imaging Technologies to learn about • Examples of FIM applications - @ @ @ @ @ aggregate detection in drug formulations - Microencapsulation process analysis - Particle differentiation in heterogeneous samples @ @ @

Researchers often turn to basic microscopy or volumetric analysis techniques to determine the shape, count, concentration, and size distribution of particles within a sample. However, manual microscopy is time-consuming and subject to human error, while volumetric techniques are unsatisfactory for samples composed of heterogeneous particle shapes. Flow imaging microscopy (FIM) for particle analysis combines the benefits of microscopy and volumetric analysis to rapidly measure particles from digital images, producing statistically significant results.
Download this ebook from Yokogawa Fluid Imaging Technologies to learn about
Particle analysis history
How flow imaging microscopy (FIM) works
Examples of FIM applications
- Aquatic organism identification
- Protein aggregate detection in drug formulations
- Microencapsulation process analysis
- Particle differentiation in heterogeneous samples
- Outlier characterization


thescientist--2020-12-21--Identifying PrognosticBiomarkers in COVID-19

COVID-19 patients exhibit a wide variety of symptoms , making it difficult to predict their disease progression .
However , @ @ @ @ @ s immune biomarkers , effective treatments can be identified and administered at early disease stages @ @ @ @ @ platform , researchers analyzed the complete immune landscape of COVID-19 patients .
They identified rare @ @ @ @ @ characterized cytokines driving the immune response , revealing novel biomarkers that improved their understanding of @ @ @ @ @ developing effective therapeutics for early intervention .
Download this research summary to learn how James @ @ @ @ @ for Systems Biology and his team used IsoPlexis ’ highly functional single-cell proteomics to identify @ @ @ @ @ COVID-19 .

COVID-19 patients exhibit a wide variety of symptoms, making it difficult to predict their disease progression. However, by understanding the disease’s immune biomarkers, effective treatments can be identified and administered at early disease stages. Using a functional proteomics platform, researchers analyzed the complete immune landscape of COVID-19 patients. They identified rare subsets of immune cells and characterized cytokines driving the immune response, revealing novel biomarkers that improved their understanding of SARS-CoV-2 infection for identifying and developing effective therapeutics for early intervention.
Download this research summary to learn how James R. Heath from the Institute for Systems Biology and his team used IsoPlexis’ highly functional single-cell proteomics to identify prognostic biomarkers of inflammation in COVID-19.


thescientist--2020-12-22--The Scientist Speaks Podcast - Episode 12

Odors bombard the human nose every day , whether the odors register consciously or not .
The way the human @ @ @ @ @ the potential to characterize disease and shape everyday human interaction .
In this month ’ @ @ @ @ @ the world of odor and how scientists use the sense of smell to better understand @ @ @ @ @ , and behavior .
Tiffany Garbutt from The Scientist ’ s Creative Services team spoke @ @ @ @ @ Professor of Neurobiology and Director of the Azrieli National Center for Human Brain Imaging and @ @ @ @ @ of Science , to learn more .
The Scientist Speaks is a podcast produced by @ @ @ @ @ Services team .
Our podcast is by scientists and for scientists .
Once a month @ @ @ @ @ stories behind news-worthy molecular biology research .
This month 's episode is supported by MilliporeSigma @ @ @ @

Odors bombard the human nose everyday, whether the odors register consciously or not. The way the human brain processes these odors has the potential to characterize disease and shape everyday human interaction. In this month’s episode, we explore the world of odor and how scientists use the sense of smell to better understand the human brain, disease, and behavior.
Tiffany Garbutt from The Scientist’s Creative Services team spoke with Noam Sobel, Sela Professor of Neurobiology and Director of the Azrieli National Center for Human Brain Imaging and Research at the Weizmann Institute of Science, to learn more.


thescientist--2020-12-23--A New Human Reference Genome Represents the Most Common Sequences

The human reference genome is a DNA blueprint used as a standard for comparison in basic research and clinical settings .
Despite improvements in accuracy and completeness that have been made over the years , it still harbors limitations that can result in erroneous findings .
In the current version of the reference , called GRCh38 or Build 38 , 93 percent of the sequence comes from just 11 individuals and 70 percent from just one man , resulting in a lack of diversity and at least 300 million missing letters of DNA .
In addition , a small percentage @ @ @ @ @ @ @ are represented by alleles that are not the most common forms of the genes .
To address these issues , some scientists are developing a new reference , called the pangenome or graph genome , that contains a vast collection of genomes representing all possible DNA sequences for any given locus .
But representing these data—the 3 billion bases in one person , times the hundreds to thousands of individuals whom scientists seek to include—is extremely complicated .
The trouble with a pangenome is that incorporating it into existing research practices and software @ @ @ @ @ @ @ requires graphical representation as opposed to a single , linear genome .
For instance , the methods used for transcriptomics , which can tell scientists which genes are active in a particular cell , would need a complete overhaul .
“ Most of the methods that do transcript expression analysis , they work on , or they expect as input , a single sequence like a single reference genome .
They don ’ t expect a graph , ” says Christina Boucher , a bioinformatics researcher at the University of Florida .
“ @ @ @ @ @ @ @ the input .
So the methods that actually do the transcript expression would have to be redeveloped , then , in order to take in a graph rather than a single reference .
The algorithms in and of themselves would have to be redeveloped.
” That ’ s why researchers such as Jesse Gillis , a computational biologist at Cold Spring Harbor Laboratory , came up with a new idea : the “ consensus genome.
” It is still a single genome just the like current reference , but it represents the most @ @ @ @ @ @ @ than whatever the few individuals used to make the current reference happened to have in their DNA .
This allows for a nearly painless adoption as far as using it in existing genome analysis software , says Gillis .
In a preprint posted to bioRxiv on December 22 , Gillis and his colleagues , including Alexander Dobin of Cold Spring Harbor Laboratory who developed the popular RNA sequence analysis software STAR , compare their consensus genome to the current reference genome , as well as to population-specific consensus genomes they created representing both @ @ @ @ @ @ @ such as Han Chinese in Beijing .
They created consensus genomes using the 1,000 Genomes Project database , which contains more than 2,500 genomes across 26 subpopulations , grouped into five superpopulations .
They tested how GRCh38 and each consensus genome performed during transcriptomics using STAR , to see if improvement in the input reference genome would improve gene expression analysis .
Like DNA analysis , data received during RNA sequencing come in pieces called reads .
To determine where these pieces come from in the genome , researchers often match these reads @ @ @ @ @ @ @ known as mapping or alignment .
Then they can count up how much messenger RNA there is for each gene to quantify gene activity .
As a baseline , Gillis and his colleagues first aligned the reads from one individual to his or her own genome and measured gene expression .
They then did the same using the reference and consensus genomes and compared the results to the baseline , quantifying the differences , or amount of error , between them .
They found that , while the inaccuracies produced by the reference @ @ @ @ @ @ @ are minor , according to Gillis , the consensus genomes had even fewer errors .
Specifically , compared with the reference genome , the consensus genomes yielded an improvement in the mapping error rate from around 9 percent to around 4 percent .
And because errors in mapping will result in errors when counting up messenger RNA , the reference also generated mistakes in gene expression measurement in almost six times as many genes as the consensus did .
“ While absolutely a decrease of a factor of two to three sounds like @ @ @ @ @ @ @ it ’ s going from what I would say is exceptionally good to slightly beyond exceptionally good , ” says Gillis .
“ And that should be a relief because we ’ ve been doing science for a long time using the reference .
If we discovered that this was a life changing difference , it would be worrying.
” Gillis and his team also found that the population-specific genomes only had a marginal improvement in error reduction beyond the general consensus , a maximum difference of about 1 percent .
This suggests @ @ @ @ @ @ @ may be unnecessary for RNA sequencing analysis .
This is good news for Elizabeth Atkinson of Massachusetts General Hospital and the Broad Institute of MIT and Harvard who studies admixed populations whose recent ancestry comes from multiple sources .
She says that not only would population-specific genomes make it difficult to compare individuals with multiple ancestries to each other , but just assigning people to those groups is challenging .
“ If you have someone of mixed ancestry , which ancestry do you choose for their population consensus genome ?
” says Atkinson @ @ @ @ @ @ @ mixed over time , so it makes sense to me that , if the pan-species [ consensus ] option appears to perform effectively as well [ as the population-specific consensus ] , that would get around some of those wrinkles in terms of comparing across populations and deciding how to even assign people to their correct population.
” Although Gillis says he believes that other researchers would be able to replicate these consensus genomes fairly quickly , he and his colleagues have developed software so they can build their own consensus and perform @ @ @ @ @ @ @ , open-source , and available on GitHub .

ABOVE: © ISTOCK.COM,
NOBI_PRIZUE
The human reference genome is a DNA blueprint used as a standard for comparison in basic research and clinical settings. Despite improvements in accuracy and completeness that have been made over the years, it still harbors limitations that can result in erroneous findings.
In the current version of the reference, called GRCh38 or Build 38, 93 percent of the sequence comes from just 11 individuals and 70 percent from just one man, resulting in a lack of diversity and at least 300 million missing letters of DNA. In addition, a small percentage of the genes in the reference genome are represented by alleles that are not the most common forms of the genes.
To address these issues, some scientists are developing a new reference, called the pangenome or graph genome, that contains a vast collection of genomes representing all possible DNA sequences for any given locus. But representing these data—the 3 billion bases in one person, times the hundreds to thousands of individuals whom scientists seek to include—is extremely complicated.
The trouble with a pangenome is that incorporating it into existing research practices and software would be a huge undertaking because it requires graphical representation as opposed to a single, linear genome. For instance, the methods used for transcriptomics, which can tell scientists which genes are active in a particular cell, would need a complete overhaul.
While absolutely a decrease of a factor of two to three sounds like an impressive difference, in reality, it’s going from what I would say is exceptionally good to slightly beyond exceptionally good. —Jesse Gillis, Cold Spring Harbor Laboratory
“Most of the methods that do transcript expression analysis, they work on, or they expect as input, a single sequence like a single reference genome. They don’t expect a graph,” says Christina Boucher, a bioinformatics researcher at the University of Florida. “That’s a huge jump in the input. So the methods that actually do the transcript expression would have to be redeveloped, then, in order to take in a graph rather than a single reference. The algorithms in and of themselves would have to be redeveloped.”
That’s why researchers such as Jesse Gillis, a computational biologist at Cold Spring Harbor Laboratory, came up with a new idea: the “consensus genome.” It is still a single genome just the like current reference, but it represents the most common alleles among thousands of individuals rather than whatever the few individuals used to make the current reference happened to have in their DNA. This allows for a nearly painless adoption as far as using it in existing genome analysis software, says Gillis.
In a preprint posted to bioRxiv on December 22, Gillis and his colleagues, including Alexander Dobin of Cold Spring Harbor Laboratory who developed the popular RNA sequence analysis software STAR, compare their consensus genome to the current reference genome, as well as to population-specific consensus genomes they created representing both superpopulations such as East Asian and subpopulations such as Han Chinese in Beijing.
They created consensus genomes using the 1,000 Genomes Project database, which contains more than 2,500 genomes across 26 subpopulations, grouped into five superpopulations. They tested how GRCh38 and each consensus genome performed during transcriptomics using STAR, to see if improvement in the input reference genome would improve gene expression analysis.
Like DNA analysis, data received during RNA sequencing come in pieces called reads. To determine where these pieces come from in the genome, researchers often match these reads to a reference genome, a process known as mapping or alignment. Then they can count up how much messenger RNA there is for each gene to quantify gene activity.
As a baseline, Gillis and his colleagues first aligned the reads from one individual to his or her own genome and measured gene expression. They then did the same using the reference and consensus genomes and compared the results to the baseline, quantifying the differences, or amount of error, between them.
They found that, while the inaccuracies produced by the reference genome during alignment and gene expression measurement are minor, according to Gillis, the consensus genomes had even fewer errors. Specifically, compared with the reference genome, the consensus genomes yielded an improvement in the mapping error rate from around 9 percent to around 4 percent. And because errors in mapping will result in errors when counting up messenger RNA, the reference also generated mistakes in gene expression measurement in almost six times as many genes as the consensus did.
“While absolutely a decrease of a factor of two to three sounds like an impressive difference, in reality, it’s going from what I would say is exceptionally good to slightly beyond exceptionally good,” says Gillis. “And that should be a relief because we’ve been doing science for a long time using the reference. If we discovered that this was a life changing difference, it would be worrying.”
Gillis and his team also found that the population-specific genomes only had a marginal improvement in error reduction beyond the general consensus, a maximum difference of about 1 percent. This suggests that having dedicated references for each population may be unnecessary for RNA sequencing analysis.
This is good news for Elizabeth Atkinson of Massachusetts General Hospital and the Broad Institute of MIT and Harvard who studies admixed populations whose recent ancestry comes from multiple sources. She says that not only would population-specific genomes make it difficult to compare individuals with multiple ancestries to each other, but just assigning people to those groups is challenging.
“If you have someone of mixed ancestry, which ancestry do you choose for their population consensus genome?” says Atkinson. “The population is getting more mixed over time, so it makes sense to me that, if the pan-species [consensus] option appears to perform effectively as well [as the population-specific consensus], that would get around some of those wrinkles in terms of comparing across populations and deciding how to even assign people to their correct population.”
Although Gillis says he believes that other researchers would be able to replicate these consensus genomes fairly quickly, he and his colleagues have developed software so they can build their own consensus and perform RNA sequencing. The programs are free, open-source, and available on GitHub.


thescientist--2020-12-23--The Biggest Science News of 2020

The Biggest Science News of 2020

ABOVE : Two fires in Argentina burned 90 percent of the San Cayetano Provincial Park , which houses a field station that has carried out long-term monitoring of local primates for decades .
BELEN NATALINI The pandemic ’ s toll on the research community Given the collective pivot the globe took toward addressing the coronavirus pandemic , we ’ re dedicating a separate post to what we heard from scientists this year—their struggles and triumphs , frustrations and joys .
Aside from research on SARS-CoV-2 itself , the pandemic had huge effects on the scientific community .
Tragically , the @ @ @ @ @ @ @ of researchers .
Lynika Strozier , whose “ hands of gold ” could extract DNA from small amounts of starting material and who identified numerous new species , was just 35 when she died of COVID-19 .
Paleobotanist Brian Axsmith died of COVID-19 at age 57 .
Paleontologist Robert Carroll , former Stanford University President Donald Kennedy , microbiologist Paul Matewele , former Babraham Institute Director Michael Wakelam , HIV researcher Gita Ramjee , and vascular biologist Stephen Schwartz were also among the 1.6 million people who have died from the disease this @ @ @ @ @ @ @ researchers found themselves struggling to do their work at times this year , others found themselves laid off or furloughed .
Women in STEM appear to have taken the greatest hit to their productivity .
Academic job opportunities shrunk and don ’ t seem to have recovered to the hiring levels of past years .
Nevertheless , a survey of scientists has found the community resilient in the face of lockdowns and other restrictions , and the astounding accomplishments in the development of drugs , vaccines , diagnostics , and research techniques related @ @ @ @ @ @ @ researchers ’ creativity and dedication .
Scientists managed to keep their science afloat by turning their homes into wet labs and finding new ways to be productive .
Scientific conferences went from cancelled or postponed to completely revamped as virtual events , with broadened inclusivity and fewer carbon emissions from travel .
The world still turned , and burned With all eyes on SARS-CoV-2 , it was easy to overlook other big events unleashed by mother nature .
Wildfires burned up and down the US West Coast .
In California , blazes damaged @ @ @ @ @ @ @ And on the other side of the globe , in Australia , efforts to shore up vulnerable koala populations suffered , perhaps irreparably .
“ There ’ s been so much research progress in recent years to try and improve the health status of these koala populations , ” Natasha Speight , a koala disease researcher and veterinarian at the University of Adelaide in South Australia , told The Scientist in January .
“ It really is a setback to have so many lost from these bushfires.
” Similarly , a park in @ @ @ @ @ @ @ groups of resident howler monkeys had been ongoing for decades saw at least five groups perish in fires this fall .
“ All these groups that we found , I knew everything about them .
I knew who was the son , the daughter , the mother .
The first [ few days ] I was crying all the time , ” Martin Kowalewski , a primate ecologist and the director of the Estación Biológica Corrientes field station , told The Scientist .
The fires were thought to have been started intentionally by @ @ @ @ @ @ @ they then burned out of control , decimating the reserve where the monkeys lived .
In February , scientists reported that they had found functioning mitochondria in people ’ s blood .
Past studies had shown that mitochondrial DNA could be found in circulation , and at times the organelles might get released from cells in response to damage , but entire , respiring organelles in the blood of healthy individuals was a novel observation .
“ The whole thing surprises me , ” Joel Riley , who studies how mitochondria can stimulate @ @ @ @ @ @ @ wasn ’ t involved in the study , told The Scientist at the time .
“ We know that bits of mitochondria can get kicked out of cells through extracellular vesicles [ when they are damaged ] , but whole mitochondria—that ’ s pretty cool.
” The next step is to figure out what the organelles are doing in circulation .
Humans continue to be full of anatomical surprises , and this year researchers added to our known components a set of salivary glands in the neck that they named the tubarial glands @ @ @ @ @ @ @ pharynx , likely went unnoticed because it is difficult to reach during surgery and was discovered with a combination of positron emission tomography ( PET ) and computed tomography ( CT ) that uses a radioactive tracer that binds to a prostate-specific membrane antigen ( PSMA ) .
Ordinarily , PSMA PET/CT is used to detect prostate cancer , but lead scientist Wouter Vogel , a radiation oncologist at the Netherlands Cancer Institute , told The Scientist in October , “ This scan is extremely sensitive for the salivary glands .
So we @ @ @ @ @ @ @ Although a perennial problem , a lack of equity in STEM gained renewed attention in 2020 as scientists advocated for inclusion , anti-racist action , and awareness of the forces that turn away people from underrepresented groups .
Black in X , a collection of initiatives to raise the profile of Black scientists in various fields and support their careers , emerged after a racist incident in May between a Black birder and a white woman who wasn ’ t following a canine leash law in New York City ’ s Central Park @ @ @ @ @ @ @ Astro , Black in Chem , and other groups have since organized virtual events and digital networking .
“ Now that we can finally see each other , we can now support each other , ” Black in Micro co-organizer Ariangela Kozik , a postdoc at the University of Michigan , told The Scientist .
This year , several academic journals also came to recognize that their name-change policies could be harming transgender individuals .
Cell Press , for instance , adopted a new policy that allows authors to change the name on @ @ @ @ @ @ @ a correction , with the author ’ s approval , which can reveal more information than authors might wish to provide .
Theresa Tanenbaum , a computer scientist at the University of California , Irvine , who has worked on name-change guidance for journals , told The Scientist she advocates for publishers keeping a private record of name changes that would be released only when needed , such as in a legal case .
The first blood test to sample for blood biomarkers indicative of Alzheimer ’ s disease became available for physicians @ @ @ @ @ @ @ s test measures the ratio of two isoforms of the amyloid-β protein , Aβ42 and Aβ40 , and the presence of isoforms of apolipoprotein E ( ApoE ) associated with Alzheimer ’ s risk .
“ If you asked me [ five or ten ] years ago if there would ever be a blood test for Alzheimer ’ s , I would have been very skeptical , ” Howard Fillit , the executive director and chief science officer of the Alzheimer ’ s Drug Discovery Foundation , which invested in C N ’ @ @ @ @ @ @ @ The Scientist .
“ So the fact that this is on the market now is just amazing.
” Because modern humans ’ interbreeding with Neanderthals took place in Eurasia thousands of years ago , geneticists had assumed that individuals with African ancestry wouldn ’ t have much Neanderthal DNA in their genomes .
Not so .
In a study that came out in January , researchers compared African genomes to the Neanderthal reference genome and found a lot more overlap than they had expected—about 17 megabases .
This is still just one-third of @ @ @ @ @ @ @ of people with European and Asian ancestry , and likely represents the migration of people from Europe and Asia who carried with them to Africa the genetic legacy of their ancestors ’ intermingling with Neanderthals .
Janet Kelso , a computational biologist at the Max Planck Institute for Evolutionary Anthropology who was not involved in the study , told The Scientist at the time , “ What ’ s surprising here is the amount .
It ’ s actually a larger proportion than I think people had imagined .
”

ABOVE: Two fires in Argentina burned 90 percent of the San Cayetano Provincial Park, which houses a field station that has carried out long-term monitoring of local primates for decades.
BELEN NATALINI
The pandemic’s toll on the research community
Given the collective pivot the globe took toward addressing the coronavirus pandemic, we’re dedicating a separate post to what we heard from scientists this year—their struggles and triumphs, frustrations and joys.
Aside from research on SARS-CoV-2 itself, the pandemic had huge effects on the scientific community. Tragically, the virus claimed the lives of a number of researchers. Lynika Strozier, whose “hands of gold” could extract DNA from small amounts of starting material and who identified numerous new species, was just 35 when she died of COVID-19. Paleobotanist Brian Axsmith died of COVID-19 at age 57. Paleontologist Robert Carroll, former Stanford University President Donald Kennedy, microbiologist Paul Matewele, former Babraham Institute Director Michael Wakelam, HIV researcher Gita Ramjee, and vascular biologist Stephen Schwartz were also among the 1.6 million people who have died from the disease this year.
While a considerable proportion of researchers found themselves struggling to do their work at times this year, others found themselves laid off or furloughed. Women in STEM appear to have taken the greatest hit to their productivity. Academic job opportunities shrunk and don’t seem to have recovered to the hiring levels of past years.
Nevertheless, a survey of scientists has found the community resilient in the face of lockdowns and other restrictions, and the astounding accomplishments in the development of drugs, vaccines, diagnostics, and research techniques related to the coronavirus are a testament to researchers’ creativity and dedication. Scientists managed to keep their science afloat by turning their homes into wet labs and finding new ways to be productive. Scientific conferences went from cancelled or postponed to completely revamped as virtual events, with broadened inclusivity and fewer carbon emissions from travel.
The world still turned, and burned
With all eyes on SARS-CoV-2, it was easy to overlook other big events unleashed by mother nature. Wildfires burned up and down the US West Coast. In California, blazes damaged field sites and threatened astronomical observatories. And on the other side of the globe, in Australia, efforts to shore up vulnerable koala populations suffered, perhaps irreparably. “There’s been so much research progress in recent years to try and improve the health status of these koala populations,” Natasha Speight, a koala disease researcher and veterinarian at the University of Adelaide in South Australia, told The Scientist in January. “It really is a setback to have so many lost from these bushfires.”
Similarly, a park in Argentina where a long-term study of 20 groups of resident howler monkeys had been ongoing for decades saw at least five groups perish in fires this fall. “All these groups that we found, I knew everything about them. I knew who was the son, the daughter, the mother. The first [few days] I was crying all the time,” Martin Kowalewski, a primate ecologist and the director of the Estación Biológica Corrientes field station, told The Scientist. The fires were thought to have been started intentionally by ranchers to stimulate grassland growth, but they then burned out of control, decimating the reserve where the monkeys lived.
Mitochondria in circulation
Electron microscopy image of mitochondria isolated from healthy human blood plasma © ALAIN THIERRY, INSERM
In February, scientists reported that they had found functioning mitochondria in people’s blood. Past studies had shown that mitochondrial DNA could be found in circulation, and at times the organelles might get released from cells in response to damage, but entire, respiring organelles in the blood of healthy individuals was a novel observation.
“The whole thing surprises me,” Joel Riley, who studies how mitochondria can stimulate inflammation at the University of Glasgow and wasn’t involved in the study, told The Scientist at the time. “We know that bits of mitochondria can get kicked out of cells through extracellular vesicles [when they are damaged], but whole mitochondria—that’s pretty cool.” The next step is to figure out what the organelles are doing in circulation.
More human salivary glands
A 3-D reconstruction from histological slides (inset on right) of the newly discovered tubarial gland (yellow; ducts in light blue). The torus tubarius cartilage is colored dark blue and muscle is pink. M. Valstar et al., Radiotherapy & Oncology , doi:10.1016/j.radonc.2020.09.034, 2020.
Humans continue to be full of anatomical surprises, and this year researchers added to our known components a set of salivary glands in the neck that they named the tubarial glands. The tissue, tucked behind the pharynx, likely went unnoticed because it is difficult to reach during surgery and was discovered with a combination of positron emission tomography (PET) and computed tomography (CT) that uses a radioactive tracer that binds to a prostate-specific membrane antigen (PSMA). Ordinarily, PSMA PET/CT is used to detect prostate cancer, but lead scientist Wouter Vogel, a radiation oncologist at the Netherlands Cancer Institute, told The Scientist in October, “This scan is extremely sensitive for the salivary glands. So we can see more than ever before.”
Inclusivity gains in STEM
Although a perennial problem, a lack of equity in STEM gained renewed attention in 2020 as scientists advocated for inclusion, anti-racist action, and awareness of the forces that turn away people from underrepresented groups. Black in X, a collection of initiatives to raise the profile of Black scientists in various fields and support their careers, emerged after a racist incident in May between a Black birder and a white woman who wasn’t following a canine leash law in New York City’s Central Park. Black in Neuro, Black in Astro, Black in Chem, and other groups have since organized virtual events and digital networking. “Now that we can finally see each other, we can now support each other,” Black in Micro co-organizer Ariangela Kozik, a postdoc at the University of Michigan, told The Scientist.
This year, several academic journals also came to recognize that their name-change policies could be harming transgender individuals. Cell Press, for instance, adopted a new policy that allows authors to change the name on their publications. It still requires issuing a correction, with the author’s approval, which can reveal more information than authors might wish to provide. Theresa Tanenbaum, a computer scientist at the University of California, Irvine, who has worked on name-change guidance for journals, told The Scientist she advocates for publishers keeping a private record of name changes that would be released only when needed, such as in a legal case.
Alzheimer’s blood test
The first blood test to sample for blood biomarkers indicative of Alzheimer’s disease became available for physicians in October. C 2 N Diagnostics’s test measures the ratio of two isoforms of the amyloid-β protein, Aβ42 and Aβ40, and the presence of isoforms of apolipoprotein E (ApoE) associated with Alzheimer’s risk. “If you asked me [five or ten] years ago if there would ever be a blood test for Alzheimer’s, I would have been very skeptical,” Howard Fillit, the executive director and chief science officer of the Alzheimer’s Drug Discovery Foundation, which invested in C 2 N’s development of the test, told The Scientist. “So the fact that this is on the market now is just amazing.”
Neanderthal DNA in Africans
Because modern humans’ interbreeding with Neanderthals took place in Eurasia thousands of years ago, geneticists had assumed that individuals with African ancestry wouldn’t have much Neanderthal DNA in their genomes. Not so. In a study that came out in January, researchers compared African genomes to the Neanderthal reference genome and found a lot more overlap than they had expected—about 17 megabases.
This is still just one-third of what’s found in the genomes of people with European and Asian ancestry, and likely represents the migration of people from Europe and Asia who carried with them to Africa the genetic legacy of their ancestors’ intermingling with Neanderthals.
Janet Kelso, a computational biologist at the Max Planck Institute for Evolutionary Anthropology who was not involved in the study, told The Scientist at the time, “What’s surprising here is the amount. It’s actually a larger proportion than I think people had imagined.”


thescientist--2020-12-23--2020 in Scientists' Own Words

2020 in Scientists' Own Words

ABOVE : Scanning electron micrograph of SARS-CoV-2 ( gold ) emerging from the surface of cells cultured in the lab .
Image captured and colorized at NIAID ’ s Rocky Mountain Laboratories in Hamilton , Montana FLICKR , NIAID We can slow it down by canceling all these events , which we completely should do .
But it ’ s still going to spread to most places .
—Maciej Boni , a biologist at Penn State University , speaking to The Scientist about how the high number of undetected cases makes it difficult to track viral spread based on confirmed @ @ @ @ @ @ @ important to screen the patients for neurological signs early and late in the course of COVID-19 .
.
.
as this could be life-saving in our fight against COVID-19 pandemic .
—Abdul Mannan Baig , a researcher at Aga Khan University in Pakistan , speaking to The Scientist about indications that SARS-CoV-2 can target the nervous system ( March 24 ) It ’ s definitely scary as someone who is looking for another postdoc or potentially applying to faculty jobs to have this looming situation .
—Kishana Taylor , a postdoc in microbiology @ @ @ @ @ @ @ California , Davis , speaking to The Scientist about pandemic-related hiring freezes in academia ( March 26 ) We all need to remember : people are more important than projects .
Our safety and that of our broader community is more important than our individual lab ’ s work right now .
—Kathleen Millen , a neuroscientist at Seattle Children ’ s Hospital Research Institute , in an email to The Scientist about how pandemic-related lab shutdowns affected the scientific community ( March 27 ) This is going to be imprinted on the @ @ @ @ @ @ @ long time .
—Anthony Fauci , director of the US National Institute of Allergy and Infectious Disease , speaking with CNN ’ s Sanjay Gupta about the effects of the COVID-19 pandemic on the psyches of his daughters and other Americans ( April 1 ) You know , the conspiracy theories out there have essentially closed down communication between scientists in China and scientists in the US .
We need that communication in an outbreak to learn from them how they control it so we can control it better .
It ’ s @ @ @ @ @ @ @ probably cost lives .
—Peter Daszak , president of the nonprofit EcoHealth Alliance , talking to “ 60 Minutes ” about the ongoing politicization of science with regard to the COVID-19 pandemic ( May 10 ) Our prior studies have suggested that blocking receptor binding is a surefire way to neutralize the virus and come up with a protective antibody .
—Erica Ollmann Saphire , an immunologist at the La Jolla Institute for Immunology , speaking to The Scientist about the promise of antibody candidates that could prevent SARS-CoV-2 from entering cells ( @ @ @ @ @ @ @ wanted to do with my life—study viruses—and then to be at home and not have a lab [ during a pandemic ] .
.
.
.
It ’ s sort of like watching a ship pass you , and you really want to be on it .
—Jillian Carmichael , a postdoc in virologist Benhur Lee ’ s lab at Mount Sinai ’ s Icahn School of Medicine , speaking with The Scientist about missing out on research during the pandemic due to the closure of daycares and schools ( June 25 ) @ @ @ @ @ @ @ beginning of an epidemic to get an accurate R0 .
—Nelly Yatich , epidemiologist in Nairobi , Kenya , discussing with The Scientist the challenges of determining the basic reproductive number , R0 , which describes the initial spread of an infection in a completely susceptible population ( July 13 ) I ’ ve been sick for three months , which just sounds so ridiculous to so many doctors .
—Hannah Davis , an artist living in Brooklyn , speaking to The Scientist about memory loss , sporadic bursts of blurred vision , @ @ @ @ @ @ @ insomnia , and various aches and pains that she experienced for months after testing positive for COVID-19 ( July 17 ) Any school that can not meet these minimum screening standards or maintain uncompromising control over good prevention practices has to ask itself if it has any business reopening .
—A .
David Paltiel of Yale School of Public Health speaking to UPI about his paper that indicated that masks , social distancing , and testing college students every two days could limit the spread of SARS-CoV-2 on campuses this fall ( July @ @ @ @ @ @ @ to be spreading the coronavirus around , but it ’ s also kind of a catch-22 because now we ’ re not doing research on the very problem that caused us to get here .
—Ravinder Sehgal , a biologist at San Francisco State University , speaking to The Scientist about how a pandemic-related university travel ban limited his field research in infectious diseases ( August 20 ) I understand that the public is frustrated .
Even my family ’ s like , ‘ Can ’ t you figure it out ?
’ @ @ @ @ @ @ @ ] much faster than any time in history where we ’ ve had a big disease [ outbreak ] like that .
So I ’ m confident that the few months to come are going to be extremely informative .
—Miriam Merad , who directs the Precision Medicine Institute at Mount Sinai , speaking to The Scientist about the rapid pace of COVID-19-related research this year ( September 16 ) Now people are so confused about what science can give you—whether hydroxychloroquine works , it doesn ’ t work , it ’ s @ @ @ @ @ @ @ it ’ s going to be very difficult for us scientists then to use any type of article or publication .
Now that they know scientists can lie , who will believe us again ?
—Patricia García , a Solidarity Trial investigator and the former health minister of Peru , speaking with The Scientist in the wake of the Surgisphere scandal ( October 1 ) The federal government is paying Dr .
Bright , one of the nation ’ s leading experts in pandemic preparedness and response , and an internationally recognized expert @ @ @ @ @ @ @ sit on his hands during a global pandemic that has , to date , killed one million people globally and over 210,000 people within the United States .
—An amended whistleblower complaint filed by attorneys representing Rick Bright , an immunologist who resigned from his post at the National Institutes of Health on October 6 It is a great day for science .
It is a great day for humanity .
When you realize your vaccine has a 90 percent effectiveness , that ’ s overwhelming .
—Albert Bourla , chairman and chief @ @ @ @ @ @ @ after the firm announced preliminary results from a Phase 3 trial of its COVID-19 vaccine , developed in collaboration with BioNTech , that suggest it is 90 percent effective in preventing the disease ( November 9 )

ABOVE: Scanning electron micrograph of SARS-CoV-2 (gold) emerging from the surface of cells cultured in the lab. Image captured and colorized at NIAID’s Rocky Mountain Laboratories in Hamilton, Montana
FLICKR, NIAID
We can slow it down by canceling all these events, which we completely should do. But it’s still going to spread to most places.
—Maciej Boni, a biologist at Penn State University, speaking to The Scientist about how the high number of undetected cases makes it difficult to track viral spread based on confirmed infections (March 12)
It is important to screen the patients for neurological signs early and late in the course of COVID-19 . . . as this could be life-saving in our fight against COVID-19 pandemic.
—Abdul Mannan Baig, a researcher at Aga Khan University in Pakistan, speaking to The Scientist about indications that SARS-CoV-2 can target the nervous system (March 24)
It’s definitely scary as someone who is looking for another postdoc or potentially applying to faculty jobs to have this looming situation.
—Kishana Taylor, a postdoc in microbiology and molecular genetics at the University of California, Davis, speaking to The Scientist about pandemic-related hiring freezes in academia (March 26)
We all need to remember: people are more important than projects. Our safety and that of our broader community is more important than our individual lab’s work right now.
—Kathleen Millen, a neuroscientist at Seattle Children’s Hospital Research Institute, in an email to The Scientist about how pandemic-related lab shutdowns affected the scientific community (March 27)
A cryogenic electron microscope-based visualization of SARS-CoV-2 spike protein is helping researchers understand precise molecular interactions with antibodies. VISUALIZATION BY RUBEN DIAZ, BASED ON WORK BY DAVID VEESLER, UNIVERSITY OF WASHINGTON
This is going to be imprinted on the personality of our nation for a very long time.
—Anthony Fauci, director of the US National Institute of Allergy and Infectious Disease, speaking with CNN’s Sanjay Gupta about the effects of the COVID-19 pandemic on the psyches of his daughters and other Americans (April 1)
You know, the conspiracy theories out there have essentially closed down communication between scientists in China and scientists in the US. We need that communication in an outbreak to learn from them how they control it so we can control it better. It’s sad to say, but it will probably cost lives.
—Peter Daszak, president of the nonprofit EcoHealth Alliance, talking to “60 Minutes” about the ongoing politicization of science with regard to the COVID-19 pandemic (May 10)
Our prior studies have suggested that blocking receptor binding is a surefire way to neutralize the virus and come up with a protective antibody.
—Erica Ollmann Saphire, an immunologist at the La Jolla Institute for Immunology, speaking to The Scientist about the promise of antibody candidates that could prevent SARS-CoV-2 from entering cells (June 2)
This is what I wanted to do with my life—study viruses—and then to be at home and not have a lab [during a pandemic]. . . . It’s sort of like watching a ship pass you, and you really want to be on it.
—Jillian Carmichael, a postdoc in virologist Benhur Lee’s lab at Mount Sinai’s Icahn School of Medicine, speaking with The Scientist about missing out on research during the pandemic due to the closure of daycares and schools (June 25)
It’s extremely difficult at the beginning of an epidemic to get an accurate R0.
—Nelly Yatich, epidemiologist in Nairobi, Kenya, discussing with The Scientist the challenges of determining the basic reproductive number, R0, which describes the initial spread of an infection in a completely susceptible population (July 13)
I’ve been sick for three months, which just sounds so ridiculous to so many doctors.
—Hannah Davis, an artist living in Brooklyn, speaking to The Scientist about memory loss, sporadic bursts of blurred vision, a racing heart, difficulties breathing, insomnia, and various aches and pains that she experienced for months after testing positive for COVID-19 (July 17)
Ravinder Sehgal holds one of the birds he studied at a site in southwest Cameroon. COURTESY OF RAVINDER SEHGAL
Any school that cannot meet these minimum screening standards or maintain uncompromising control over good prevention practices has to ask itself if it has any business reopening.
—A. David Paltiel of Yale School of Public Health speaking to UPI about his paper that indicated that masks, social distancing, and testing college students every two days could limit the spread of SARS-CoV-2 on campuses this fall (July 31)
We don’t want to be spreading the coronavirus around, but it’s also kind of a catch-22 because now we’re not doing research on the very problem that caused us to get here.
—Ravinder Sehgal, a biologist at San Francisco State University, speaking to The Scientist about how a pandemic-related university travel ban limited his field research in infectious diseases (August 20)
I understand that the public is frustrated. Even my family’s like, ‘Can’t you figure it out?’ . . . We are [learning] much faster than any time in history where we’ve had a big disease [outbreak] like that. So I’m confident that the few months to come are going to be extremely informative.
—Miriam Merad, who directs the Precision Medicine Institute at Mount Sinai, speaking to The Scientist about the rapid pace of COVID-19-related research this year (September 16)
Rick Bright (center) with National Institute of Allergy and Infectious Diseases Director Anthony Fauci (left) and Marilyn Serafini, former president and co-CEO of the Alliance for Health Reform WIKIMEDIA, ALLIANCE FOR HEALTH POLICY
Now people are so confused about what science can give you—whether hydroxychloroquine works, it doesn’t work, it’s fake, it’s not fake—that it’s going to be very difficult for us scientists then to use any type of article or publication. Now that they know scientists can lie, who will believe us again?
—Patricia García, a Solidarity Trial investigator and the former health minister of Peru, speaking with The Scientist in the wake of the Surgisphere scandal (October 1)
The federal government is paying Dr. Bright, one of the nation’s leading experts in pandemic preparedness and response, and an internationally recognized expert in vaccine and diagnostic development, to sit on his hands during a global pandemic that has, to date, killed one million people globally and over 210,000 people within the United States.
—An amended whistleblower complaint filed by attorneys representing Rick Bright, an immunologist who resigned from his post at the National Institutes of Health on October 6
It is a great day for science. It is a great day for humanity. When you realize your vaccine has a 90 percent effectiveness, that’s overwhelming.
—Albert Bourla, chairman and chief executive of Pfizer, speaking to CNBC after the firm announced preliminary results from a Phase 3 trial of its COVID-19 vaccine, developed in collaboration with BioNTech, that suggest it is 90 percent effective in preventing the disease (November 9)


thescientist--2020-12-30--Promoting Effective Project Teams for Drug Discovery

Drug discovery is a difficult process .
It takes , on average , 10-12 years for an experimental drug to @ @ @ @ @ , only 1 in 1,000 drug candidates that enter preclinical testing move to human testing @ @ @ @ @ ten of those drugs getting to the market .
To further complicate the process , @ @ @ @ @ expertise must work together to generate multiple types of data .
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Drug discovery is a difficult process. It takes, on average, 10-12 years for an experimental drug to come to market. Moreover, only 1 in 1,000 drug candidates that enter preclinical testing move to human testing, with only one in ten of those drugs getting to the market. To further complicate the process, researchers with different areas of expertise must work together to generate multiple types of data. A good data management strategy is vital for making drug discovery more efficient and less costly.
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thescientist--2020-12-30--First US Case of UK SARS-CoV-2 Variant Detected

Colorado officials yesterday reported the first known US case , followed by an additional suspected case today ( December 30 ) , of the COVID-19 variant that has swept across the UK , leading dozens of countries to restrict UK arrivals .
Although the variant appears to transmit more efficiently between people , it is no more likely to cause a more severe infection , according to a preliminary report from Public Health England ( PHE ) released on Monday .
“ It didn ’ t teleport across the Atlantic , ” Harvard University epidemiologist William Hanage tells The New @ @ @ @ @ @ @ “ should not be cause for panic , ” he says , adding , “ it is cause to redouble our efforts at preventing the virus from getting the opportunity to spread.
” Both the confirmed case and the suspected case are members of the Colorado National Guard who had been deployed to help with a COVID-19 outbreak at the Good Samaritan Society assisted living facility in Simla , about 45 miles northeast of Colorado Springs , state health officials announced during a Wednesday news conference .
The confirmed case is a man @ @ @ @ @ @ @ history , according to a tweet from the office of Colorado governor Jared Polis .
Additional cases with the new variant will be detected in the United States in coming days , the US Centers for Disease Control and Prevention predicted in a statement to The Washington Post Tuesday .
The variant ’ s apparent increase in contagiousness “ could lead to more cases and place greater demand on already strained health care resources , ” the agency says .
Researchers had detected the more transmissible variant in at least 17 countries outside @ @ @ @ @ @ @ Australia , Canada , and South Korea .
“ Now I ’ m worried there will be another spring wave due to the variant , ” epidemiologist Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle tells Associated Press .
“ It ’ s a race with the vaccine , but now the virus has just gotten a little bit faster.
” It is unlikely that people who were previously infected with COVID-19 will be reinfected if exposed to the variant , according to the PHE report .
Experts say that @ @ @ @ @ @ @ against the variant .
The arrival of the new variant “ doesn ’ t fundamentally change the nature of the threat , ” Johns Hopkins Bloomberg School of Public Health epidemiologist Justin Lessler tells the Post .
“ It ’ s no more deadly than the virus was before , and it doesn ’ t look like it infects people who are immune.
” Lessler says he would be “ astounded ” if this were the only case of the variant in the US .
“ We know that the virus spreads easily @ @ @ @ @ @ @ says , and the patient ’ s lack of travel history indicates “ this strain has gotten here sometime in the past , and there are chains of transmission ongoing.
” Preliminary UK contact tracing data suggest that of people known to have been exposed to someone infected with the variant , 15.1 percent became infected , whereas those exposed to someone infected with other strains had a 9.8 percent infection rate .
That difference suggests the variant is more contagious , but PHE says it needs more data to confirm this .
@ @ @ @ @ @ @ in a separate study , published to a preprint server last week and not yet peer reviewed , that estimated that the variant , known as B.1.1.7 or VOC 202012/01 , is 56 percent more transmissible but not more severe or lethal than other variants .
Of the 17 mutations found in the variant , eight are in the segment of the virus ’ s genome that codes for the spike protein that protrudes from the virus and allows it to bind to cellular receptors and infiltrate cells , according to a preliminary @ @ @ @ @ @ @ .
Some scientists theorize these mutations may explain its enhanced transmissibility .
British public health officials first detected B.1.1.7 in September , meaning the variant has had ample time to spread outside the country .
Despite having the highest number of recorded cases in the world , the US sequences far fewer SARS-CoV-2 genomes than the UK , leading scientists to suspect that the variant may already have been spreading across the country undetected before yesterday ’ s announcement .
Harvard ’ s Hanage tells the Times that the US would have to @ @ @ @ @ @ @ of viruses to track their spread in real time .
“ The United States is hobbled by the inconsistency of its approach , ” he says .
“ Unless we turn on the lights , we won ’ t know it ’ s there.
” Many scientists say the arrival of B.1.1.7 is a wake-up call .
“ The lack of virus sequencing and case tracking in the US is a scandal , ” University of Massachusetts virologist Jeremy Luban tells the Post .

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Update (December 31): California officials announced a case of the variant in a 30-year-old San Diego County man who had not traveled outside the country, suggesting the virus was transmitted by someone else in the community. A household contact has also developed symptoms, officials said, and is being tested. Trevor Bedford, an evolutionary virologist at the Fred Hutchinson Cancer Research Center in Seattle tells The New York Times that he expects a similar trajectory of the variant in the US as in the UK: the variant accounts for few cases now, but might constitute the majority of cases in a few months, due to its increased transmissibility.
Colorado officials yesterday reported the first known US case, followed by an additional suspected case today (December 30), of the COVID-19 variant that has swept across the UK, leading dozens of countries to restrict UK arrivals. Although the variant appears to transmit more efficiently between people, it is no more likely to cause a more severe infection, according to a preliminary report from Public Health England (PHE) released on Monday.
“It didn’t teleport across the Atlantic,” Harvard University epidemiologist William Hanage tells The New York Times. The newly reported case “should not be cause for panic,” he says, adding, “it is cause to redouble our efforts at preventing the virus from getting the opportunity to spread.”
Both the confirmed case and the suspected case are members of the Colorado National Guard who had been deployed to help with a COVID-19 outbreak at the Good Samaritan Society assisted living facility in Simla, about 45 miles northeast of Colorado Springs, state health officials announced during a Wednesday news conference. The confirmed case is a man in his 20s that has no travel history, according to a tweet from the office of Colorado governor Jared Polis.
Additional cases with the new variant will be detected in the United States in coming days, the US Centers for Disease Control and Prevention predicted in a statement to The Washington Post Tuesday. The variant’s apparent increase in contagiousness “could lead to more cases and place greater demand on already strained health care resources,” the agency says.
Researchers had detected the more transmissible variant in at least 17 countries outside the UK as of Tuesday, including Australia, Canada, and South Korea.
“Now I’m worried there will be another spring wave due to the variant,” epidemiologist Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle tells Associated Press. “It’s a race with the vaccine, but now the virus has just gotten a little bit faster.”
It is unlikely that people who were previously infected with COVID-19 will be reinfected if exposed to the variant, according to the PHE report. Experts say that COVID-19 vaccines will most likely confer immunity against the variant.
The arrival of the new variant “doesn’t fundamentally change the nature of the threat,” Johns Hopkins Bloomberg School of Public Health epidemiologist Justin Lessler tells the Post. “It’s no more deadly than the virus was before, and it doesn’t look like it infects people who are immune.”
Lessler says he would be “astounded” if this were the only case of the variant in the US. “We know that the virus spreads easily and quickly between countries,” he says, and the patient’s lack of travel history indicates “this strain has gotten here sometime in the past, and there are chains of transmission ongoing.”
Preliminary UK contact tracing data suggest that of people known to have been exposed to someone infected with the variant, 15.1 percent became infected, whereas those exposed to someone infected with other strains had a 9.8 percent infection rate. That difference suggests the variant is more contagious, but PHE says it needs more data to confirm this.
PHE’s data mirror the findings in a separate study, published to a preprint server last week and not yet peer reviewed, that estimated that the variant, known as B.1.1.7 or VOC 202012/01, is 56 percent more transmissible but not more severe or lethal than other variants.
Of the 17 mutations found in the variant, eight are in the segment of the virus’s genome that codes for the spike protein that protrudes from the virus and allows it to bind to cellular receptors and infiltrate cells, according to a preliminary report on the variant published December 18. Some scientists theorize these mutations may explain its enhanced transmissibility.
British public health officials first detected B.1.1.7 in September, meaning the variant has had ample time to spread outside the country. Despite having the highest number of recorded cases in the world, the US sequences far fewer SARS-CoV-2 genomes than the UK, leading scientists to suspect that the variant may already have been spreading across the country undetected before yesterday’s announcement.
Harvard’s Hanage tells the Times that the US would have to improve how it monitors the genetic sequences of viruses to track their spread in real time. “The United States is hobbled by the inconsistency of its approach,” he says. “Unless we turn on the lights, we won’t know it’s there.”
Many scientists say the arrival of B.1.1.7 is a wake-up call. “The lack of virus sequencing and case tracking in the US is a scandal,” University of Massachusetts virologist Jeremy Luban tells the Post.