thescientist--2020-09-24--Y Chromosome from Early Modern Humans Replaced Neanderthal Y

ABOVE : Upper molar of a male Neanderthal from which researchers extracted Y chromosome DNA I. CREVECOEUR The Neanderthal Y chromosome is much more closely related to the Y of modern humans than to the Y of Denisovans , another archaic hominin that lived in Eurasia at the same time as Neanderthals , according to a study published today ( September 24 ) in Science .
This stands in stark contrast to the rest of the nuclear genome , which has clearly placed Neanderthals and Denisovans as sister groups in a lineage that split from the ancestors of modern humans @ @ @ @ @ @ @ Denisovans and the first high-coverage from Neanderthals—suggest that earlier Neanderthals had a Denisovan-like Y chromosome , but that this was replaced by the Y chromosome of modern humans after Neanderthals interbred with them between 370,000 and 100,000 years ago .
“ It ’ s a really a great surprise , ” says Mikkel Heide Schierup , an evolutionary biologist at Aarhus University who did not participate in the study but wrote an accompanying commentary .
Only a few percent of the rest of the Neanderthal genome appears to be made up of modern @ @ @ @ @ @ @ that three different Neanderthal individuals , unearthed at sites spread across Eurasia and dating to periods tens of thousands of years apart , all carried modern human–like Y chromosomes .
This suggests the widespread replacement of the Y across the Neanderthal population , he explains .
“ It ’ s a pretty dramatic event.
” Recent years have seen the publication of a handful of high-coverage Neanderthal and Denisovan genomes , but because they were female , there was very little , if any , sequence data on the archaic hominins ’ Y @ @ @ @ @ @ @ of Y chromosome makeup , computational biologist Janet Kelso of the Max Planck Institute for Evolutionary Anthropology and her colleagues dug deeper into samples from archaic male hominins that had been found over the years .
See “ Neanderthal DNA in Modern Human Genomes Is Not Silent ” From samples of three relatively recent Neanderthal remains , all dating to less than 53,000 years ago , and two older Denisovans , the researchers used various techniques to enrich for hominin DNA , and Kelso ’ s PhD student Martin Petr designed probes to @ @ @ @ @ @ @ The researchers then compiled about 7 million base pairs of sequence data for each archaic individual ’ s Y and compared the sequences with those from modern humans of African and non-African descent .
“ The most striking thing that immediately popped up is that all three Neanderthal Y chromosomes are more closely related to the modern human or present-day human Y chromosomes than the Denisovan Y chromosomes , ” says Petr .
While this wasn ’ t what the researchers were expecting , he notes that this is not the first time @ @ @ @ @ @ @ mitochondrial genome of Neanderthals is also more similar to the mitochondrial sequences of modern humans than to those of their sister group .
“ It is remarkable to see that both uniparental markers , so both [ the ] Y chromosome and mitochondrial DNA , they show the same story , ” says Cosimo Posth , a paleogeneticist at University of Tübingen in Germany .
In 2017 , he and colleagues analyzed material from a very early group of Neanderthals and revealed their mitochondrial DNA ( mtDNA ) to be more similar to @ @ @ @ @ @ @ led to what Petr says is “ currently the most widely accepted model ” for the patterns of mtDNA similarity : Neanderthals originally carried a Denisovan-like mitochondrial genome , but it was replaced by gene flow by mtDNA from an early lineage of modern humans that had left Africa and migrated to Eurasia , where they interbred with Neanderthals .
Petr , Kelso , and their colleagues suspect the Y chromosome followed a parallel fate .
“ I think it ’ s highly plausible that it could have happened at the same time @ @ @ @ @ @ @ event , but one period of time , ” Kelso says .
Tony Capra , an evolutionary geneticist at the University of California , San Francisco , who was not involved in the study , agrees .
“ I think that that definitely adds support to this hypothesis [ of replacement ] —that we see that same pattern with the Denisovan being the outgroup to the modern humans and Neanderthals for both the mitochondria and the Y chromosome.
” See “ Genetics Steps In to Help Tell the Story of Human Origins ” @ @ @ @ @ @ @ unlikely that both the mitochondrial genome and the Y chromosome spread through the Neanderthal population due to chance .
More probable is that the modern human DNA provided a selective advantage to those Neanderthals who carried it .
“ We don ’ t know what was the selective agent but it seems like you need one , ” Schierup tells The Scientist , “ because it ’ s a relatively short time ” to see a chromosome sweep through a population , with interbreeding with modern humans estimated to have taken place at @ @ @ @ @ @ @ ago and the modern Y chromosome becoming widespread by about 50,000 years ago .
Exactly when the replacement started is impossible to pin down at this point , however , notes Posth .
Petr ran several simulations that showed even a slight fitness advantage of the modern human Y would strongly favor its spread after introgression .
He explains that Neanderthals experienced long periods of very small population sizes , which makes natural selection less efficient at weeding out deleterious mutations .
Combined with the Y chromosome ’ s inability to recombine , @ @ @ @ @ @ @ Y had accumulated deleterious mutations that the modern human Y was free of .
Going forward , Petr , Kelso , and others say they hope that Y chromosome sequence data from older Neanderthal individuals will reveal if they carry the original Y chromosome before it was replaced by the modern human variety .
“ If we have good enough Y chromosomes , we could even compare the deleterious mutations , ” Kelso says , and see if the older Neanderthal Y chromosome did indeed have more .
“ That ’ s what @ @ @ @ @ @ @ ” says Capra , “ it makes a very specific prediction about what the Y chromosomes from the older Neanderthals should look like.
” He adds that he ’ d also like to see more functional analyses of the Y chromosome sequences we do have , for example , by looking at genetic differences between the Denisovan Y chromosome and the Y chromosomes of Neanderthals and modern humans .
“ I ’ m really curious to know what did these variants on these Y chromosomes do.
” The new findings highlight the dynamic @ @ @ @ @ @ @ .
“ We need to stop thinking of continents as isolated entities .
.
.
.
Through time , there ’ s been multiple contact between Africa and Eurasia , and this is leaving a trace , a detectable trace , in the genome of Neanderthals ” and of modern humans .
M. Petr et al.
, “ The evolutionary history of Neanderthal and Denisovan Y chromosomes , ” Science , 369:1653–56 , 2020 .

ABOVE: Upper molar of a male Neanderthal from which researchers extracted Y chromosome DNA
I. CREVECOEUR
The Neanderthal Y chromosome is much more closely related to the Y of modern humans than to the Y of Denisovans, another archaic hominin that lived in Eurasia at the same time as Neanderthals, according to a study published today (September 24) in Science. This stands in stark contrast to the rest of the nuclear genome, which has clearly placed Neanderthals and Denisovans as sister groups in a lineage that split from the ancestors of modern humans. The Y chromosome data—the first from Denisovans and the first high-coverage from Neanderthals—suggest that earlier Neanderthals had a Denisovan-like Y chromosome, but that this was replaced by the Y chromosome of modern humans after Neanderthals interbred with them between 370,000 and 100,000 years ago.
“It’s a really a great surprise,” says Mikkel Heide Schierup, an evolutionary biologist at Aarhus University who did not participate in the study but wrote an accompanying commentary. Only a few percent of the rest of the Neanderthal genome appears to be made up of modern human DNA, yet this study found that three different Neanderthal individuals, unearthed at sites spread across Eurasia and dating to periods tens of thousands of years apart, all carried modern human–like Y chromosomes. This suggests the widespread replacement of the Y across the Neanderthal population, he explains. “It’s a pretty dramatic event.”
Recent years have seen the publication of a handful of high-coverage Neanderthal and Denisovan genomes, but because they were female, there was very little, if any, sequence data on the archaic hominins’ Y chromosomes. To get a better understanding of Y chromosome makeup, computational biologist Janet Kelso of the Max Planck Institute for Evolutionary Anthropology and her colleagues dug deeper into samples from archaic male hominins that had been found over the years.
See “Neanderthal DNA in Modern Human Genomes Is Not Silent”
Matthias Meyer, a coauthor on the new study, works in the clean laboratory at the Max Planck Institute for Evolutionary Anthropology. MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY
From samples of three relatively recent Neanderthal remains, all dating to less than 53,000 years ago, and two older Denisovans, the researchers used various techniques to enrich for hominin DNA, and Kelso’s PhD student Martin Petr designed probes to specifically fish out Y chromosome sequences. The researchers then compiled about 7 million base pairs of sequence data for each archaic individual’s Y and compared the sequences with those from modern humans of African and non-African descent.
“The most striking thing that immediately popped up is that all three Neanderthal Y chromosomes are more closely related to the modern human or present-day human Y chromosomes than the Denisovan Y chromosomes,” says Petr. While this wasn’t what the researchers were expecting, he notes that this is not the first time researchers have seen this pattern; the mitochondrial genome of Neanderthals is also more similar to the mitochondrial sequences of modern humans than to those of their sister group.
“It is remarkable to see that both uniparental markers, so both [the] Y chromosome and mitochondrial DNA, they show the same story,” says Cosimo Posth, a paleogeneticist at University of Tübingen in Germany. In 2017, he and colleagues analyzed material from a very early group of Neanderthals and revealed their mitochondrial DNA (mtDNA) to be more similar to the Denisovan mitochondrial genome. This finding led to what Petr says is “currently the most widely accepted model” for the patterns of mtDNA similarity: Neanderthals originally carried a Denisovan-like mitochondrial genome, but it was replaced by gene flow by mtDNA from an early lineage of modern humans that had left Africa and migrated to Eurasia, where they interbred with Neanderthals.
Map showing the locations where the archaic individuals investigated in the new study were found and the estimated dates when they lived (ka ago = thousands of years ago) REPRINTED WITH PERMISSION FROM M. PETR ET AL., SCIENCE , 369:1653–56, 2020
Petr, Kelso, and their colleagues suspect the Y chromosome followed a parallel fate. “I think it’s highly plausible that it could have happened at the same time . . . maybe not one breeding event, but one period of time,” Kelso says.
Tony Capra, an evolutionary geneticist at the University of California, San Francisco, who was not involved in the study, agrees. “I think that that definitely adds support to this hypothesis [of replacement]—that we see that same pattern with the Denisovan being the outgroup to the modern humans and Neanderthals for both the mitochondria and the Y chromosome.”
See “Genetics Steps In to Help Tell the Story of Human Origins”
Researchers agree that it’s very unlikely that both the mitochondrial genome and the Y chromosome spread through the Neanderthal population due to chance. More probable is that the modern human DNA provided a selective advantage to those Neanderthals who carried it. “We don’t know what was the selective agent but it seems like you need one,” Schierup tells The Scientist, “because it’s a relatively short time” to see a chromosome sweep through a population, with interbreeding with modern humans estimated to have taken place at most only a few hundred thousand years ago and the modern Y chromosome becoming widespread by about 50,000 years ago. Exactly when the replacement started is impossible to pin down at this point, however, notes Posth.
View of the valley from above the Denisova Cave archaeological site, Russia B. VIOLA MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY
Petr ran several simulations that showed even a slight fitness advantage of the modern human Y would strongly favor its spread after introgression. He explains that Neanderthals experienced long periods of very small population sizes, which makes natural selection less efficient at weeding out deleterious mutations. Combined with the Y chromosome’s inability to recombine, it’s possible that the Neanderthal Y had accumulated deleterious mutations that the modern human Y was free of.
Going forward, Petr, Kelso, and others say they hope that Y chromosome sequence data from older Neanderthal individuals will reveal if they carry the original Y chromosome before it was replaced by the modern human variety. “If we have good enough Y chromosomes, we could even compare the deleterious mutations,” Kelso says, and see if the older Neanderthal Y chromosome did indeed have more.
“That’s what I really like about this result,” says Capra, “it makes a very specific prediction about what the Y chromosomes from the older Neanderthals should look like.” He adds that he’d also like to see more functional analyses of the Y chromosome sequences we do have, for example, by looking at genetic differences between the Denisovan Y chromosome and the Y chromosomes of Neanderthals and modern humans. “I’m really curious to know what did these variants on these Y chromosomes do.”
See “The Peopling of South America”
The new findings highlight the dynamic nature of hominin history, says Posth. “We need to stop thinking of continents as isolated entities. . . . Through time, there’s been multiple contact between Africa and Eurasia, and this is leaving a trace, a detectable trace, in the genome of Neanderthals” and of modern humans.
M. Petr et al., “The evolutionary history of Neanderthal and Denisovan Y chromosomes,” Science, 369:1653–56, 2020.


thescientist--2020-09-24--Astrocytes, Not Just Neurons, Play a Role in Sleep

ABOVE : Astrocytes in the mouse brain generate a fluorescent calcium indicator ( gold ) captured with a two-photon microscope .
ASHLEY INGIOSI , COURTESY OF CURRENT BIOLOGY For years , researchers have assumed that the signals in the brain that make mammals sleep come from neurons and that astrocytes , glial cells that outnumber neurons five to one in the brain , were following neuronal cues .
In a study published today ( September 24 ) in Current Biology , researchers show that calcium levels—a marker of signaling activity between cells—change in astrocytes as mice sleep and wake .
@ @ @ @ @ @ @ don ’ t make up for lost sleep like they normally do , indicating that these cells in the brain have much more influence on sleep than previously thought .
“ There was this idea for a long time .
.
.
that astrocytes were just glue , pulling the brain together and are more like passive cells , but it ’ s not true , ” says Sejal Davla , a postdoc at the City University of New York who was not involved in the work .
“ It was very intriguing @ @ @ @ @ @ @ you see in astrocytes are not directly coordinated with the neuronal activity .
It looks like the cells do something at their own rhythm in their own manner.
” Astrocytes use waves of calcium to talk to each other because they aren ’ t electrically excitable like neurons .
Around the time that Ashley Ingiosi started a postdoc in the lab of Marcos Frank , a neuroscientist at Washington State University , in 2015 , tools that enabled researchers to look at astrocytic calcium were just becoming available , including a fluorescent sensor @ @ @ @ @ @ @ to how much calcium is present in cells .
The elevation of calcium concentrations in an astrocyte is a form of activation , and this rise in calcium is a step in processes that allow astrocytes to communicate with each other and with other cell types , including neurons .
So the brighter the fluorescence , the more active the cells .
Ingiosi , Frank , and colleagues used those tools to explore how astrocytes behave during the sleep-wake cycle in mice .
They monitored calcium activity in the frontal cortex of mice @ @ @ @ @ @ @ which allowed them to get a detailed look at individual astrocytes .
And they fitted other animals with a miniscope—a microscope about as big as a Lego that attaches to the head—to monitor astrocyte activity as the animals moved and behaved as usual , including falling asleep and waking up .
With “ the miniscope on the head , they truly have freely behaving mice , ” says Philip Haydon , a neuroscientist at Tufts University and past collaborator of Frank who did not participate in the study .
“ They don ’ @ @ @ @ @ @ @ , so they ’ re actually seeing natural transitions between these states .
It takes us a long way to seeing what the astrocyte is doing.
” The researchers determined that astrocytic calcium was higher during wakefulness and lower during sleep , when calcium signals were also less synchronized among astrocytes .
When they sleep deprived mice , they saw an immediate increase in calcium levels when the mouse ’ s sleep need was highest .
They then dropped as the mice slept .
The synchrony of the calcium signals in astrocytes across @ @ @ @ @ @ @ not exactly in line with the synchronization of neuronal electrical activity .
If changes in astrocyte synchrony were driven by neurons , the authors write , they might have expected slower oscillations consistent with how neural activity changes in sleep , rather than less coordination among astrocytes .
“ In the past , it was thought that astrocytes were just passively responding to neuronal activity , ” Ingiosi says , “ but now that we see that the synchrony isn ’ t just mimicking what we see in terms of neuronal synchrony in @ @ @ @ @ @ @ that astrocytes might actually be playing a more direct role in regulating our sleep-wake behavior than we had previously considered.
” When the team monitored mice whose astrocytes were missing a protein that allows calcium into cells , these mice had lower levels of astrocytic calcium during waking , but they still spent about the same amount of time in various sleep states as wildtype mice did .
Sometimes , though , defects in sleep regulation don ’ t show up unless mice are kept awake , after which they respond to increased @ @ @ @ @ @ @ compensate for the sleep loss .
When the researchers sleep deprived the mice with impaired calcium entry , those animals slept less than sleep-deprived wildtype mice did , indicating that astrocytic calcium plays a role in regulating the compensatory response to sleep deprivation .
“ There ’ s a whole other level of brain organization that we were unaware of that is just as dynamic as neurons .
We never could measure it because all we had at the time were the tools that could measure neurons , ” says Frank .
In @ @ @ @ @ @ @ 6 , researchers also found a role for astrocytic calcium signaling in sleep .
Those authors used two-photon imaging and a different knockout mouse to show that astrocytic calcium is involved in regulating slow wave sleep .
Taken together , the two studies indicate that these cells may have more control over sleep than was previously believed .
“ It ’ s really nice when two independent groups come up with the same results .
It makes you want to believe them , ” says Haydon , adding that both studies point to @ @ @ @ @ @ @ With this paper and other recent work , the field is poised to tackle some fascinating , and interrelated , questions about the mechanisms by which astrocytes regulate neuronal activity in sleep , ” agrees Kira Poskanzer , a neuroscientist at the University of California , San Francisco , who did not participate in the study , in an email to The Scientist .
“ These mechanistic goals include identifying the intracellular signaling mechanisms in astrocytes that influence sleep , describing which specific features of sleep are astrocyte-mediated , characterizing the circuit mechanisms @ @ @ @ @ @ @ .
.
.
broad an influence astrocytes exert on the neuronal activity that defines sleep.
” A.M. Ingiosi et al.
, “ A role for astroglial calcium in mammalian sleep and sleep regulation , ” Current Biology , doi:10.1016/j.cub.2020.08.052 , 2020 .
Correction ( September 24 ) : The article has been updated to clarify how mice with impaired calcium entry in astrocytes respond to sleep deprivation .
The Scientist regrets the error .

ABOVE: Astrocytes in the mouse brain generate a fluorescent calcium indicator (gold) captured with a two-photon microscope.
ASHLEY INGIOSI, COURTESY OF CURRENT BIOLOGY
For years, researchers have assumed that the signals in the brain that make mammals sleep come from neurons and that astrocytes, glial cells that outnumber neurons five to one in the brain, were following neuronal cues. In a study published today (September 24) in Current Biology, researchers show that calcium levels—a marker of signaling activity between cells—change in astrocytes as mice sleep and wake. Without this cross-talk between astrocytes, mice don’t make up for lost sleep like they normally do, indicating that these cells in the brain have much more influence on sleep than previously thought.
“There was this idea for a long time . . . that astrocytes were just glue, pulling the brain together and are more like passive cells, but it’s not true,” says Sejal Davla, a postdoc at the City University of New York who was not involved in the work. “It was very intriguing to see that the activity patterns that you see in astrocytes are not directly coordinated with the neuronal activity. It looks like the cells do something at their own rhythm in their own manner.”
Astrocytes use waves of calcium to talk to each other because they aren’t electrically excitable like neurons. Around the time that Ashley Ingiosi started a postdoc in the lab of Marcos Frank, a neuroscientist at Washington State University, in 2015, tools that enabled researchers to look at astrocytic calcium were just becoming available, including a fluorescent sensor that glows with an intensity that corresponds to how much calcium is present in cells. The elevation of calcium concentrations in an astrocyte is a form of activation, and this rise in calcium is a step in processes that allow astrocytes to communicate with each other and with other cell types, including neurons. So the brighter the fluorescence, the more active the cells.
Ingiosi, Frank, and colleagues used those tools to explore how astrocytes behave during the sleep-wake cycle in mice. They monitored calcium activity in the frontal cortex of mice held in place for two-photon imaging, which allowed them to get a detailed look at individual astrocytes. And they fitted other animals with a miniscope—a microscope about as big as a Lego that attaches to the head—to monitor astrocyte activity as the animals moved and behaved as usual, including falling asleep and waking up.
With “the miniscope on the head, they truly have freely behaving mice,” says Philip Haydon, a neuroscientist at Tufts University and past collaborator of Frank who did not participate in the study. “They don’t have to put them under anesthesia, so they’re actually seeing natural transitions between these states. It takes us a long way to seeing what the astrocyte is doing.”
The researchers determined that astrocytic calcium was higher during wakefulness and lower during sleep, when calcium signals were also less synchronized among astrocytes. When they sleep deprived mice, they saw an immediate increase in calcium levels when the mouse’s sleep need was highest. They then dropped as the mice slept.
The synchrony of the calcium signals in astrocytes across sleep states and after sleep deprivation was not exactly in line with the synchronization of neuronal electrical activity. If changes in astrocyte synchrony were driven by neurons, the authors write, they might have expected slower oscillations consistent with how neural activity changes in sleep, rather than less coordination among astrocytes.
“In the past, it was thought that astrocytes were just passively responding to neuronal activity,” Ingiosi says, “but now that we see that the synchrony isn’t just mimicking what we see in terms of neuronal synchrony in the brain across states that tells us that astrocytes might actually be playing a more direct role in regulating our sleep-wake behavior than we had previously considered.”
There’s a whole other level of brain organization that we were unaware of that is just as dynamic as neurons. —Marcos Frank, Washington State University
When the team monitored mice whose astrocytes were missing a protein that allows calcium into cells, these mice had lower levels of astrocytic calcium during waking, but they still spent about the same amount of time in various sleep states as wildtype mice did. Sometimes, though, defects in sleep regulation don’t show up unless mice are kept awake, after which they respond to increased sleep pressure by sleeping for longer to compensate for the sleep loss. When the researchers sleep deprived the mice with impaired calcium entry, those animals slept less than sleep-deprived wildtype mice did, indicating that astrocytic calcium plays a role in regulating the compensatory response to sleep deprivation.
“There’s a whole other level of brain organization that we were unaware of that is just as dynamic as neurons. We never could measure it because all we had at the time were the tools that could measure neurons,” says Frank.
In another paper published in Nature Communications July 6, researchers also found a role for astrocytic calcium signaling in sleep. Those authors used two-photon imaging and a different knockout mouse to show that astrocytic calcium is involved in regulating slow wave sleep. Taken together, the two studies indicate that these cells may have more control over sleep than was previously believed.
“It’s really nice when two independent groups come up with the same results. It makes you want to believe them,” says Haydon, adding that both studies point to a range of open questions.
“With this paper and other recent work, the field is poised to tackle some fascinating, and interrelated, questions about the mechanisms by which astrocytes regulate neuronal activity in sleep,” agrees Kira Poskanzer, a neuroscientist at the University of California, San Francisco, who did not participate in the study, in an email to The Scientist. “These mechanistic goals include identifying the intracellular signaling mechanisms in astrocytes that influence sleep, describing which specific features of sleep are astrocyte-mediated, characterizing the circuit mechanisms that astrocytes regulate, and defining how . . . broad an influence astrocytes exert on the neuronal activity that defines sleep.”
A.M. Ingiosi et al., “A role for astroglial calcium in mammalian sleep and sleep regulation,” Current Biology, doi:10.1016/j.cub.2020.08.052, 2020.
Correction (September 24): The article has been updated to clarify how mice with impaired calcium entry in astrocytes respond to sleep deprivation. The Scientist regrets the error.


thescientist--2020-09-25--Thwarting AAV-Neutralizing Antibodies Could Improve Gene Therapy

A little more than a decade ago , seven patients with hemophilia B—a disease caused by a mutation on the F9 gene that prevents patients from forming crucial clotting proteins—volunteered to be the first humans to receive a gene therapy delivered using an adeno-associated virus as a vector .
This particular treatment didn ’ t move past the Phase 1/2 trial because , while it was deemed safe , the patients did not sustain expression of the gene .
But two other gene therapies based on an adeno-associated virus ( AAV ) , Luxturna for rare forms of blindness and @ @ @ @ @ @ @ since been approved by the US Food and Drug Administration ( FDA ) , and several pharmaceutical companies are now pursuing regulatory approval of AAV-carried gene therapies for hemophilia B .
Recently , scientists followed up with four of those original patients .
In a study published in Molecular Therapy in September , they report that the men are still free of any worrisome toxicities related to the treatment .
The study wasn ’ t all good news , though .
The team also found that after all these years , the men @ @ @ @ @ @ @ .
That means that if an AAV gene therapy is approved to treat their illness , they likely won ’ t be able to benefit from it—the antibodies would chew up the vector before it could insert the corrective gene .
Administration of an AAV gene therapy is essentially a vaccine against AAV , says Lindsey George , a hematologist at the Children ’ s Hospital of Philadelphia who led the research .
Hers was not the first study to identify antibodies as a problem for those receiving AAV gene therapies , but @ @ @ @ @ @ @ elevated titers can last this long .
“ This role of AAV neutralizing antibodies is huge , ” says George , as it stands to undermine the effectiveness of gene therapies .
Because AAVs are viruses , the human immune system creates antibodies upon exposure that recognize and neutralize them in subsequent encounters .
Sometimes patients have neutralizing antibodies in their blood before ever having received a gene therapy because they ’ re exposed to AAVs in the environment .
Along with high levels of antibodies to the specific AAV vector that they @ @ @ @ @ @ @ team evaluated also had neutralizing antibodies to several other commonly used AAV vectors , namely , AAV5 and AAV8 , she tells The Scientist .
Andrew Davidoff , a pediatric surgeon at St. Jude Children ’ s Research Hospital who studies AAV gene therapies but was not involved in the study , says , “ This paper suggests that not only will they not be able to receive a second dose of vector of the same [ type of AAV ] , but potentially even other [ types ] .
” If scientists @ @ @ @ @ @ @ , they would not only give patients like these another opportunity to receive a more effective dose of gene therapy , but “ it will expand the patients that we can treat with the therapy ” to include the 30–50 percent of patients who have already been exposed to AAVs in the environment , says Giuseppe Ronzitti , who heads a lab focused on gene therapy research at Genethon .
But , Davidoff says , “ nobody has found a suitable solution yet that is likely to be accepted by patients .
The @ @ @ @ @ @ @ , this immune system that helps fight off infections .
So to overcome that , even temporarily , is not an easy task.
” Some immunosuppressant drugs won ’ t work if the body has already developed specific antibodies to a particular pathogen , such as AAV .
Scientists are therefore testing combinations of different types of immunosuppressants they hope will prevent the body from attacking AAVs , but these are likely to come with major risks , chiefly , susceptibility to infection .
Another option is plasmapheresis—a process in which a person @ @ @ @ @ @ @ body and the cells separated from the plasma so that they can be reinfused without the antibodies found in the plasma—but , like immunosuppressant drugs , the technique is nonspecific and comes with similar risks .
“ It ’ s a matter of risk-benefit with the continued immunosuppression , ” says Ronzitti .
So scientists have been looking for other ways to control the body ’ s response to these gene therapy vectors .
Ronzitti and his team recently proposed a solution in Nature Medicine .
The scientists used the imlifidase ( IdeS @ @ @ @ @ @ @ European Commission , to degrade immunoglobulin G ( IgG ) antibodies that are developed after the body encounters a specific antigen so that it can remember and target that antigen in the future , and thus might cause a patient to reject a transplanted kidney .
IgG antibodies are responsible for the immune system ’ s response to AAVs .
It ’ s a “ newer , less invasive alternative to plasmapheresis , ” Ronzitti tells The Scientist in an email .
The team injected monkeys with the IdeS protein before administering a @ @ @ @ @ @ @ .
The treatment appeared safe , the monkeys ’ levels of preexisting AAV antibodies went down , and the AAV vector successfully made its way to the liver .
To model a scenario in which a patient would need more than one dose of gene therapy , the scientists administered an AAV gene therapy to another group of monkeys before giving them the IdeS protein to degrade the antibodies they ’ d developed in response , then readministered the gene therapy .
Again , AAV antibodies diminished after the IdeS treatment and the @ @ @ @ @ @ @ .
One drawback to the approach is that IgGs are the most prevalent type of antibody found in the blood , and destroying all of them may have undesirable side effects .
In an attempt to develop a more targeted therapy , one group published a study in January demonstrating that a specialized version of plasmapheresis could reduce the levels of antibodies against human AAVs in mice to the point where a new gene therapy should be effective , without depleting all other immunoglobulins that formed in response to infections .
More recently @ @ @ @ @ @ @ University of Pittsburgh Medical Center made use of CRISPR-Cas9 to increase the efficacy of AAV gene therapy in mice .
Pathologist Samira Kiani and her team weren ’ t looking for ways to improve gene therapy , but instead were seeking to temporarily modulate immunity in hopes of changing the course of diseases such as septicemia , a precursor to sepsis that occurs when an infection makes its way to the blood .
The researchers aimed to temporarily downregulate the Myeloid differentiation primary response 88 ( Myd88 ) gene , which would briefly @ @ @ @ @ @ @ remove the brakes .
“ The gene that we chose to target is known to a be a central gene for innate and adaptive immunity , ” says Kiani .
It controls the production of IgG antibodies in response to AAV exposure , which provided a simple way to measure whether the strategy was effective .
If the team administered an AAV to an animal shortly after it had received the CRISPR-Cas9 treatment , it should have a substantially lower antibody response to the virus .
First , they administered the CRISPR to @ @ @ @ @ @ @ reduction in the expression of the Myd88 gene , as they ’ d expected .
Then , the team used the technique to treat mice just before giving them a dose of AAV-based gene therapy that was designed to lower their cholesterol .
Weeks later , the researchers administered a second dose of the same AAV vector to determine if the temporary immunosuppression during the first dose had prevented the mice from making enough antibodies to thwart a second dose .
The mice that were pretreated with the immune-modulating CRISPR showed lower levels @ @ @ @ @ @ @ to the cholesterol-lowering AAV treatment .
The study was published in Nature Cell Biology in September .
If given prior to the administration of an AAV gene therapy , “ this approach would prevent the formation of new antibodies , ” so the patient could receive a second dose later , if needed , says Kiani .
Given that the CRISPR treatment only prevents the development of antibodies temporarily , it shouldn ’ t cause any long-term suppression of the rest of the immune system .
On the flip side , because it @ @ @ @ @ @ @ “ if the patients have already pre-existing antibodies [ from natural exposure ] this approach might not be the best approach.
” All of the potential solutions have a long way to go , including still needing to be tested in human patients , but the ability to effectively modulate the antibody-mediated immune response could make AAV gene therapies far more effective for far more patients than they are now , says Ronzitti .
The immune response to these vectors is “ quite a complex story , ” he says .
“ But @ @ @ @ @ @ @ one.
” L. George et al.
, “ Long-term follow-up of the first in human intravascular delivery of AAV for gene transfer : AAV2-hFIX16 for severe hemophilia B , ” Molecular Therapy , doi:10.1016/j.ymthe.2020.06.001 , 2020 .
F. Moghadam et al.
, “ Synthetic immunomodulation with a CRISPR super-repressor in vivo , ” Nature Cell Biology , doi:10.1038/s41556-020-0563-3 , 2020 .

ABOVE: Illustration of adeno-associated virus
© ISTOCK.COM, YABUSAKA DESIGN
A little more than a decade ago, seven patients with hemophilia B—a disease caused by a mutation on the F9 gene that prevents patients from forming crucial clotting proteins—volunteered to be the first humans to receive a gene therapy delivered using an adeno-associated virus as a vector. This particular treatment didn’t move past the Phase 1/2 trial because, while it was deemed safe, the patients did not sustain expression of the gene. But two other gene therapies based on an adeno-associated virus (AAV), Luxturna for rare forms of blindness and Zolgensma for spinal muscular atrophy, have since been approved by the US Food and Drug Administration (FDA), and several pharmaceutical companies are now pursuing regulatory approval of AAV-carried gene therapies for hemophilia B.
Recently, scientists followed up with four of those original patients. In a study published in Molecular Therapy in September, they report that the men are still free of any worrisome toxicities related to the treatment. The study wasn’t all good news, though. The team also found that after all these years, the men still had elevated levels of AAV-neutralizing antibodies. That means that if an AAV gene therapy is approved to treat their illness, they likely won’t be able to benefit from it—the antibodies would chew up the vector before it could insert the corrective gene.
Administration of an AAV gene therapy is essentially a vaccine against AAV, says Lindsey George, a hematologist at the Children’s Hospital of Philadelphia who led the research. Hers was not the first study to identify antibodies as a problem for those receiving AAV gene therapies, but it is the first to show that elevated titers can last this long. “This role of AAV neutralizing antibodies is huge,” says George, as it stands to undermine the effectiveness of gene therapies.
Because AAVs are viruses, the human immune system creates antibodies upon exposure that recognize and neutralize them in subsequent encounters. Sometimes patients have neutralizing antibodies in their blood before ever having received a gene therapy because they’re exposed to AAVs in the environment.
The ability to effectively modulate the antibody-mediated immune response could make AAV gene therapies far more effective for far more patients than they are now.
Along with high levels of antibodies to the specific AAV vector that they’d received—AAV2—the patients George’s team evaluated also had neutralizing antibodies to several other commonly used AAV vectors, namely, AAV5 and AAV8, she tells The Scientist.
Andrew Davidoff, a pediatric surgeon at St. Jude Children’s Research Hospital who studies AAV gene therapies but was not involved in the study, says, “This paper suggests that not only will they not be able to receive a second dose of vector of the same [type of AAV], but potentially even other [types].”
If scientists can prevent antibodies from neutralizing the AAV, they would not only give patients like these another opportunity to receive a more effective dose of gene therapy, but “it will expand the patients that we can treat with the therapy” to include the 30–50 percent of patients who have already been exposed to AAVs in the environment, says Giuseppe Ronzitti, who heads a lab focused on gene therapy research at Genethon.
But, Davidoff says, “nobody has found a suitable solution yet that is likely to be accepted by patients. The body has evolved over millions of years, this immune system that helps fight off infections. So to overcome that, even temporarily, is not an easy task.”
Some immunosuppressant drugs won’t work if the body has already developed specific antibodies to a particular pathogen, such as AAV. Scientists are therefore testing combinations of different types of immunosuppressants they hope will prevent the body from attacking AAVs, but these are likely to come with major risks, chiefly, susceptibility to infection.
Another option is plasmapheresis—a process in which a person’s blood is removed from the body and the cells separated from the plasma so that they can be reinfused without the antibodies found in the plasma—but, like immunosuppressant drugs, the technique is nonspecific and comes with similar risks. “It’s a matter of risk-benefit with the continued immunosuppression,” says Ronzitti.
So scientists have been looking for other ways to control the body’s response to these gene therapy vectors.
Degradation or prevention of AAV antibodies
Ronzitti and his team recently proposed a solution in Nature Medicine. The scientists used the imlifidase (IdeS) protein, conditionally approved by the European Commission, to degrade immunoglobulin G (IgG) antibodies that are developed after the body encounters a specific antigen so that it can remember and target that antigen in the future, and thus might cause a patient to reject a transplanted kidney. IgG antibodies are responsible for the immune system’s response to AAVs. It’s a “newer, less invasive alternative to plasmapheresis,” Ronzitti tells The Scientist in an email.
The team injected monkeys with the IdeS protein before administering a dose of gene therapy targeting the liver. The treatment appeared safe, the monkeys’ levels of preexisting AAV antibodies went down, and the AAV vector successfully made its way to the liver. To model a scenario in which a patient would need more than one dose of gene therapy, the scientists administered an AAV gene therapy to another group of monkeys before giving them the IdeS protein to degrade the antibodies they’d developed in response, then readministered the gene therapy. Again, AAV antibodies diminished after the IdeS treatment and the second gene therapy dose was successfully delivered.
One drawback to the approach is that IgGs are the most prevalent type of antibody found in the blood, and destroying all of them may have undesirable side effects. In an attempt to develop a more targeted therapy, one group published a study in January demonstrating that a specialized version of plasmapheresis could reduce the levels of antibodies against human AAVs in mice to the point where a new gene therapy should be effective, without depleting all other immunoglobulins that formed in response to infections.
More recently, a team of researchers at the University of Pittsburgh Medical Center made use of CRISPR-Cas9 to increase the efficacy of AAV gene therapy in mice. Pathologist Samira Kiani and her team weren’t looking for ways to improve gene therapy, but instead were seeking to temporarily modulate immunity in hopes of changing the course of diseases such as septicemia, a precursor to sepsis that occurs when an infection makes its way to the blood. The researchers aimed to temporarily downregulate the Myeloid differentiation primary response 88 (Myd88) gene, which would briefly dampen the immune response, and then remove the brakes.
“The gene that we chose to target is known to a be a central gene for innate and adaptive immunity,” says Kiani. It controls the production of IgG antibodies in response to AAV exposure, which provided a simple way to measure whether the strategy was effective. If the team administered an AAV to an animal shortly after it had received the CRISPR-Cas9 treatment, it should have a substantially lower antibody response to the virus.
First, they administered the CRISPR to tamp down Myd88 activity and measured a reduction in the expression of the Myd88 gene, as they’d expected. Then, the team used the technique to treat mice just before giving them a dose of AAV-based gene therapy that was designed to lower their cholesterol.
Weeks later, the researchers administered a second dose of the same AAV vector to determine if the temporary immunosuppression during the first dose had prevented the mice from making enough antibodies to thwart a second dose. The mice that were pretreated with the immune-modulating CRISPR showed lower levels of AAV-neutralizing antibodies and more dramatic responses to the cholesterol-lowering AAV treatment. The study was published in Nature Cell Biology in September.
If given prior to the administration of an AAV gene therapy, “this approach would prevent the formation of new antibodies,” so the patient could receive a second dose later, if needed, says Kiani. Given that the CRISPR treatment only prevents the development of antibodies temporarily, it shouldn’t cause any long-term suppression of the rest of the immune system. On the flip side, because it doesn’t clear existing antibodies, “if the patients have already pre-existing antibodies [from natural exposure] this approach might not be the best approach.”
All of the potential solutions have a long way to go, including still needing to be tested in human patients, but the ability to effectively modulate the antibody-mediated immune response could make AAV gene therapies far more effective for far more patients than they are now, says Ronzitti. The immune response to these vectors is “quite a complex story,” he says. “But we are solving the issues one by one.”
L. George et al., “Long-term follow-up of the first in human intravascular delivery of AAV for gene transfer: AAV2-hFIX16 for severe hemophilia B,” Molecular Therapy, doi:10.1016/j.ymthe.2020.06.001, 2020.
F. Moghadam et al., “Synthetic immunomodulation with a CRISPR super-repressor in vivo,” Nature Cell Biology, doi:10.1038/s41556-020-0563-3, 2020.


thescientist--2020-09-25--Understanding and Optimizing PCR

Understanding and Optimizing PCR

PCR is one of the most commonly used techniques in biological studies .
However , its ubiquity belies its complexity @ @ @ @ @ of moving parts to every PCR experiment , including DNA template , primers , reagents @ @ @ @ @ Each of these parts has a specific role and purpose .
Difficulties with any of @ @ @ @ @ end-products in specific ways .
Download this eBook from The Scientist 's Creative Services team @ @ @ @

PCR is one of the most commonly used techniques in biological studies. However, its ubiquity belies its complexity. There are a lot of moving parts to every PCR experiment, including DNA template, primers, reagents, and cycling conditions. Each of these parts has a specific role and purpose. Difficulties with any of the reaction components affect PCR end-products in specific ways.
Download this eBook from The Scientist's Creative Services team and Merck to explore


thescientist--2020-09-25--Western Blot Protein Detection: Enzymatic vs. Fluorescence Methods

Western blotting is a popular technique in cell and molecular biology for detecting proteins .
Historically , researchers used a @ @ @ @ @ detect binding .
With advances in technology such as charge-coupled devices and new labels , @ @ @ @ @ and chemifluorescence are becoming more common .
Scientists must consider cost , equipment and reagent @ @ @ @ @ detection parameters required before deciding on a detection method .
Download this article from Analytik @ @ @ @ @ The major differences between enzymatic and fluorescence methods • When to use chemiluminescent , colorimetric @ @ @ @ @ detection

Western blotting is a popular technique in cell and molecular biology for detecting proteins. Historically, researchers used a chemiluminescent signal and darkrooms to detect binding. With advances in technology such as charge-coupled devices and new labels, other detection methods including fluorescence and chemifluorescence are becoming more common. Scientists must consider cost, equipment and reagent availability, and the specific detection parameters required before deciding on a detection method.
Download this article from Analytik Jena to learn about


thescientist--2020-09-25--p53 as an Immune System Modulator in Cancer

p53 is best known as a cell cycle regulator and an initiator of apoptosis and senescence .
p53 dysfunction often @ @ @ @ @ , the relationship between p53 and oncogenesis goes beyond cell cycle dysregulation .
In homeostatic @ @ @ @ @ prominent immune regulator , from facilitating effector cell recognition to stimulating paracrine activity .
As @ @ @ @ @ only unshackle cancer cell proliferation , but also aid tumorigenesis , growth , and metastasis @ @ @ @ @ deleterious ways .
Characterizing this immune function is essential in order to identify the unique @ @ @ @ @ .
IsoPlexis ’ platform is able to identify these rare cell subsets which correlate to @ @ @ @ @ to disease progression , enabling and accelerating the development of curative medicines .
Download this @ @ @ @ @ more about the p53-mediated pathways that impact immune system responses to cancer .

p53 is best known as a cell cycle regulator and an initiator of apoptosis and senescence. p53 dysfunction often leads to cancer; however, the relationship between p53 and oncogenesis goes beyond cell cycle dysregulation. In homeostatic conditions, p53 is a prominent immune regulator, from facilitating effector cell recognition to stimulating paracrine activity. As such, p53 mutations not only unshackle cancer cell proliferation, but also aid tumorigenesis, growth, and metastasis by impacting immune function in deleterious ways. Characterizing this immune function is essential in order to identify the unique superhero and supervillain cell subsets. IsoPlexis’ platform is able to identify these rare cell subsets which correlate to anti-tumor response or those contributing to disease progression, enabling and accelerating the development of curative medicines.
Download this poster from IsoPlexis to learn more about the p53-mediated pathways that impact immune system responses to cancer.


thescientist--2020-09-25--Robert Simoni, Cellular Membrane Biochemist, Dies at 81

Robert Simoni , a biochemist at Stanford University whose research helped illustrate how cholesterol is metabolized by mammalian cells , died September 18 at age 81 after undergoing a recent surgery .
Simoni spent much of his professional career working at Stanford , first as a researcher and later as chair of the biology department , chair of the Faculty Senate , and acting provost , before retiring in 2013 .
His scientific contributions earned him a Fulbright Fellowship and a Research Career Development Award from the National Institutes of Health ( NIH ) , while his administrative work was @ @ @ @ @ @ @ highest awards , the Kenneth M. Cuthbertson Award for Exceptional Contributions to Stanford .
“ We have a large department , about 60 faculty members , and I think I ’ ve had at least 30 emails passed through .
Everybody has a very personal story to tell about how Bob touched them , ” Martha Cyert , the current chair of Stanford ’ s biology department , tells The Scientist .
“ He recruited a lot of us when he was chair of the department , and he was just so knowledgeable @ @ @ @ @ @ @ to Bob when you had a problem.
” Born in San Jose , California , in 1939 , Simoni credited an “ unusually inspirational ” high school science teacher for his initial interest in science , according to a 2014 interview with the Stanford Historical Society .
He attended San Jose State College , where he majored in biology .
Initially , Simoni struggled to find his niche , considering dentistry before he failed the required dexterity test .
Having enjoyed his biochemistry classes at San Jose State , Simoni completed a PhD @ @ @ @ @ @ @ , Davis , studying the synthesis of fatty acids in plants .
Following his graduation in 1966 , Simoni worked for several years researching the structure and function of cell membranes at Johns Hopkins University , first as a postdoc and later as a research associate .
In 1971 , he returned to California to join the faculty at Stanford University , where he taught introductory biochemistry to more than 16,000 students over the next four decades .
In an interview with the Stanford Daily ahead of his retirement at 74 , Simoni @ @ @ @ @ @ @ sustained me the entire [ 41 ] years I ’ ve been at Stanford.
” At the end of his final lecture , he received a sendoff from the Stanford Marching Band , flanked by colleagues who had affectionately donned wigs emblematic of Simoni ’ s signature curly , white hair .
As a researcher , Simoni is most well-known for his studies of cholesterol , a critical component of mammalian cell membranes .
“ Bob was very much a basic scientist looking for fundamental information , but some of his biggest contributions @ @ @ @ @ @ @ involved in making cholesterol and all the different mechanisms that lead to their regulation , ” Cyert says .
Simoni ’ s work helped show that the production of cholesterol in mammalian cells is controlled by regulating both the synthesis and the degradation of the first enzyme in the biosynthetic pathway , 3-hydroxy-3-methyl-glutaryl-CoA reductase .
When these systems become dysregulated , imbalances in cholesterol production that cause health problems such as cardiovascular disease can result .
After publishing many of his papers in the Journal of Biological Chemistry , Simoni became a member @ @ @ @ @ @ @ as an associate editor .
In the early 1990s , he helped the journal transition from a print publication to a digital format , the first journal to do so , ushering in a new era of academic publishing .
Later in his career , Simoni also began to take on administrative duties .
As chair of the biology department , he was involved in the hiring of new faculty and played a key role in the building of both the Gilbert Biological Sciences Building and the Anne T. and Robert M. Bass @ @ @ @ @ @ @ house the department today .
In addition , Simoni served as the principal investigator on an NIH-funded grant that paid for training for the department ’ s graduate students for more than 30 years .
“ Those are a lot of work , ” Cyert tells The Scientist .
“ I took over for him , so I am uniquely qualified to say what a great job he did running that.
” In 1994 , Simoni became the chair of the Faculty Senate , a group he was a part of for more @ @ @ @ @ @ @ , he pushed for grading policy reform after a nationwide reckoning with widespread college grade inflation , debated the teaching of western civilization courses as a requirement , and oversaw a science core curriculum reform .
Speaking to the Stanford Daily ahead of his retirement at age 74 , Simoni reflected back on his long career .
“ When I first started , it was traditional that people retired at the age of 65—in fact , it was mandatory .
I never really thought I ’ d work this long , but I @ @ @ @ @ @ @ teaching so much.
” Simoni is survived by his wife of 59 years , Diane Simoni , his three children , and five grandchildren .

Robert Simoni Linda A. Cicero / Stanford News Service
Robert Simoni, a biochemist at Stanford University whose research helped illustrate how cholesterol is metabolized by mammalian cells, died September 18 at age 81 after undergoing a recent surgery.
Simoni spent much of his professional career working at Stanford, first as a researcher and later as chair of the biology department, chair of the Faculty Senate, and acting provost, before retiring in 2013. His scientific contributions earned him a Fulbright Fellowship and a Research Career Development Award from the National Institutes of Health (NIH), while his administrative work was acknowledged with one of Stanford’s highest awards, the Kenneth M. Cuthbertson Award for Exceptional Contributions to Stanford.
“We have a large department, about 60 faculty members, and I think I’ve had at least 30 emails passed through. Everybody has a very personal story to tell about how Bob touched them,” Martha Cyert, the current chair of Stanford’s biology department, tells The Scientist. “He recruited a lot of us when he was chair of the department, and he was just so knowledgeable. You never felt hesitant about coming to Bob when you had a problem.”
Born in San Jose, California, in 1939, Simoni credited an “unusually inspirational” high school science teacher for his initial interest in science, according to a 2014 interview with the Stanford Historical Society. He attended San Jose State College, where he majored in biology. Initially, Simoni struggled to find his niche, considering dentistry before he failed the required dexterity test. Having enjoyed his biochemistry classes at San Jose State, Simoni completed a PhD in biochemistry at the University of California, Davis, studying the synthesis of fatty acids in plants.
Following his graduation in 1966, Simoni worked for several years researching the structure and function of cell membranes at Johns Hopkins University, first as a postdoc and later as a research associate.
In 1971, he returned to California to join the faculty at Stanford University, where he taught introductory biochemistry to more than 16,000 students over the next four decades. In an interview with the Stanford Daily ahead of his retirement at 74, Simoni said, “teaching that class has sustained me the entire [41] years I’ve been at Stanford.” At the end of his final lecture, he received a sendoff from the Stanford Marching Band, flanked by colleagues who had affectionately donned wigs emblematic of Simoni’s signature curly, white hair.
Robert Simoni receives a surprise at the end of his final introductory biochemistry lecture after teaching the class for 41 years. stanford university
As a researcher, Simoni is most well-known for his studies of cholesterol, a critical component of mammalian cell membranes. “Bob was very much a basic scientist looking for fundamental information, but some of his biggest contributions are understanding these key proteins that are involved in making cholesterol and all the different mechanisms that lead to their regulation,” Cyert says.
Simoni’s work helped show that the production of cholesterol in mammalian cells is controlled by regulating both the synthesis and the degradation of the first enzyme in the biosynthetic pathway, 3-hydroxy-3-methyl-glutaryl-CoA reductase. When these systems become dysregulated, imbalances in cholesterol production that cause health problems such as cardiovascular disease can result.
After publishing many of his papers in the Journal of Biological Chemistry, Simoni became a member of the editorial board and later served as an associate editor. In the early 1990s, he helped the journal transition from a print publication to a digital format, the first journal to do so, ushering in a new era of academic publishing.
Later in his career, Simoni also began to take on administrative duties. As chair of the biology department, he was involved in the hiring of new faculty and played a key role in the building of both the Gilbert Biological Sciences Building and the Anne T. and Robert M. Bass Biology Research Building, both of which house the department today. In addition, Simoni served as the principal investigator on an NIH-funded grant that paid for training for the department’s graduate students for more than 30 years. “Those are a lot of work,” Cyert tells The Scientist. “I took over for him, so I am uniquely qualified to say what a great job he did running that.”
In 1994, Simoni became the chair of the Faculty Senate, a group he was a part of for more than three decades. As a member, he pushed for grading policy reform after a nationwide reckoning with widespread college grade inflation, debated the teaching of western civilization courses as a requirement, and oversaw a science core curriculum reform.
Speaking to the Stanford Daily ahead of his retirement at age 74, Simoni reflected back on his long career. “When I first started, it was traditional that people retired at the age of 65—in fact, it was mandatory. I never really thought I’d work this long, but I have in large part because I enjoy teaching so much.”
Simoni is survived by his wife of 59 years, Diane Simoni, his three children, and five grandchildren.


thescientist--2020-09-28--Vast Majority in US Remain Susceptible to COVID-19: Study

Fewer than 10 percent of dialysis patients sampled in the US showed signs of having had COVID-19 as of late July , a sign that much of the population remains susceptible to the novel coronavirus , according to one of the largest studies of its kind published Friday ( September 25 ) in The Lancet .
Researchers studied the prevalence of antibodies against SARS-CoV-2 in a random subset of thousands of dialysis patients across the country .
Their findings do not indicate exactly how many in the US are immune to the virus , as it is unclear how long @ @ @ @ @ @ @ develops antibodies .
“ We are still in the middle of the fight , ” Eli Rosenberg , an epidemiologist at the State University of New York at Albany who was not part of the study , tells The Washington Post .
“ We ’ re all tired , and we ’ re all hoping for a vaccine .
This shows us how it ’ s not over here , not even by a long shot.
” Researchers from Stanford University and Ascend Clinical , a laboratory that processes tests for kidney dialysis @ @ @ @ @ @ @ from 28,500 patients who underwent dialysis at any of 1,300 centers across 46 states in July .
Dialysis patients undergo routine monthly laboratory studies , making it easy for researchers to gather samples .
The plasma indicated that about 8 percent had antibodies against SARS-CoV-2 , which extrapolates to about 9 percent of all US adults , according to Stanford biostatistician and study coauthor Maria Montez-Rath , who used patient demographics to translate that result to the broader population .
Despite more than 7 million documented US coronavirus cases , the results suggest @ @ @ @ @ @ @ herd immunity threshold required to prevent large-scale resurgences of the virus .
Researchers have not yet determined the ideal number of the populace that would need immunity , but some epidemiologists have estimated it to be upward of 75 percent , Shweta Bansal , a Georgetown University epidemiologist , told Vox .
The study authors urged public health efforts to target interventions toward racial and ethnic minority populations , as those groups had a disproportionate incidence of coronavirus antibodies : 16 percent of those who live in majority Black and Hispanic communities , @ @ @ @ @ @ @ majority Hispanic communities , and 4 percent of patients from majority white communities .
Infectious disease doctor Barnaby Flower and public health expert Christina Atchison , Imperial College London researchers who were not involved with the study , describe in an accompanying comment in The Lancet the limitations of studying only dialysis patients .
“ Attending a health-care facility three times a week would seem like a good way to encounter SARS-CoV-2 , as has been shown elsewhere , ” they write , which would mean researchers overestimated the population with antibodies .
@ @ @ @ @ @ @ authors could have undercounted , as patients who require dialysis are more likely to die of the virus and , therefore , would be excluded from the study .

ABOVE: © ISTOCK.COM,
PICSFIVE
Fewer than 10 percent of dialysis patients sampled in the US showed signs of having had COVID-19 as of late July, a sign that much of the population remains susceptible to the novel coronavirus, according to one of the largest studies of its kind published Friday (September 25) in The Lancet.
Researchers studied the prevalence of antibodies against SARS-CoV-2 in a random subset of thousands of dialysis patients across the country. Their findings do not indicate exactly how many in the US are immune to the virus, as it is unclear how long immunity lasts and not every infected individual develops antibodies.
“We are still in the middle of the fight,” Eli Rosenberg, an epidemiologist at the State University of New York at Albany who was not part of the study, tells The Washington Post. “We’re all tired, and we’re all hoping for a vaccine. This shows us how it’s not over here, not even by a long shot.”
Researchers from Stanford University and Ascend Clinical, a laboratory that processes tests for kidney dialysis patients, studied leftover blood plasma samples from 28,500 patients who underwent dialysis at any of 1,300 centers across 46 states in July. Dialysis patients undergo routine monthly laboratory studies, making it easy for researchers to gather samples.
The plasma indicated that about 8 percent had antibodies against SARS-CoV-2, which extrapolates to about 9 percent of all US adults, according to Stanford biostatistician and study coauthor Maria Montez-Rath, who used patient demographics to translate that result to the broader population.
Despite more than 7 million documented US coronavirus cases, the results suggest that the country is nowhere near the herd immunity threshold required to prevent large-scale resurgences of the virus. Researchers have not yet determined the ideal number of the populace that would need immunity, but some epidemiologists have estimated it to be upward of 75 percent, Shweta Bansal, a Georgetown University epidemiologist, told Vox.
The study authors urged public health efforts to target interventions toward racial and ethnic minority populations, as those groups had a disproportionate incidence of coronavirus antibodies: 16 percent of those who live in majority Black and Hispanic communities, 11 percent of participants who live in majority Hispanic communities, and 4 percent of patients from majority white communities.
Infectious disease doctor Barnaby Flower and public health expert Christina Atchison, Imperial College London researchers who were not involved with the study, describe in an accompanying comment in The Lancet the limitations of studying only dialysis patients.
“Attending a health-care facility three times a week would seem like a good way to encounter SARS-CoV-2, as has been shown elsewhere,” they write, which would mean researchers overestimated the population with antibodies. But, they also concede that the authors could have undercounted, as patients who require dialysis are more likely to die of the virus and, therefore, would be excluded from the study.


Optimizing Protein Characterization

Scientists must efficiently produce recombinant proteins , such as monoclonal antibodies , on a large scale for biotherapeutics development .
@ @ @ @ @ compromise protein stability and lead to protein unfolding and aggregation .
Luckily , there are @ @ @ @ @ eliminating protein aggregates .
Download this ebook from Enzo to learn about • Techniques for @ @ @ @ @ pharmaceuticals • How to detect protein and bacterial aggregates

Scientists must efficiently produce recombinant proteins, such as monoclonal antibodies, on a large scale for biotherapeutics development. Many chemical and physical factors compromise protein stability and lead to protein unfolding and aggregation. Luckily, there are several methods for detecting and eliminating protein aggregates.
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thescientist--2020-09-28--The Anatomy of GenElute-E Single Spin DNA and RNA Purification

Silica-based DNA and RNA purification protocols , with all their spins and washes , can be tedious .
GenEluteTM-E technology @ @ @ @ @ and retain contaminants in a column while nucleic acids flow through .
When combined with @ @ @ @ @ nucleic acids can be prepared for downstream analysis in no time at all .
Download @ @ @ @ @ it all works !
Better results , fewer steps .
Learn more at www.sigmaaldrich.com/

Silica-based DNA and RNA purification protocols, with all their spins and washes, can be tedious. GenEluteTM-E technology uses negative chromatography to absorb and retain contaminants in a column while nucleic acids flow through. When combined with SmartLyseTM extraction reagents, purified nucleic acids can be prepared for downstream analysis in no time at all.
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thescientist--2020-09-28--Nucleic acid purification with GenEluteTM-E Single Spin Technology

Silica-based nucleic acid extraction techniques , with all their spins and washes , can be laborious .
Learn how GenEluteTM-E @ @ @ @ @ to extract and purify nucleic acid samples with only a single centrifugation step .
Learn @ @ @

Silica-based nucleic acid extraction techniques, with all their spins and washes, can be laborious. Learn how GenEluteTM-E single spin technology allows researchers to extract and purify nucleic acid samples with only a single centrifugation step. Learn more at www.sigmaaldrich.com/ singlespin


thescientist--2020-09-28--Newly Found Alzheimer's Plaque Type Linked to Early-Onset Disease

ABOVE : The newly described plaque ( green , red , and yellow ) with its direct connection with blood vessels ( blue ) B.D.C .
BOON ET AL.
, ACTA NEUROPATHOLOGICA , DOI:10.1007/S00401-020-02198-8 , 2020 Scientists have discovered a type of amyloid-β plaque in the brains of people with early-onset Alzheimer ’ s disease that has not been observed before .
These “ coarse-grained ” plaques , described in a study published last week in Acta Neuropathologica , have a different structure , composition , and distribution from the typical amyloid plaques that have been well-studied in the disease @ @ @ @ @ @ @ we were looking into the neuroinflammatory response in early-onset AD cases , ” says Baayla Boon , a PhD candidate in pathology at Amsterdam UMC and the lead author of the study .
Examining post-mortem brain slices from this small group of similar cases , she noticed a lot of plaques that appeared darker than expected under the microscope .
“ We realized that these plaques look different from what we actually knew , ” she says .
The researchers then followed up by comparing the brains of 74 people who had recently @ @ @ @ @ @ @ 38 with early-onset , and 21 with late-onset .
Most of the early-onset samples contained large amounts of these coarse-grained plaques , while most late-onset cases had little or none .
“ We couldn ’ t really find studies reporting these plaques , ” says Boon .
“ We ’ ve been looking at this disease for so many years—how can it be that we now suddenly find a new plaque ?
We were mostly flabbergasted by that.
” Plaques made up of amyloid-β peptides are one of the hallmarks of Alzheimer ’ @ @ @ @ @ @ @ neurodegeneration is unclear .
Boon and her colleagues probed the molecular make-up of the new plaques to understand how they might form .
A key difference they uncovered is that the coarse-grained plaques have more of a shorter version of amyloid-β , compared to the plaques usually seen in brain tissue .
The coarse-grained plaques bear resemblance to the amyloid-β build-up in the brain ’ s blood vessels seen in a disease known as cerebral amyloid angiopathy , which causes brain bleeds in older people .
In addition , most of the coarse-grained @ @ @ @ @ @ @ vessels and the researchers found markers of vascular damage .
“ It ’ s absolutely interesting .
It adds to the understanding and increasing evidence for the links between the brain ’ s vascular system and the development of Alzheimer ’ s pathology , ” says Tormod Fladby , who researches the development of Alzheimer ’ s disease at the University of Oslo and was not involved in the study .
“ It also adds to the differentiation between distinct types of Alzheimer ’ s pathologies , which may turn out to be @ @ @ @ @ @ @ intervention strategies.
” Boon also says she thinks that doctors may need a different strategy to find treatments for cases with these coarse-grained deposits , including helping to remove them from the brain .
If the different plaques need different treatment approaches , this mixture of disease subtypes may be a reason why so many potential treatments appear to have failed in clinical trials .
“ It could definitely be an explanation because we now put all the AD cases into one pile .
I think we need to find something so that @ @ @ @ @ @ @ deposits are in the brain so that we can stratify these patients better , ” says Boon .
The team used different antibodies to identify the presence of the longer and shorter versions of amyloid-β in the plaques , as well as markers of damage to the brain .
This approach is useful for producing a qualitative image for the distribution of the peptides , but other techniques are required to produce reliable figures on the amount of protein present , such as mass spectrometry .
“ That , I think , is @ @ @ @ @ @ @ days .
I ’ m quite surprised that they did not do that and that they relied solely on antibodies , ” says Jörg Hanrieder , a neurochemist at the University of Gothenburg in Sweden who was not involved with the study .
“ Because from our experience , these antibodies are not specific enough , particularly not in tissue.
” There is only a two-amino-acid difference between the longer and shorter versions of amyloid-β , making it challenging to distinguish them using antibodies .
Better quantification of the composition of the plaques @ @ @ @ @ @ @ mechanisms at work .
Boon and her colleagues are now planning to use mass spectrometry to do this , as well as trying to recreate these plaques in mice to test the idea that the development of these plaques are closely linked to the blood vessels .
“ We can ’ t prove our hypothesis on how it develops in this kind of study ; you need models for that .
”

ABOVE: The newly described plaque (green, red, and yellow) with its direct connection with blood vessels (blue)
B.D.C. BOON ET AL., ACTA NEUROPATHOLOGICA, DOI:10.1007/S00401-020-02198-8, 2020
Scientists have discovered a type of amyloid-β plaque in the brains of people with early-onset Alzheimer’s disease that has not been observed before. These “coarse-grained” plaques, described in a study published last week in Acta Neuropathologica, have a different structure, composition, and distribution from the typical amyloid plaques that have been well-studied in the disease.
“For a different study, we were looking into the neuroinflammatory response in early-onset AD cases,” says Baayla Boon, a PhD candidate in pathology at Amsterdam UMC and the lead author of the study. Examining post-mortem brain slices from this small group of similar cases, she noticed a lot of plaques that appeared darker than expected under the microscope. “We realized that these plaques look different from what we actually knew,” she says.
The researchers then followed up by comparing the brains of 74 people who had recently died—15 without Alzheimer’s disease, 38 with early-onset, and 21 with late-onset. Most of the early-onset samples contained large amounts of these coarse-grained plaques, while most late-onset cases had little or none. “We couldn’t really find studies reporting these plaques,” says Boon. “We’ve been looking at this disease for so many years—how can it be that we now suddenly find a new plaque? We were mostly flabbergasted by that.”
Plaques made up of amyloid-β peptides are one of the hallmarks of Alzheimer’s disease, although their role in neurodegeneration is unclear. Boon and her colleagues probed the molecular make-up of the new plaques to understand how they might form. A key difference they uncovered is that the coarse-grained plaques have more of a shorter version of amyloid-β, compared to the plaques usually seen in brain tissue. The coarse-grained plaques bear resemblance to the amyloid-β build-up in the brain’s blood vessels seen in a disease known as cerebral amyloid angiopathy, which causes brain bleeds in older people.
In addition, most of the coarse-grained plaques were in direct contact with blood vessels and the researchers found markers of vascular damage.
“It’s absolutely interesting. It adds to the understanding and increasing evidence for the links between the brain’s vascular system and the development of Alzheimer’s pathology,” says Tormod Fladby, who researches the development of Alzheimer’s disease at the University of Oslo and was not involved in the study. “It also adds to the differentiation between distinct types of Alzheimer’s pathologies, which may turn out to be very relevant when it comes to developing intervention strategies.”
The authors’ proposed model for three types of amyloid-β deposits in the brain: the classic plaque well-known in Alzheimer’s disease, the newly discovered coarse-grained plaque, and plaques seen in cerebral amyloid angiopathy (CAA), a disease of the brain’s blood vessels. The coarse-grained plaque shares features of the CAA plaque in that it has more of the short version of amyloid-β (Aβ 40 ) than the long one (Aβ 42 ) and is situated near blood vessels in the brain. The model also represents damage in the brain, including dystrophic neurites (damaged parts of neurons), norrin (a marker of vascular damage), and complement (a marker for neuroinflammation). B.D.C. BOON ET AL., ACTA NEUROPATHOLOGICA , DOI:10.1007/S00401-020-02198-8, 2020
Boon also says she thinks that doctors may need a different strategy to find treatments for cases with these coarse-grained deposits, including helping to remove them from the brain. If the different plaques need different treatment approaches, this mixture of disease subtypes may be a reason why so many potential treatments appear to have failed in clinical trials.
“It could definitely be an explanation because we now put all the AD cases into one pile. I think we need to find something so that we can predict what kind of amyloid-β deposits are in the brain so that we can stratify these patients better,” says Boon.
The team used different antibodies to identify the presence of the longer and shorter versions of amyloid-β in the plaques, as well as markers of damage to the brain. This approach is useful for producing a qualitative image for the distribution of the peptides, but other techniques are required to produce reliable figures on the amount of protein present, such as mass spectrometry.
“That, I think, is the gold standard to quantify proteins these days. I’m quite surprised that they did not do that and that they relied solely on antibodies,” says Jörg Hanrieder, a neurochemist at the University of Gothenburg in Sweden who was not involved with the study. “Because from our experience, these antibodies are not specific enough, particularly not in tissue.”
There is only a two-amino-acid difference between the longer and shorter versions of amyloid-β, making it challenging to distinguish them using antibodies. Better quantification of the composition of the plaques will give a clearer idea of the mechanisms at work.
Boon and her colleagues are now planning to use mass spectrometry to do this, as well as trying to recreate these plaques in mice to test the idea that the development of these plaques are closely linked to the blood vessels. “We can’t prove our hypothesis on how it develops in this kind of study; you need models for that.”
B.D.C. Boon et al. “The coarse-grained plaque: a divergent Aβ plaque-type in early-onset Alzheimer’s disease,” Acta Neuropathol, doi:10.1007/s00401-020-02198-8, 2020.