#OriginOfComplexMalariaInfection;  #SingleCellSequencingApproach; #TexasBiomedicalResearchInstitute;


Texas (U.S.), Jan 10 (Canadian-Media): New technology employing single cell genome sequencing of the parasite that causes malaria has yielded some surprising results and helps pave the way for possible new intervention strategies for this deadly infectious disease, according to Texas Biomedical Research Institute Assistant Professor Ian Cheeseman, Ph.D. Dr. Cheeseman was Principal Investigator of a three-year study published in the January 2020 edition of Cell Host & Microbe, a high-impact peer-reviewed publication, phys.org news reports said.

A chart of single cell sequencing on malaria parasites. Credit: Texas Biomedical Research Institute

Malaria is caused by Plasmodium parasites spread to people by the bite of infected Anopheles mosquitoes.

"We don't know what is inside malaria infections," Dr. Cheeseman said. "We don't know how many different genetically distinct strains of parasites there are. We don't know how related they are to each other. We don't know how many mosquitoes they came from."

To help answer these questions, Dr. Cheeseman and his collaborators turned to single cell genome sequencing. Using this technology, individual malaria parasite cells are isolated and their genome amplified before being analyzed by a genome sequencer. Single cell sequencing allows researchers to capture the genetic mutations present in a single cell, and has been adopted by cancer researchers to understand how tumors evolve. This is the first time the technology was used to study malaria transmission.

Dr. Cheeseman and his international team studied single malaria-infected cells from malaria patients in Malawi, a country heavily burdened by this infectious disease. Malaria patients, who donated malaria-infected blood samples used in this study reside in Chikhwawa, a region with a large mosquito population. In this region, people may be bitten by a malaria-infected mosquito every 48 hours.

Assistant Professor Ian Cheeseman, Ph.D.Texas Biomedical Research Institute Credit: Texas Biomedical Research Institute

The single cell sequencing approach applied in this study provides a fresh picture of how often bites from an infected mosquito lead to a malaria infection. What researchers discovered went against conventional wisdom. Nearly all the infections they studied likely came from one mosquito bite.

"We found that complex malaria infections are predominantly caused by a single mosquito bite transmitting many genetically diverse but related parasites into the blood stream of a patient," , lead author on the study and a Malawian national, stated.

Knowing this enables scientists to design more effective interventions to block mosquitoes from spreading malaria and build more sophisticated models to predict the spread of antimalarial drug resistance and malaria transmission patterns. The rise of antimalarial drug resistance is a major threat to malaria control globally as resistance to the antimalarial drugs artemisinin and piperaquine continue to spread.

Malaria infects an estimated 200 million people worldwide each year and kills more than 400,000 people, most of them children, according to the World Health Organization. "Any strides we can make in understanding this disease will make an enormous impact," Dr. Cheeseman concluded.

This was confirmed by Yarimar Carrasquillo, the paper's senior author and a scientist for the National Center for Complementary and Integrative Health (NCCIH), told AFP the region responsible was the central amygdala, which according to her work appeared to play a dual role.

By better understanding the brain mechanisms responsible for pain modulation, researchers hope to eventually find better cures. For example whereas stress or anxiety can amplify pain, being focussed on a task that diverts your attention can reduce pain.

"The healthy response is you get pain, it tells you something is wrong, it heals, and the pain goes away," said Carrasquillo.

"In chronic pain, that doesn't happen, the system gets stuck. If we can identify what makes the system gets stuck, then we can reverse it."

The centre will focus on two key areas of research such as how genetic and environmental factors come together to produce symptoms associated with autism and related disorders, as well as how the fundamental features of these disorders develop both within and outside the brain.

The new centre will be named after them. Lisa Yang and Hock Tan who donated a $20 million for its  establishment.  Yang and Tan also helped set up a similar center at MIT’s McGovern Institute for Brain Research in 2017.

#ChampalimaudCentreForTheUnknownInLisbon; #BeyondWebstersLaw; #TimeintensityEquivalenceInDiscrimination 

Germany, Aug 13 (Canadian-Media): For centuries, the mental world of the mind and the physical world were treated as utterly distinct, ScienceXNewsletter reports said.

Time holds the key to the explanation of Weber's law. Credit: Diogo Matias, Champalimaud Foundation

​While the movement of inanimate objects could be measured and ultimately predicted with the help of mathematics, the behavior of organisms appeared to be shaped by different forces under the control of the will.
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About 200 years ago, the German physician Ernst Heinrich Weber made a seemingly innocuous observation that led to the birth of the discipline of psychophysics—the science relating physical stimuli in the world and the sensations they evoke in the mind of a subject. Weber asked subjects to say which of two slightly different weights was heavier. From these experiments, he discovered that the probability that a subject will make the right choice only depends on the ratio between the weights.

For instance, if a subject is correct 75 percent of the time when comparing a weight of 1 Kg and a weight of 1.1 Kg, then she will also be correct 75 percent of the time when comparing two weights of 2 and 2.2 Kg—or, in general, any pair of weights where one is 10 percent heavier than the other. This simple but precise rule opened the door to the quantification of behavior in terms of mathematical laws.

Weber's observations have since been generalised to all sensory modalities across many animal species, leading to what is now known as Weber's Law. It is the oldest and most firmly established law in psychophysics. Psychophysical laws describe precise rules of perception and are important because they can be used to obtain mathematical explanations of behavior in terms of brain processes, just as the precise patterns of movement of the planets in the sky were useful to understand gravitation.

Many explanations for Weber's law have been proposed through the years. Although they can all account for Weber's findings, no experimental test had been found to identify which model was correct. Thus, the puzzle of a mathematical explanation of Weber's law remained open.

Now, a team of researchers at the Champalimaud Centre for the Unknown in Lisbon, Portugal, has discovered that Weber's Law can be described as the consequence of a new psychophysical rule involving the time that it takes to make a choice, not just the outcome of the decision. The team has shown that this new rule is sufficient to derive a unique and accurate mathematical model describing the cognitive process underlying Weber's Law. Their results are described in an article published in the scientific journal Nature Neuroscience.

Time is key

In this new study, the team of Alfonso Renart trained rats to discriminate between two sounds of slightly different intensities. They constructed miniscule headphones specially adapted to the heads of rats, and used them to deliver sounds simultaneously to both ears.
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In each trial, the sound on one of the two speakers would be slightly louder, and the rat's job was to report which speaker played the louder sound by orienting toward the corresponding side. "This behaviour is natural to rats, because they orient their heads toward the source of a sound, just like we do," explains José Pardo-Vazquez, one of the article's co-authors. The rats could experience the sound as long as they needed in order to make up their mind. Thus, every attempt provided a choice and a decision time.

"Our experiments confirmed that the animals' behaviour matched Weber's Law," says Pardo-Vazquez. "Their ability to tell which of the two sounds was louder only depended on the ratio between the sounds' intensities. If the rat had to compare the intensities of two sounds that were played softly, its accuracy was just as good as with a pair of sounds that were played loudly, as long as both pairs had the same intensity ratio."

Then, the team started to analyze in detail how long the rats took to make their decisions, a step that turned out to be critical. "Typically, studies of Weber's law focused on the accuracy of the discrimination, which is what Weber himself described," Pardo-Vazquez explains. "Surprisingly, the time taken to decide has received little attention."
The team realized decision times and the loudness of the pair of sounds were linked—the louder the sounds, the shorter the decision time. In fact, they showed that the nature of this link was unique and mathematically precise, making the decision times observed in a discrimination between two quiet sounds, for instance, exactly proportional to the decision times measured when the subject discriminated between two loud sounds—as long as their relative intensities were constant.

Beyond Weber's Law

The team had, in fact, discovered a new psychophysical law, which they call "time-intensity equivalence in discrimination" (TIED), because it links the overall intensity of a pair of sounds and the time it took to discriminate between them. The TIED is more stringent than Weber's Law, because it not only links the accuracy of pairs of discriminations, it also links their associated decision times. "The precision of this relationship between the decision times in our experiments is amazing," says Pardo-Vazquez. "It is unusual that the behavior of animals can be described with such mathematical precision."

To investigate if the TIED held also in different conditions, the team ran the same kind of experiment with human subjects, obtaining similar results. They also analyzed experiments done by others in which rats perform olfactory discriminations of odor mixtures, again with the same outcome. "It is still early to say if the TIED is as general as Weber's law, but the fact that we obtained the same results in two species and across two sensory modalities is an encouraging first step," Pardo-Vazquez said.

Closing in on the right model

Dozens of mathematical models have been proposed through the years to explain Weber's law, but there was no clear experimental test to distinguish them. The researchers say that the TIED offers a way forward. Their analysis revealed that in order to be consistent with the TIED, a mathematical model of the discrimination task would need to satisfy a set of strict conditions.

"This was fantastic," says Juan Castiñeiras, another co-author of the study. "The TIED constrained the world of possible explanations, and thereby resolved the ambiguity between the many proposed models of Weber's law." A previously proposed model by the psychologist Stephen Link at the end of the 1980s came close to the solution, but missed an important condition describing how the intensity of sensory stimuli is encoded by the activity of sensory neurons.

The final step was to take this set of conditions and construct a model to test how accurately it accounted for the behavior of the rats. "We analyzed the simplest model with the fewest possible number of parameters," explains Castiñeiras. When the values of these parameters were chosen to maximize the similarity to the behavior of the rats, they discovered that the fit of the model was remarkable. "Even the simplest model effectively captured everything we could measure with almost no error. This greatly strengthened our confidence that the model describes something true about how perception works," says Renart.

Precise experiments and theories lead to definite progress

These results stand out in their field because of the precision of both the new psychophysical rule and of the mathematical model that describes the experimental data. "Although less frequently observed, in biology and in the study of behavior—like in physics—precise experimental results permit precise explanations which resolve previous ambiguities and therefore constitute progress," says Renart. For instance, their results suggest that one of the main theories in psychophysics was not adequate to describe the TIED. "Producing mathematical explanations that rule out competing theories is very rare in neuroscience, because there is always the possibility to slightly modify one model to make it compatible with the experimental data," Castiñeiras says. "We showed that a very influential theory in psychophysics (called Signal Detection Theory) did not model decision times and could therefore not describe the TIED. It missed the essence of the explanation of Weber's law."
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One of the next goals of the team is to understand how the mathematical model they have identified is implemented by the brain: "We want to determine which brain areas are important in our task, and how neurons in these circuits carry out the different computational elements of the model," Renart concludes.

#unsupervisedlearning; #nextAIrevolution; #MITTechnologyReview 

Massachusetts (U.S.), July 28 (Canadian-Media): Yann LeCun, Facebook’s chief AI scientist, believes unsupervised learning will bring about the next AI revolution, MIT Technology Review reports said.

Yann LeCun/Twitter

“Nobody tells the baby that objects are supposed to fall,” said Yann LeCun, the chief AI scientist at Facebook and a professor at NYU, during a webinar on Thursday organized by the Association for Computing Machinery, an industry body. And because babies don’t have very sophisticated motor control, he hypothesizes, “a lot of what they learn about the world is through observation.”

That theory could could ;ead researchers to advance the boundaries of artificial intelligence.

Deep learning, the category of AI algorithm, has increased the possibility of giving machines perceptual abilities like vision. The next step is to instill them with sophisticated reasoning.

New techniques of giving machines a kind of working memory are helping to overcome this limitation.

“Obviously we’re missing something,” LeCun said.  

The answer, he thinks, is in  deep-learning subcategory known as unsupervised learning. LeCun prefers the term “self-supervised learning” because it essentially uses part of the training data to predict the rest of the training data.

In recent years, such algorithms have facilitated in natural-language processing because of their ability to find the relationships between billions of words. 

“Everything we learn as humans—almost everything—is learned through self-supervised learning. There’s a thin layer we learn through supervised learning, and a tiny amount we learn through reinforcement learning,” he said. “If machine learning, or AI, is a cake, the vast majority of the cake is self-supervised learning.”

What does this look like in practice? Researchers should begin by focusing on temporal prediction.

“This is kind of a simulation of what’s going on in your head, if you want,” LeCun said.

“It's a good idea to do video prediction in the context of self-driving cars because you might want to know in advance what other cars on the streets are gonna do,” he said.

Ultimately, unsupervised learning will help machines develop a model of the world that can then predict future states of the world, he said.  LeCun is confident: “The next revolution of AI will not be supervised.”

#UniversityofGothenburg; #interleukin-6; #IL-6;

Sweden (Switzerland), May 5 (Canadian-Media): Researchers at the University of Gothenburg, Sweden, have clarified the link between the molecule interleukin-6 (IL-6) in the brain and obesity; Science X Newsletter reported.

In experiments on rats and mice, they show that the molecule does affect the risk of obesity, and also where this effect occurs in the brain.

interleukin-6 (IL-6) is a well-known pro-inflammatory molecule, and an integral element of body's first line of defense during infection. Intriguingly, the brain may govern and utilize IL-6 differently from the rest of the body. Researchers led by the laboratory of Karolina Skibicka at the Sahlgrenska Academy, Sweden wondered what happens to IL-6 levels in the brain following a diet that leads to obesity.

Rats and mice were offered a high-calorie palatable food, a mix of fat and sugar, in addition to their regular low-calorie diet. Like many humans, rodents choose to overeat when presented with calorie-dense foods.

"What we found was that the rats and mice that became obese had reduced IL-6, but only in one brain region called the lateral parabrachial nucleus (lPBN)," says Devesh Mishra, postdoctoral fellow leading the study. "To understand whether this reduction of IL-6 is a good or bad thing for the metabolic health of the rodents, we viro-genetically reduced IL-6 levels very selectively in the lPBN; this led to increased body weight and body fat, even in rodents fed a healthy diet."

Therefore, the researchers have concluded that the reduced levels of lPBN IL-6 in obesity are problematic, and likely contribute to metabolic dysfunction and weight gain. Since body weight is a result of the amount of food consumed, i.e., energy intake, versus how much energy we use, i.e. energy expenditure, weight gain can follow dysfunction of either one of these branches of energy balance.

What makes local parabrachial nucleus-produced IL-6 extra important, the study found, is that it affects both branches simultaneously: It decreases food intake and increases energy expenditure, the latter by increasing brown fat activity, so body's energy is utilized for heat generation or fat burning. Hence, reduced levels of lPBN IL-6 disrupt the entire energy balance equation.

These findings may be relevant not only for mice but also men, since an earlier study from University of Gothenburg revealed that blood serum IL-6 levels in obese and overweight men are increased, yet brain IL-6 levels measured in cerebrospinal fluid are reduced.

There is one unresolved issue related to these findings—researchers found that the obesity-associated reduction in IL-6 was only present in males. Female rats and mice had normal IL-6 levels. The Sahlgrenska team is now investigating why females are protected from the obesity-associated IL-6-driven dysfunction.
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Given that obesity is a major global disorder with 1.9 billion overweight individuals out of which 650 million are obese, effective anti-obesity treatments are desperately needed to minimize the amount of personal and medical burden on individuals and societies. On the scientific end, researchers think that IL-6 as a satiety-mediating substance with brain region specificity is an important discovery, and can open new directions in the quest for more effective anti-obesity strategies.

#marineviralspecies; #journalCell, #ScienceXNewsletter; #polarcircle; #TaraOcean; #OhioStateUniversity; #biodiversityhotspot; #ArcticOcean; #climatechange; #biogeochemistry 
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​United States, Apr 26 (Canadian-Media): An international team of scientists were able to identify nearly 200,000 marine viral species, according to the  findings which appeared on April 25 in the journal Cell, Science X Newsletter reports said.

These findings help create a new picture of our planet and how it may be impacted by interactions among organisms and point to issues ranging from evolution to climate change.

Image  Credit: A. Deniaud Garcia/ Fondation Tara Ocean: The Tara sailing on its Polar Circle expedition in 2013. 

"Viruses are these tiny things that you can't even see, but because they're present in such huge numbers, they really matter," says senior author Matthew Sullivan, a microbiologist at the Ohio State University. "We've developed a distribution map that is foundational for anyone who wants to study how viruses manipulate the ecosystem. There were many things that surprised us about our findings."

​Among the surprises was the existence of these nearly 200,000 marine viral species. Additionally, meta-community analysis showed that the viruses were organized into five distinct ecological zones throughout the entire ocean, which was unexpected given the fluid nature of the oceans and the complexity of many of the marine regions. Also, despite the paradigm from larger organisms that species diversity is highest near the equator and lowest near the poles, the researchers collected an extensive number of samples in the Arctic compared to previous studies of ocean life and found a biodiversity hotspot in the Arctic Ocean.

The samples were collected between 2009 and 2013 on the Tara as part of the Tara Oceans effort. Begun in 2006, the Tara project aims to conduct unique and innovative ocean science with the goal of predicting and better anticipating the impacts of climate change. In the current effort, a rotating team of scientists spent time on the boat collecting ocean water samples from different depths across many geographical regions. After being collected, the samples for this study were filtered and shipped back to about a dozen different labs for analysis.

The investigators studied not only the water samples for viruses, but also other microbes and other living creatures. "We filtered the samples to analyze organisms ranging in size from viruses to fish eggs," Sullivan says. He adds that papers reporting some of the other microbial components from the samples are forthcoming.
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Another noteworthy aspect of the project was the extensive number of samples collected in the Arctic, a highlight that has not been part of earlier studies of ocean life.

Image  Credit: A. Deniaud/Fondation Tara Ocean: Samples being collected on the Tara.

This research has significant implications for understanding how ocean microorganisms affect the earth's atmosphere. "In the last 20 years or so, we've learned that half of the oxygen that we breathe comes from marine organisms," Sullivan notes. "Additionally, the oceans soak up half of the carbon dioxide from the atmosphere."

"Because of complex chemistry, increased levels of carbon dioxide at the surface acidify the oceans," Sullivan adds. "However, if carbon dioxide instead is converted to organic carbon and biomass, then it can become particulate and sink into the deep oceans. That's a good result for helping mitigate human-induced climate change—and we're learning that viruses can help facilitate this sinking. Having a new map of where these viruses are located can help us understand this ocean carbon "pump" and, more broadly, biogeochemistry that impacts the planet."

The investigators say that having a more complete picture of marine viral distribution and abundance will help them to determine which viruses they should be focusing on for further studies. Additionally, the maps based on this research establish a baseline for other collection efforts going forward, which can help to answer questions about how levels of microorganisms change over time, in response to both seasonal variation and climate change.
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"Previous ocean ecosystem models have commonly ignored microbes, and rarely included viruses, but we now know they are a vital component to include," Sullivan concludes.
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​#​Alzheimer; #amyloidprecursorprotein; #pathologicalcontributors; #aging; #Abeta; #synapticdysfunction;
#neuronalloss; #Florida'sAlzheimer'sAssociation
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Florida (US), Apr 24 (Canadian-Media): Worldwide, 50 million people are living with Alzheimer's disease and other dementias and every 65 seconds someone in the United States develops this disease, which causes problems with memory, thinking and behavior, Florida's Alzheimer's Association reports said.

Image Credit: Qi Zhang, Ph.D. and Claire E. DelBove/The background is an image of neurons (blue). Some of them express the new amyloid precursor protein reporter (green) and a synapse-marker, Synaptophysin-pHTomato (red). The rendering at the lower left corner illustrates the Alzheimer's disease etiology model derived from the study, in which a variety of pathological contributors like aging and Abeta converge on presynaptic cholesterol and the disruption of cholesterol homeostasis diverges to various pathological outcomes like synaptic dysfunction and neuronal loss.

It has been more than 100 years since Alois Alzheimer, M.D., a German psychiatrist and neuropathologist, first reported the presence of senile plaques in an Alzheimer's disease patient brain. It led to the discovery of amyloid precursor protein that produces deposits or plaques of amyloid fragments in the brain, the suspected culprit of Alzheimer's disease. Since then, amyloid precursor protein has been extensively studied because of its association with Alzheimer's disease. However, amyloid precursor protein distribution within and on neurons and its function in these cells remain unclear.
A team of neuroscientists led by Florida Atlantic University's Brain Institute sought to answer a fundamental question in their quest to combat Alzheimer's disease—"Is amyloid precursor protein the mastermind behind Alzheimer's disease or is it just an accomplice?"

​Mutations found in amyloid precursor protein have been linked to rare cases of familial Alzheimer's disease. Although scientists have gained a lot knowledge about how this protein turns into amyloid plaques, little is known about its native function in neurons. In the case of more common sporadic Alzheimer's disease, the highest genetic risk factor is a protein that is involved in cholesterol transportation and not this amyloid precursor protein. Moreover, various clinical trials designed to address Alzheimer's disease by minimizing amyloid plaque formation have failed, including one from Biogen announced last month.

​In a study published in the journal Neurobiology of Disease, Qi Zhang, Ph.D., senior author, an investigator at the FAU Brain Institute, and an assistant research professor in FAU's Schmidt College of Medicine, along with collaborators from Vanderbilt University, tackle this Alzheimer's disease mystery by devising a multi-functional reporter for amyloid precursor protein and tracking the protein's localization and mobility using quantitative imaging with unprecedented accuracy.
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For the study, Zhang and collaborators genetically disrupted the interaction between cholesterol and amyloid precursor protein. Surprisingly, by disengaging the two, they discovered that this manipulation not only disrupts the trafficking of amyloid precursor protein but also messes up cholesterol distribution at the neuronal surface. Neurons with an altered distribution of cholesterol exhibited swollen synapses and fragmented axons and other early signs of neurodegeneration.
"Our study is intriguing because we noticed a peculiar association between amyloid precursor protein and cholesterol that resides in the cell membrane of synapses, which are points of contact among neurons and the biological basis for learning and memory," said Zhang. "Amyloid precursor protein may just be one of the many accomplices partially contributing to cholesterol deficiency. Strangely, the heart and brain seem to meet again in the fight against bad cholesterol."

Given the broad involvement of cholesterol in almost all aspects of neurons' life, Zhang and collaborators have proposed a new theory about the amyloid precursor protein connection in Alzheimer's disease, especially in the surface of those tiny synapses, which triggers neurodegeneration.

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"Although still in early stages, this cutting-edge research by Dr. Zhang and his collaborators at Vanderbilt University may have implications for the millions of people at risk for or suffering with Alzheimer's disease," said Randy D. Blakely, Ph.D., executive director of the FAU Brain Institute and a professor of biomedical science in FAU's Schmidt College of Medicine. "The number of people in Florida alone who are age 65 and older with Alzheimer's disease is expected to increase 41.2 percent by 2025 to a projected 720,000, highlighting the urgency of finding a medical breakthrough."

Locally, Alzheimer's disease affects 11.5 percent of Medicare beneficiaries in Palm Beach County and 12.7 percent of Medicare beneficiaries in Broward County (a nearly 18 percent increase over national average).

According to the Alzheimer's Association, Florida is number one in per capita cases of Alzheimer's disease in the U.S.
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#geneediting; #CRISPR-Cas9; #research; #ArizonaStateUniversity; #ScienceXNewsletter; #guideRNA; #genedrives; 

Arizona (US), Apr 24 (Canadian-Media): A method of rendering the gene editing tool CRISPR-Cas9 "immunosilent," potentially allowing the editing and repair of genes to be accomplished reliably and stealthily has been described in research appearing in the advanced online edition of the journal Nature Communications, Karen Andersen, Samira Kiani and their colleagues at Arizona State University, Science X Newsletter reported. 

Image Credit: Jason Drees/The graphic illustrates the technique described in the new study. A version of the Cas9 protein used in CRISPR gene editing has been mutated. While this protein, seen in blue, retains its proper functioning, it remains "immunosilent"--hidden from predation as a foreign entity by the immune system's T cells (seen in brown). 

​The study is the first to accurately predict the dominant binding sites or epitopes responsible for immune recognition of the Cas9 protein and experimentally target them for modification. The findings bring CRISPR a step closer to safe, clinical application.

The advance of science is something like the wandering of an explorer through an uncharted jungle. Often, the dense undergrowth can seem impenetrable, but at certain privileged moments, a clearing opens, and an entirely new landscape emerges.

Something like this is occurring in the field of biology with the recent discovery of powerful techniques for intervening in the genetic code of life. A new method for editing genes with the ease of a computer's cut-and-paste functions may prove more momentous than the splitting of the atom and represents a major advance in the war against deadly diseases.
The breakthrough—known as CRISPR—has been greeted with ecstatic optimism and grave apprehension.

Anderson is a professor in the Biodesign Virginia G. Piper Center for Personalized Diagnostics and ASU's School of Life Sciences. She is also associate professor of medicine at the Mayo Clinic Arizona. Kiani recently joined the Biodesign Institute in addition to her appointments at ASU's School of Life Sciences and the School of Biological and Health Systems Engineering. Her research interests include the use of synthetic biology methods to improve CRISPR safety.

Ancient tool, futuristic science

Back in 1987, a team of researchers in Osaka, Japan found something peculiar. Identical genetic sequences appeared to be cropping up repeatedly in the bacterial genome of E. coli. These palindromic sequences were separated by abbreviated snippets of DNA of varying composition.
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The nature of these strange repeated sequences and the curious DNA phrases separating them were an enigma. Remarkably, they started showing up in other bacteria. Indeed, the phenomenon seemed to be ubiquitous, and the race for an explanation was on.

Today we know that the researchers had stumbled on a previously unknown bacterial immune system—CRISPR (for clustered regularly interspaced short palindromic repeats).
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CRISPR relies on two primary components. The first, known as a guide RNA, is a sort of molecular bloodhound, responsible for locating a particular site in the genome to be modified or disabled. The second component, known as Cas9, is a special type of protein known as an endonuclease. It functions like a pair of razor-sharp pruning shears, cutting through the double stranded DNA at the desired site located by the guide RNA

Nature 2.0

Clever researchers soon recognized the potential of CRISPR-Cas9 to serve as an all-purpose gene editing tool, useful not only for modifying selected regions throughout the entire bacterial genome, but the genomes of all living organisms, including humans. The possibilities are staggering and are not limited to effective treatments for a broad range of genetic diseases. For the first time, it may be possible to correct Nature's genetic typos, curing many of these diseases outright and preventing others from ever arising.

CRISPR also holds the potential to radically transform ecosystems and has been suggested as a means of wiping out diseases like malaria by driving the mosquitos that carry them to extinction, through CRISPR-aided techniques known as gene drives.

When a bacterium like E. coli is invaded by an unfamiliar virus—known as a bacteriophage—the CRISPR system is activated. If bacterial defense mechanisms successfully disable the virus, CRISPR chops the invader's DNA into pieces and stores these fragments in a kind of genomic library. A subsequent viral assault on the bacterium will cause CRISPR to compare DNA segments of the offending virus with the bacterium's data bank of DNA fragments from previous viral attacks. When the guide RNA finds a match along the virus' DNA, it binds with the complementary sequence and the Cas9 protein severs the DNA, terminating the virus.

For the first time in earth's history, one species holds the key to directing the course of its own evolution, (not to mention the evolution of bacteria, giraffes, redwood trees and all planetary life). Currently, there are prohibitions on gene editing efforts in humans that could be passed through the germline to successive generations, but in at least one case, these boundaries have been ominously overstepped. So powerful and versatile is the CRISPR method, there are likely few domains of applied biology that will remain untouched by it.

But before CRISPR can take its first tentative steps in the clinic, a number of safety issues must be addressed, beginning with the gene-slicing protein Cas9.

"Being as much a societal revolution as a technological revolution, many researchers have started to look into ethical, societal, safety and regulatory considerations related to CRISPR usage,"Kiani says. "Safety engineering to address controllability, specificity and side effects of CRISPR treatments have gained significant momentum and ethical debates have arisen to ensure correct use of technology. My lab is interested to address both issues."

Managing immunity

Cas9 is a precise and versatile tool, replacing early, inaccurate and inefficient gene editing techniques with a rapid, inexpensive and deadly-accurate cutting device. But Cas9 in its native form may not be well tolerated by the human body.
Making CRISPR technology safe for clinical use is a central concern and the issue is challenging. One necessity is to ensure that the central machinery of CRISPR is not recognized by a patient's immune system as a foreign entity and attacked. An immune response of this kind could cause significant toxicity. (An early, pre-CRISPR method of introducing altered genes to correct a rare genetic disorder resulted in tragedy when an immune system revolt caused multiple organ failure and death. Today, improved vectors for gene therapy have resulted in safer treatments for a range of genetic disorders, though "off-target" effects of these interventions remain an important concern.)
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The Cas9 protein is derived from a common bacterium, streptococcus pyogenes. "The problem," Anderson says, "is that many of us are already immune to streptococcus. If you have had a Group A strep infection, you may have preexisting immunity to that protein."

S. pyogenes is a round bacterium that commonly colonizes the throat, genital mucosa, rectum and skin, affecting 700 million people annually worldwide. It is responsible for diseases ranging from rheumatic fever and rheumatic heart disease to scarlet fever and streptococcal pharyngitis—commonly known as strep throat.
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In previous gene editing efforts, cells were removed from human tissue, reengineered and replaced in the body. The power of CRISPR allows researchers to modify DNA within a living person's tissue and even to target multiple gene modifications with a single CRISPR intervention. "If you want to think about repairing cells that are in an organ, like a liver cell or kidney or brain," Anderson says, "then you have to express the bacterial protein there." This is where the threat of triggering an immune response to Cas9 becomes a formidable obstacle.

Cas9 goes incognito

The new study affirms that Cas9 is indeed immunogenic in humans and that preexisting exposure to S. pyogenes can drive the body's T cells to launch an immune attack against the bacterial protein. When 143 samples of blood were screened, 82 of them (or 57.3 percent) showed detectable levels of antibody to S. pyogenes.

The study next describes an effort to produce a fully functional version of Cas9, suitable for gene editing, which is not recognized and targeted by the immune system. To do this, the researchers identified the regions of antibody binding on the Cas9 molecule, (known as epitopes), that were directly implicated in triggering T cell recognition and attack.

Two mutations in so-called anchor residues of the Cas9 epitope were explored individually and in combination to assess their effect on immunogenicity. Modifying these regions by just a single amino acid produced a version of Cas9 that could operate undercover. T-cell reactivity to the mutated peptide showed a 25-30 fold reduction, while leaving Cas9's DNA-cutting ability intact.

"That's the unique part of what we've done," Anderson says. "We took those dominant epitopes and tried to silence them—just by doing one or two mutations in the Cas9 gene. But we rebuilt it, so the gene was still functional. It's not immunologically silent, but its more quiet." Indeed, the study results confirmed that in cultured cells, the reengineered Cas9 was less immunologically active, while retaining its functional properties. The author's stress that the technique could be combined with other strategies to further improve CRISPR safety and reduce the need for immunosuppressant drugs.

Exciting new avenues of research are being explored that would enable CRISPR to be used to induce epigenetic changes, turning on silent genes, altering the activity of disrupted genes or otherwise modifying gene expression without permanent changes to the DNA. Such interventions will require the CRISPR system to remain much longer in the body to be effective, perhaps weeks or months. Here, potential immunity to Cas9 will be even more of a critical consideration. Custom tailoring of epitopes to silence the immune response to Cas9 offers an attractive approach.

"We are hoping that this study is the beginning of many efforts that when combined can address the immunogenicity of CRISPR for clinical trials," Kiani says.

#Irvine study; #mediaviolenece; #mediaexposure; #ScienceAdvances


 New York, Apr 23 (Canadian-Media): Repeated exposure to media coverage of collective traumas, such as mass shootings or natural disasters, can fuel a cycle of distress, according to a University of California, Irvine study. ​

Researchers found that individuals can become more emotionally responsive to news reports of subsequent incidents, resulting in heightened anxiety and worry about future occurrences.

The report appears in Science Advances, a peer-reviewed, multidisciplinary, open-access journal published by the American Association for the Advancement of Science.
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“It’s natural for people to experience feelings of concern and uncertainty when a terrorist attack or a devastating hurricane occurs,” said senior author Roxane Cohen Silver, UC Irvine professor of psychological science. “Media coverage of these events, fueled by the 24-hour news cycle and proliferation of mobile technologies, is often repetitious and can contain graphic images, video and sensationalized stories, extending the impact to populations beyond those directly involved.”
Earlier research has shown that consumption of media coverage of a collective trauma is a rational response for individuals seeking information as a way to mitigate their apprehension and cope with their stress. However, this strategy may backfire. According to this new study, repeated exposure to explicit content may exacerbate fear about future adversities, which promotes future media consumption and greater anxiety when they do occur. There is an even greater risk of falling into this pattern for those who have experienced violence in their lives or have been diagnosed with mental health ailments.

“The cycle of media exposure and distress appears to have downstream implications for public health as well,” said Rebecca R. Thompson, a UC Irvine postdoctoral scholar in psychological science and lead author of the report. “Repeated exposure to news coverage of collective traumas has been linked to poor mental health consequences — such as flashbacks — in the immediate aftermath and posttraumatic stress responses and physical health problems over time, even among individuals who did not directly experience the event.”

A national longitudinal study of more than 4,000 U.S. residents was conducted by Thompson, Silver and their colleagues over a three-year period following the 2013 Boston Marathon bombings and the 2016 massacre at the Pulse nightclub in Orlando, Florida. Participants were surveyed four times, enabling the team to capture responses to both tragedies and examine how responses to the first incident affected reactions to news coverage of the second.

“Our findings suggest that media organizations should seek to balance the sensationalistic aspects of their coverage, such as providing more informational accounts as opposed to lengthy descriptions of carnage, as they work to inform the public about breaking news events,” Silver said. “This may lessen the impact of exposure to one event, reducing the likelihood of increased worry and media-seeking behavior for subsequent events.”

Also conducting the study were Nickolas M. Jones, former UC Irvine psychological science doctoral student, and E. Alison Holman, UC Irvine associate professor of nursing. Project funding was provided by National Science foundation grants BCS-1342637, BCS-385 1451812 and BCS-1650792.
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