New genes out of nothing

One key question in evolutionary biology is how novel genes arise and develop. Swedish researchers now show how new genes and functions that are advantageous to bacteria can be selected from random DNA sequences. The results are presented in the scientific journal mBio.

How do new genes and functional proteins arise and develop? This is one of the most fundamental issues in evolutionary biology. Two different types of mechanism have been proposed: (1) new genes with novel functions arise from existing genes, and (2) new genes and proteins evolve from random DNA sequences with no similarity to existing genes and proteins. In the present study, the researchers explored the latter type of mechanism: evolution of new genes and proteins from randomised DNA sequences -- de novo evolution, as it is called. It is fairly easy to understand that when a gene already exists, it can be modified and acquire a new function. But how does "nothing" turn into a function affording a small advantage that is favoured by natural selection?

The raw material for the experiment was an big library of some 500 million randomised gene sequences, from which peptide sequences with a biological function were identified. In the experiment, random gene sequences were placed on a plasmid and overexpressed. The scientists then investigated whether they could give bacteria a specific, defined property. Were they, for example, able to give the bacteria antibiotic resistance? They identified several short peptides (22-25 amino acids long) that could give the bacteria a high degree of resistance to aminoglycosides, an important class of antibiotics used for severe infections.

"When the project started, we had low expectations. We were amazed when we found peptides able to confer a resistance level 48 times higher," says Dr Michael Knopp, the study's lead author.

Through a combination of genetic and functional experiments, the scientists were able to demonstrate that the peptides cause resistance by attaching themselves to bacterial cell membranes and affecting the proton potential across the membrane. The disruption of the proton potential causes a decrease in antibiotic uptake, rendering the bacteria resistant.

"This study is important because it shows that completely random sequences of amino acids can give rise to new, advantageous functions, and that this process of de novo evolution can be studied experimentally in the laboratory," says Dan I. Andersson, Professor of Medical Bacteriology, who is chiefly responsible for the study.

From Science Daily

A treasure map to understanding the epigenetic causes of disease

DNA illustration.

More than 15 years after scientists first mapped the human genome, most diseases still cannot be predicted based on one's genes, leading researchers to explore epigenetic causes of disease. But the study of epigenetics cannot be approached the same way as genetics, so progress has been slow. Now, researchers at the USDA/ARS Children's Nutrition Research Center at Baylor College of Medicine and Texas Children's Hospital have determined a unique fraction of the genome that scientists should focus on. Their report, which provides a "treasure map" to accelerate research in epigenetics and human disease, was published in Genome Biology.

Epigenetics is a system for molecular marking of DNA -- it tells the different cells in the body which genes to turn on or off in that cell type. But the cell-specific nature of epigenetics makes it challenging to study. Whereas a blood sample can be used to 'genotype' an individual, most epigenetic marks in blood DNA provide no clues about epigenetic dysregulation in other parts of the body, such as the brain or heart.

Dr. Robert A. Waterland, professor of pediatrics -- nutrition and of molecular and human genetics at Baylor, and his team identified special regions of the genome where a blood sample can be used to infer epigenetic regulation throughout the body, allowing scientists to test for epigenetic causes of disease.

To do this, they focused on the most stable form of epigenetic regulation -- DNA methylation. This addition of methyl groups to the DNA molecule occurs in the embryonic state and can impact health for your entire life.

To identify genomic regions in which DNA methylation differs between people but is consistent across different tissues, they profiled DNA methylation throughout the genome in three tissues (thyroid, heart and brain) from each of 10 cadavers.

"Since these tissues each represent a different layer of the early embryo, we're essentially going back in time to events that occurred during early embryonic development," Waterland said. "To map DNA methylation we converted methylation information into a genetic signal, then sequenced the genomes. Our atlas required massive amounts of sequencing data -- 370 times more than were used for the first map of the human genome in 2001."

The nearly 10,000 regions the researchers mapped out, called correlated regions of systemic interindividual variation (CoRSIVs), comprise a previously unrecognized level of molecular individuality in humans.

"Recent studies are already showing that methylation at these regions is associated with a range of human diseases including obesity, cancer, autism, Alzheimer's disease and cleft palate," said Dr. Cristian Coarfa, associate professor of molecular and cell biology at Baylor and co-leader of the project

Waterland believes these findings will transform the study of epigenetics and disease, as researchers will now know where in the genome to look.

"Because epigenetic marking has the power to stably silence or stably activate genes, any disease that has a genetic basis could equally likely have an epigenetic basis," Waterland said. "There is incredible potential for us to understand disease processes from an epigenetic perspective. CoRSIVs are the entryway to that."

Read more at Science Daily

Carbon dioxide levels in atmosphere hit record high in May

Earth.

Atmospheric carbon dioxide continued its rapid rise in 2019, with the average for May peaking at 414.7 parts per million (ppm) at NOAA's Mauna Loa Atmospheric Baseline Observatory.

The measurement is the highest seasonal peak recorded in 61 years of observations on top of Hawaii's largest volcano and the seventh consecutive year of steep global increases in concentrations of carbon dioxide (CO2), according to data published today by NOAA and Scripps Institution of Oceanography. The 2019 peak value was 3.5 ppm higher than the 411.2 ppm peak in May 2018 and marks the second-highest annual jump on record.

Monthly CO2 values at Mauna Loa first breached the 400 ppm threshold in 2014.

"It's critically important to have these accurate, long-term measurements of CO2 in order to understand how quickly fossil fuel pollution is changing our climate," said Pieter Tans, senior scientist with NOAA's Global Monitoring Division. "These are measurements of the real atmosphere. They do not depend on any models, but they help us verify climate model projections, which if anything, have underestimated the rapid pace of climate change being observed."

The concentration of CO2 in the atmosphere increases every year, and the rate of increase is accelerating. The early years at Mauna Loa saw annual increases averaging about 0.7 ppm per year, increasing to about 1.6 ppm per year in the 1980s and 1.5 ppm per year in the 1990s. The growth rate rose to 2.2 ppm per year during the last decade. There is abundant and conclusive evidence that the acceleration is caused by increased emissions, Tans said.

The Mauna Loa data, together with measurements from sampling stations around the world, are collected by NOAA's Global Greenhouse Gas Reference Network and produce a foundational research dataset for international climate science.

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Oldest flaked stone tools point to the repeated invention of stone tools

Ethiopia map.

A new archaeological site discovered by an international and local team of scientists working in Ethiopia shows that the origins of stone tool production are older than 2.58 million years ago. Previously, the oldest evidence for systematic stone tool production and use was 2.58 to 2.55 million years ago.

Analysis by the researchers of early stone age sites, published this week in the Proceedings of the National Academy of Sciences, suggests that stone tools may have been invented many times in many ways before becoming an essential part of the human lineage.

The excavation site, known as Bokol Dora 1 or BD 1, is close to the 2013 discovery of the oldest fossil attributed to our genus Homo discovered at Ledi-Geraru in the Afar region of northeastern Ethiopia. The fossil, a jaw bone, dates to about 2.78 million years ago, some 200,000 years before the then oldest flaked stone tools. The Ledi-Geraru team has been working for the last five years to find out if there is a connection between the origins of our genus and the origins of systematic stone tool manufacture.

A significant step forward in this search was uncovered when Arizona State University geologist Christopher Campisano saw sharp-edged stone tools sticking out of the sediments on a steep, eroded slope.

"At first we found several artifacts lying on the surface, but we didn't know what sediments they were coming from," says Campisano. "But when I peered over the edge of a small cliff, I saw rocks sticking out from the mudstone face. I scaled up from the bottom using my rock hammer and found two nice stone tools starting to weather out."

It took several years to excavate through meters of sediments by hand before exposing an archaeological layer of animal bones and hundreds of small pieces of chipped stone representing the earliest evidence of our direct ancestors making and using stone knives. The site records a wealth of information about how and when humans began to use stone tools.

Preservation of the artifacts comes from originally being buried close to a water source.

"Looking at the sediments under a microscope, we could see that the site was exposed only for a very short time. These tools were dropped by early humans at the edge of a water source and then quickly buried. The site then stayed that way for millions of years," noted geoarchaeologist Vera Aldeias of the Interdisciplinary Center for Archaeology and Behavioral Evolution at the University of Algarve, Portugal.

Kaye Reed, who studies the site's ecology, is director of the Ledi-Geraru Research Project and a research associate with Arizona State University's Institute of Human Origins along with Campisano, notes that the animals found with these tools were similar to those found only a few kilometers away with the earliest Homo fossils.

"The early humans that made these stone tools lived in a totally different habitat than 'Lucy' did," says Reed. "Lucy" is the nickname for an older species of hominin known as Australopithecus afarensis, which was discovered at the site of Hadar, Ethiopia, about 45 kilometers southwest of the new BD 1 site. "The habitat changed from one of shrubland with occasional trees and riverine forests to open grasslands with few trees. Even the fossil giraffes were eating grass!"

In addition to dating a volcanic ash several meters below the site, project geologists analyzed the magnetic signature of the site's sediments. Over the Earth's history, its magnetic polarity has reversed at intervals that can be identified. Other earlier archaeological sites near the age of BD 1 are in "reversed" polarity sediments. The BD 1 site is in "normal" polarity sediments. The reversal from "normal" to "reversed" happened at about 2.58 million years ago, geologists knew that BD 1 was older than all the previously known sites.

The recent discovery of older hammering or "percussive" stone tools in Kenya dated to 3.3 million years ago, described as "Lomekwian," and butchered bones in Ethiopia shows the deep history of our ancestors making and using tools. However, recent discoveries of tools made by chimpanzees and monkeys have challenged "technological ape" ideas of human origins.

Archaeologists working at the BD 1 site wondered how their new stone tool discovery fit into this increasingly complex picture. What they found was that not only were these new tools the oldest artifacts yet ascribed to the "Oldowan," a technology originally named after finds from Olduvai Gorge in Tanzania, but also were distinct from tools made by chimpanzees, monkeys or even earlier human ancestors.

"We expected to see some indication of an evolution from the Lomekwian to these earliest Oldowan tools. Yet when we looked closely at the patterns, there was very little connection to what is known from older archaeological sites or to the tools modern primates are making," said Will Archer of the Max Planck Institute for Evolutionary Anthropology in Leipzig and the University of Cape Town.

The major differences appear to be the ability for our ancestors to systematically chip off smaller sharp-edged tools from larger nodules of stone. Chimpanzees and monkeys generally use tools for percussive activities, to hammer and bash food items like nuts and shellfish, which seems to have been the case with the 3.3 million year old Lomekwian tools as well.

Something changed by 2.6 million years ago, and our ancestors became more accurate and skilled at striking the edge of stones to make tools. The BD 1 artifacts captures this shift.

It appears that this shift in tool making occurred around the same time that our ancestor's teeth began to change. This can be seen in the Homo jaw from Ledi-Geraru. As our ancestors began to process food prior to eating using using stone tools, we start to see a reduction in the size of their teeth. Our technology and biology were intimately intertwined even as early as 2.6 million years ago.

The lack of clear connections with earlier stone tool technology suggests that tool use was invented multiple times in the past.

David Braun, an archaeologist with George Washington University and the lead author on the paper, noted, "Given that primate species throughout the world routinely use stone hammers to forage for new resources, it seems very possible that throughout Africa many different human ancestors found new ways of using stone artifacts to extract resources from their environment. If our hypothesis is correct then we would expect to find some type of continuity in artifact form after 2.6 million years ago, but not prior to this time period. We need to find more sites."

Read more at Science Daily

Downpours of torrential rain more frequent with global warming

The frequency of downpours of heavy rain -- which can lead to flash floods, devastation, and outbreaks of waterborne disease -- has increased across the globe in the past 50 years, research led by the Global Institute for Water Security at the University of Saskatchewan (USask) has found.

The number of extreme downpours increased steadily between 1964 and 2013 -- a period when global warming also intensified, according to research published in the journal Water Resources Research.

The frequency of 'extreme precipitation events' increased in parts of Canada, most of Europe, the Midwest and northeast region of the U.S., northern Australia, western Russia and parts of China, (see maps and graphics).

"By introducing a new approach to analyzing extremes, using thousands of rain records, we reveal a clear increase in the frequency extreme rain events over the recent 50 years when global warming accelerated," said Simon Papalexiou, a hydro-climatologist in USask's College of Engineering, and an expert in hydroclimatic extremes and random processes.

Papalexiou, who led the research, added: "This upward trend is highly unlikely to be explained by natural climatic variability. The probability of this happening is less than 0.3 per cent under the model assumptions used."

The USask study of over 8,700 daily rain records from 100,000 stations monitoring rain worldwide found the frequency of torrential rain between 1964 and 2013 increased as the decades progressed.

Between 2004 and 2013, there were seven per cent more extreme bouts of heavy rain overall than expected globally. In Europe and Asia, there were 8.6 per cent more 'extreme rain events' overall, during this decade.

Global warming can lead to increased precipitation because more heat in the atmosphere leads to more atmospheric water which, in turn, leads to rain.

Torrents of rain not only lead to flooding, but can threaten public health, overwhelming sewage treatment plants and increasing microbial contaminants of water. More than half a million deaths were caused by rain-induced floods between 1980 and 2009.

Heavy rain can also cause landslides, damage crops, collapse buildings and bridges, wreck homes, and lead to chaos on roads and to transport, with huge financial losses.

Co-author Alberto Montanari, professor of hydraulic works and hydrology at the University of Bologna and president of the European Geoscience Union, said:

"Our results are in line with the assumption that the atmosphere retains more water under global warming. The fact that the frequency, rather the magnitude, of extreme precipitation is significantly increasing has relevant implications for climate adaptation. Human systems need to increase their capability to react to frequent shocks."

The researchers screened data for quality and consistency, selecting the most robust and complete records from the 100,000 stations worldwide monitoring precipitation. Regions in South America and Africa were excluded from the study, as records for the study period were not complete or robust.

Papalexiou said planning for more frequent 'extreme' rain should be a priority for governments, local authorities and emergency services.

"If global warming progresses as climate model projections predict, we had better plan strategies for dealing with frequent heavy rain right now," said Papalexiou. "Our study of records from around the globe shows that potentially devastating bouts of extreme rain are increasing decade by decade.

Read more at Science Daily

In hot pursuit of dinosaurs: Tracking extinct species on ancient Earth via biogeography

Dinosaurs illustration.

One researcher at the University of Tokyo is in hot pursuit of dinosaurs, tracking extinct species around ancient Earth. Identifying the movements of extinct species from millions of years ago can provide insights into ancient migration routes, interaction between species, and the movement of continents.

"If we find fossils on different continents from closely related species, then we can guess that at some point there must have been a connection between those continents," said Tai Kubo, Ph.D., a postdoctoral researcher affiliated with the University Museum at the University of Tokyo.

A map of life -- biogeography

Previous studies in biogeography -- the geographic distribution of plants and animals -- had not considered the evolutionary relationships between ancient species. The new method that Kubo designed, called biogeographical network analysis, converts evolutionary relationships into geographical relationships.

For example, cats and dogs are more closely related to each other than to kangaroos. Therefore, a geographical barrier must have separated the ancestors of kangaroos from the ancestors of cats and dogs well before cats and dogs became separate species.

Most fossils are found in just a few hot-spot locations around the world and many ancient species with backbones (vertebrates) are known from just one fossil of that species. These limitations mean that a species' fossils cannot reveal the full area of where it was distributed around the world.

"Including evolutionary relationships allows us to make higher resolution maps for where species may have migrated," said Kubo.

The analysis used details from evolutionary studies, the location of fossil dig sites, and the age of the fossils. Computer simulations calculated the most likely scenarios for the migration of species between continents on the Cretaceous-era Earth, 145 to 66 million years ago.

North and south divide

This new analysis verified what earlier studies suggested: nonavian dinosaurs were divided into a group that lived in the Northern Hemisphere and another that lived in the Southern Hemisphere, and that those two groups could still move back and forth between Europe and Africa during the Early Cretaceous period (145 to 100 million years ago), but became isolated in the Late Cretaceous period (100 to 66 million years ago).

During the Early Cretaceous period, there were three major supercontinents: North America-Europe-Asia, South America-Africa, and Antarctica-India-Australia.

By the Late Cretaceous period, only the North America-Europe-Asia supercontinent remained. The other supercontinents had separated into the continents we know today, although they had not yet drifted to their current locations.

"During the Late Cretaceous period, high sea levels meant that Europe was a series of isolated islands. It makes sense that nonavian dinosaur species differentiated between Africa and Europe during that time," said Kubo.

Read more at Science Daily

Sponges collect penguin, seal, and fish DNA from the water they filter

Sea sponges, Aplysina aerophoba.

Just like humans leave DNA in the places we inhabit, water-dwelling animals leave DNA behind in the water column. In a paper published June 3 in the journal Current Biology, scientists report that sponges, which can filter 10,000 liters of water daily, catch DNA in their tissues as they filter-feed. This proof-of-concept study identified fish, seal, and penguin DNA in sponges from the Antarctic and Mediterranean, demonstrating that sponges can be used to monitor biodiversity.

"Sponges are ideal sampling units because you find them everywhere and in every aquatic habitat, including freshwater," says Stefano Mariani, a marine ecologist and population geneticist at the University of Salford. "Also, they're not very selective filter-feeders, they don't run away, and they don't get hurt by sampling -- you can just grab a piece, and they will regenerate nicely."

Additionally, the authors found that the presence of sponge DNA did not interfere with their ability to identify the DNA of other species caught within its tissue. Instead, they found that by using a particular DNA primer, which is a short sequence of nucleic acid that probes the DNA of specific organisms, they could selectively amplify vertebrate DNA while avoiding amplifying the sponge's DNA itself.

Using this process in tandem with metabarcoding, which sorts the jumble of DNA from the tissue sample into distinguishable, species-specific piles, Mariani and his team were able to identify 31 taxa. Mostly, the species identified were fish, but one sponge sample from Antarctica included DNA from Weddell seals and chinstrap penguins. The sample was later identified to be located offshore of a penguin breeding colony. "This was a really exciting find and also makes a lot of sense," says Mariani, "because the penguins would be in and out of the water a lot, eating, swimming, and pooing."

Currently, machines with large water-sampling capabilities are being developed to allow scientists to sample DNA from water, but the authors think using a natural sampler could be just as effective. Because the DNA found in water is extremely diluted, it needs to undergo extensive filtering -- but with filtering, Mariani warns, comes the danger of DNA contamination. Further, preserving water samples risks degrading the DNA. Sponge tissue, however, has already filtered out the water, greatly reducing both the processing time as well as the risk of contamination.

Further, bringing machines into some regions might not be feasible and may be too disruptive to fragile ecosystems. "If you want to study an endangered species of sawfish or a manatee in a mangrove forest in Mozambique, you can't go there with massive robots. You have to use a very low-tech approach," Mariani says.

Moving forward, the authors would like to investigate the ability of other animals to act as DNA samplers, particularly in open waters where sponges are either rare or unreachable by humans for sampling. Mariani suggests that other organisms such as jelly fish or salps, which also sieve water but float through the water column, may be more accessible in the open ocean.

Read more at Science Daily

Physicists can predict the jumps of Schrödinger's cat (and finally save it)

Schrödinger's cat concept.

Yale researchers have figured out how to catch and save Schrödinger's famous cat, the symbol of quantum superposition and unpredictability, by anticipating its jumps and acting in real time to save it from proverbial doom. In the process, they overturn years of cornerstone dogma in quantum physics.

The discovery enables researchers to set up an early warning system for imminent jumps of artificial atoms containing quantum information. A study announcing the discovery appears in the June 3 online edition of the journal Nature.

Schrödinger's cat is a well-known paradox used to illustrate the concept of superposition -- the ability for two opposite states to exist simultaneously -- and unpredictability in quantum physics. The idea is that a cat is placed in a sealed box with a radioactive source and a poison that will be triggered if an atom of the radioactive substance decays. The superposition theory of quantum physics suggests that until someone opens the box, the cat is both alive and dead, a superposition of states. Opening the box to observe the cat causes it to abruptly change its quantum state randomly, forcing it to be either dead or alive.

The quantum jump is the discrete (non-continuous) and random change in the state when it is observed.

The experiment, performed in the lab of Yale professor Michel Devoret and proposed by lead author Zlatko Minev, peers into the actual workings of a quantum jump for the first time. The results reveal a surprising finding that contradicts Danish physicist Niels Bohr's established view -- the jumps are neither abrupt nor as random as previously thought.

For a tiny object such as an electron, molecule, or an artificial atom containing quantum information (known as a qubit), a quantum jump is the sudden transition from one of its discrete energy states to another. In developing quantum computers, researchers crucially must deal with the jumps of the qubits, which are the manifestations of errors in calculations.

The enigmatic quantum jumps were theorized by Bohr a century ago, but not observed until the 1980s, in atoms.

"These jumps occur every time we measure a qubit," said Devoret, the F.W. Beinecke Professor of Applied Physics and Physics at Yale and member of the Yale Quantum Institute. "Quantum jumps are known to be unpredictable in the long run."

"Despite that," added Minev, "We wanted to know if it would be possible to get an advance warning signal that a jump is about to occur imminently."

Minev noted that the experiment was inspired by a theoretical prediction by professor Howard Carmichael of the University of Auckland, a pioneer of quantum trajectory theory and a co-author of the study.

In addition to its fundamental impact, the discovery is a potential major advance in understanding and controlling quantum information. Researchers say reliably managing quantum data and correcting errors as they occur is a key challenge in the development of fully useful quantum computers.

The Yale team used a special approach to indirectly monitor a superconducting artificial atom, with three microwave generators irradiating the atom enclosed in a 3D cavity made of aluminum. The doubly indirect monitoring method, developed by Minev for superconducting circuits, allows the researchers to observe the atom with unprecedented efficiency.

Microwave radiation stirs the artificial atom as it is simultaneously being observed, resulting in quantum jumps. The tiny quantum signal of these jumps can be amplified without loss to room temperature. Here, their signal can be monitored in real time. This enabled the researchers to see a sudden absence of detection photons (photons emitted by an ancillary state of the atom excited by the microwaves); this tiny absence is the advance warning of a quantum jump.

"The beautiful effect displayed by this experiment is the increase of coherence during the jump, despite its observation," said Devoret. Added Minev, "You can leverage this to not only catch the jump, but also reverse it."

This is a crucial point, the researchers said. While quantum jumps appear discrete and random in the long run, reversing a quantum jump means the evolution of the quantum state possesses, in part, a deterministic and not random character; the jump always occurs in the same, predictable manner from its random starting point.

"Quantum jumps of an atom are somewhat analogous to the eruption of a volcano," Minev said. "They are completely unpredictable in the long term. Nonetheless, with the correct monitoring we can with certainty detect an advance warning of an imminent disaster and act on it before it has occurred.

Read more at Science Daily

Transgenic fungus rapidly killed malaria mosquitoes in West African study

Mosquito.

According to the World Health Organization, malaria affects hundreds of millions of people around the world, killing more than 400,000 annually. Decades of insecticide use has failed to control mosquitoes that carry the malaria parasite and has led to insecticide-resistance among many mosquito strains. In response, scientists began genetically modifying mosquitoes and other organisms that can help eradicate mosquitoes. Until now, none of these transgenic approaches made it beyond laboratory testing.

In a research paper published in the May 31, 2019, issue of the journal Science, a team of scientists from the University of Maryland and Burkina Faso described the first trial outside the laboratory of a transgenic approach to combating malaria. The study showed that a naturally occurring fungus engineered to deliver a toxin to mosquitoes safely reduced mosquito populations by more than 99% in a screen-enclosed, simulated village setting in Burkina Faso, West Africa.

"No transgenic malaria control has come this far down the road toward actual field testing," said Brian Lovett, a graduate student in UMD's Department of Entomology and the lead author of the paper. "This paper marks a big step and sets a precedent for this and other transgenic methods to move forward."

"We demonstrated that the efficacy of the transgenic fungi is so much better than the wild type that it justifies continued development," said Raymond St. Leger, a Distinguished University Professor of Entomology at UMD and co-author of the study.

The fungus is a naturally occurring pathogen that infects insects in the wild and kills them slowly. It has been used to control various pests for centuries. The scientists used a strain of the fungus that is specific to mosquitoes and engineered it to produce a toxin that kills mosquitoes more rapidly than they can breed. This transgenic fungus caused mosquito populations in their test site to collapse to unsustainable levels within two generations.

"You can think of the fungus as a hypodermic needle we use to deliver a potent insect-specific toxin into the mosquito," said St. Leger.

The toxin is an insecticide called Hybrid. It is derived from the venom of the Australian Blue Mountains funnel-web spider and has been approved by the Environmental Protection Agency (EPA) for application directly on crops to control agricultural insect pests.

"Simply applying the transgenic fungus to a sheet that we hung on a wall in our study area caused the mosquito populations to crash within 45 days," Lovett said. "And it is as effective at killing insecticide-resistant mosquitoes as non-resistant ones."

Lovett said laboratory tests suggest that the fungus will infect the gamut of malaria-carrying mosquitoes. The abundance of species that transmit malaria has hindered efforts to control the disease, because not all species respond to the same treatment methods.

To modify the fungus Metarhizium pingshaense so that it would produce and deliver Hybrid, the University of Maryland research team used a standard method that employs a bacterium to intentionally transfer DNA into fungi. The DNA the scientists designed and introduced into the fungi provided the blueprints for making Hybrid along with a control switch that tells the fungus when to make the toxin.

The control switch is a copy of the fungus' own DNA code. Its normal function is to tell the fungus when to build a defensive shell around itself so that it can hide from an insect's immune system. Building that shell is costly for the fungus, so it only makes the effort when it detects the proper surroundings -- inside the bloodstream of a mosquito.

By combining the genetic code for that switch with the code for making Hybrid, the scientists were able to ensure that their modified fungus only produces the toxin inside the body of a mosquito. They tested their modified fungus on other insects in Maryland and Burkina Faso, and found that the fungus was not harmful to beneficial species such as honeybees.

"These fungi are very selective," St. Leger said. "They know where they are from chemical signals and the shapes of features on an insect's body. The strain we are working with likes mosquitoes. When this fungus detects that it is on a mosquito, it penetrates the mosquito's cuticle and enters the insect. It won't go to that trouble for other insects, so it's quite safe for beneficial species such as honeybees."

After demonstrating the safety of their genetically modified fungus in the lab, Lovett and St. Leger worked closely with scientific colleagues and government authorities in Burkina Faso to test it in a controlled environment that simulated nature. In a rural, malaria-endemic area of Burkina Faso, they constructed a roughly 6,550-square-foot, screened-in structure they called MosquitoSphere. Inside, multiple screened chambers contained experimental huts, plants, small mosquito-breeding pools and a food source for the mosquitoes.

In one set of experiments, the researchers hung a black cotton sheet coated with sesame oil on the wall of a hut in each of three chambers. One sheet received oil mixed with the transgenic fungus Metarhizium pingshaense, one received oil with wild-type Metarhizium and one received only sesame oil. Then, they released 1,000 adult male and 500 adult female mosquitoes into each chamber of MosquitoSphere to establish breeding populations. The researchers then counted mosquitoes in each chamber every day for 45 days.

In the chamber containing the sheet treated with the transgenic fungus, mosquito populations plummeted over 45 days to just 13 adult mosquitoes. That is not enough for the males to create a swarm, which is required for mosquitoes to breed. By comparison, the researchers counted 455 mosquitoes in the chamber treated with wild-type fungus and 1,396 mosquitoes in the chamber treated with plain sesame oil after 45 days. They ran this experiment multiple times with the same dramatic results.

In similar experiments in the lab, the scientists also found that females infected with transgenic fungus laid just 26 eggs, only three of which developed into adults, whereas uninfected females laid 139 eggs that resulted in 74 adults.

According to the researchers, it is critically important that new anti-malarial technologies, such as the one tested in this study, are easy for local communities to employ. Black cotton sheets and sesame oil are relatively inexpensive and readily available locally. The practice also does not require people to change their behavior, because the fungus can be applied in conjunction with pesticides that are commonly used today.

"By following EPA and World Health Organization protocols very closely, working with the central and local government to meet their criteria and working with local communities to gain acceptance, we've broken through a barrier," Lovett said. "Our results will have broad implications for any project proposing to scale up new, complex and potentially controversial technologies for malaria eradication."

Read more at Science Daily

Combination of three gene mutations results in deadly human heart disease

Heart and DNA concept

Congenital heart disease occurs in up to 1% of live births, and the infants who are affected may require multiple surgeries, life-long medication, or heart transplants. In many patients, the exact cause of congenital heart disease is unknown. While it is becoming increasingly clear that these heart defects can be caused by genetic mutations, it is not well understood which genes are involved and how they interact. Genetic mutations, also called genetic variants, can also cause poor heart function, but the type and severity of dysfunction varies widely even among those with the same mutation.

The Human Genome project allowed scientists to identify some rare cases of disease caused by severe mutations of a single gene, but scientists believe that more common forms of disease may be the result of a combination of more subtle genetic mutations that act together. Yet experimental proof for this concept of human disease has remained elusive -- until now.

In a paper published May 31 in the journal Science, scientists from the Gladstone Institutes and the University of California, San Francisco (UCSF) used technological advances to prove that three subtle genetic variants inherited within a family worked together to cause heart disease in multiple siblings at a very young age.

"The idea that several genetic variants are necessary to cause most complex diseases has been around for a long time, but proving it has been difficult," said Casey Gifford, PhD, a staff scientist at Gladstone who is the first author on the paper. "With the advent of CRISPR genome editing and improvements in human pluripotent stem cell technology, we felt that we finally had the right tools to test this hypothesis once we found the right case to study."

The right case turned out to be a family in which multiple children suffered from the same form of severe congenital heart disease that resulted in poor pumping of the heart. Gladstone President and UCSF Benioff Children's Hospitals cardiologist Deepak Srivastava, MD, first encountered the family when he treated a two-month-old child for left ventricular noncompaction, a type of heart disease where the cells in the left ventricle don't mature fully and therefore can't contract well leading to heart failure. While this child survived after requiring emergent life-support, she had a sibling who died from the same condition as a fetus in the third trimester, and her 4-year-old sister also had a similar condition. After running tests on both parents' hearts, the researchers learned that the father also had a milder, adult-onset version of the disease, while the mother's heart was normal.

"Given the severity of the disease in the children and the fact that one of the parents had an asymptomatic form, we suspected that the condition in the children was caused by a combination of the mother and the father's genes," says Srivastava, who is the senior author on the paper.

To test this theory, the researchers sequenced the genome of the family and discovered that the father had mutations in two genes, MKL2 and MYH7, that placed him at risk for heart disease. There are normally two copies of each gene in our genome, and in this case only one copy of MKL2 and MYH7 was mutated, resulting in a change of just one of hundreds of amino acids. All three children not only inherited both of these mutations from their father, but also a third mutation from the mother disrupting one copy of the gene NKX2-5. This mutation also affected just one amino acid and has been reported in the general population without heart disease. But the children also shared many other genetic variants in common, so whether altering just one copy of these three genes was enough to cause disease remained an open question.

Using CRISPR genome editing, Srivastava's team created the exact same mutations on one copy of each gene in mice. The mice that only harbored one copy of the father's two variants or the mother's variant didn't show any signs of heart disease. Remarkably, mice that had all three variants showed heart defects that mimicked those observed in the children. There was not only damage to the structure and function of the heart similar to the human disease, but also changes in the expression of hundreds of other genes essential for development of the heart and coronary vasculature.

"Our findings suggest that the gene inherited from the mother exacerbated the problem caused by the father's genes, resulting in a much more severe form of heart disease in the children," explained Gifford, who was a Damon Runyon Cancer Research Foundation Fellow when she performed the research.

In a final step, the researchers generated induced pluripotent stem cells from each of the family members and then turned the stem cells into beating heart cells. The cells from the children, which carried all three mutations, showed signs of disease, while the parents' cells did not.

The researchers say the study also answers an important question about how people with the same gene mutation can have different forms of the disease. For example, mutations of the gene MYH7 have previously been implicated in several different types of both congenital and adult-onset heart disease. The new data suggests that a modifier gene, in this case, NKX2-5, influences the effect of MYH7 variants to change how disease manifests.

Read more at Science Daily