Genetic Study may Track Dogs' Travels with Humans

A genetic study of a sexually transmitted canine cancer has offered clues to how dogs may have traveled around the world with their humans. Scientists analyzed the DNA of 440 nine tumors that exist today. Additional mutation allowed the scientists to trace the tumor's family tree. 

The research estimated the time since the mitochondrial transfer events by counting the number of mutations. One of them really seems to just track around maritime trade routes, in the last few hundred years. We found it along the coast of West Africa, in the Cape Vede Islands, Brazil, South Africa, India and some parts of southern Europe.

Genome Analysis lighted up the Arrivals and Spreading of first Americans

An international team of researchers compared the genomes of 31 living Native Americans, Siberians and people from Oceania with 23 Native Americans genome to establish a timeline for the arrival and spread of Amerindian populations. They concluded that the first Americans arrived after about 23,000 years ago and diverged around 13,000 years ago into two populations. They found no admixture of Polynesian or European genes, but did find some East Asian gene flow.

Source: University of California

Genetic ancestry of tigers explored

A 10-year study looked at DNA similarities of tigers -- living and extinct -- in order to better understand these animals as well as provide a new, more powerful tool for wildlife protection.

study, which is published online in the Journal of Heredity and will appear in the print edition May 1, 2015 describes DNA signatures for 145 individual tigers, including "voucher specimens" of tigers from verified geographic origins including Eurasian museum specimens that represented extinct subspecies

Tigers -- they are some of nature's most beautiful, deadly and endangered species. In fact, living tigers are severely endangered in fragmented geographic areas across Asia -- some reports show their numbers as low as 3,000 wild individuals. While there are efforts to help protect these magnificent creatures, more was needed in terms of research into the genetics of tigers.

 

The study's first results appeared in 2004 that showed Malayan tigers splitting from its Indochinese counterpart as a distinct, new fifth-living tiger subspecies. The latest results show that extinct Javan (1980s) and Bali (1940s) tigers were nearly indistinguishable from a molecular standpoint from Sumatran tigers just as the extinct Caspian tigers are nearly identical to surviving Amur tiger subspecies.

Source: Science Daily

New information changes few opinions on GMOs, global warming

First impressions are critical. So much so that for many people, even when they are given scientific information, they won't change their minds. This is particularly true for issues such as genetically modified foods and global warming. In fact, some people get even more defiant. 

In fact, some grow even more stubborn in their beliefs that GMOs are unsafe, said Brandon McFadden, an assistant professor in food and resource economics in the UF Institute of Food and Agricultural Sciences.
After they read scientific information stating that genetically modified foods are safe, 12 percent of the study's participants said they felt such foods were less safe -- not more, much to McFadden's astonishment.
That's partly because people form beliefs and often never let go of them, he said.
"This is critical and hopefully demonstrates that as a society we should be more flexible in our beliefs before collecting information from multiple sources," McFadden said. "Also, this indicates that scientific findings about a societal risk likely have diminishing value over time."
For the study, published in the current issue of the journal Food Policy, McFadden led a research project that surveyed 961 people across the U.S. via the Internet in April 2013.
To assess their beliefs about genetically modified foods, participants were asked to respond to statements such as: "Genetically modified crops are safe to eat." To gauge their beliefs about humans and global warming, they responded to statements such as: "Earth is getting warmer because of human actions."
Then they were given scientific information about genetically modified foods and global warming.
For example, researchers showed them this quote from the National Research Council regarding genetically modified food: "To date, no adverse health effects attributed to genetic engineering have been documented in the human population."
Respondents read several quotes about global warming, including this one from the American Association for the Advancement of Science: "The scientific evidence is clear: Global climate change caused by human activities is occurring now, and it is a growing threat to society."
After reading statements from scientific groups, participants were asked about their beliefs regarding the safety of genetically modified foods. The choices ranged from "much less safe" to "much more safe."
The results showed that before they received the information, 32 percent believed GM foods were safe to eat; 32 percent were not sure and 36 percent did not believe GM foods were safe to eat. After they received scientific information, about 45 percent believed genetically modified foods were safer to eat and 43 percent were not swayed by the information.
Then they were asked to assess the extent to which they believe human involvement caused global warming. They were given choices ranging from "much less involved" to "much more involved."
The study showed that before they received the information, 64 percent believed human actions are causing global warming; 18 percent were not sure and 18 percent did not believe human actions are to blame. After receiving scientific information about global warming, about 50 percent of participants believed even more strongly that human actions lead to global warming, while 44 percent were not swayed by the information, the study showed.
"Possibly, the best indicator for whether a person will adopt scientific information is simply what a person believes before receiving the information," McFadden said.

This story is taken from Science Daily

Quasi-sexual gene transfer drives genetic diversity of hot spring bacteria

New work from a multidisciplinary team of scientists used massive DNA sequencing of bacterial populations that grow in the hot springs in Yellowstone National Park to determine their genetic diversity and explore the underlying evolutionary dynamics. They found an unexpectedly high degree of sharing and exchange of genetic material between the tiny, green, photosynthetic cyanobacteria Synechococcus, which are abundant in these scalding, inhospitable environments. 

The team discovered that the pattern of differences in genome organization between various individuals of the same species indicates that the bacteria transfer DNA, including whole genes, back and forth. This swapping or "recombination" allows gene variations to spread rapidly through a population. Their findings are published by Science.
There is a great deal of small-scale genetic diversity in naturally occurring bacterial populations--as opposed to the carefully managed bacterial clones used in laboratory research and clinical work. Bacterial populations in the natural environment represent a dynamic genetic resource that changes over time, but the quantification of this diversity, and the exact mechanisms creating its dynamics, has remained elusive.
"Biologists have long been interested in determining the evolutionary and ecological forces that drive the population genetics of bacterial communities," Bhaya explained.
The research team, which also included lead author Michael Rosen as well as Daniel Fisher, both of the Applied Physics Department at Stanford University, set out to investigate this question by combining the power of so-called "deep sequencing" ( highly detailed and extensive DNA sequence determination) with powerful statistical analysis.
Several possible scenarios were considered. For instance, one theory predicts that bacterial populations are genetically diverse because they adapt to their surrounding conditions on a very small-scale, local level, leading to the establishment of distinct subpopulations, called ecotypes.
Another possibility was that all of the diversity in the bacterial genes is 'neutral'--no particular version of a gene makes an organism more or less fit for its environment. Bacteria reproduce by asexual division, which means that each new generation is stuck with a nearly exact replica of its sole parent's genetic material. Genetic changes can occur through mutation or the transfer of segments of DNA between individual organisms.
Using sophisticated statistical analysis of the massive "DNA deep sequencing" data enabled the team to trace the evolutionary forces that shaped these natural Synechococcus populations. They found that neither models of neutral drift, nor the concept of micro-niches of different ecotypes fit the data.
Rather, the population occupies a broad niche that includes a range of environmental conditions. Diversity is created by frequent swapping of genetic material between organisms. This apparently happens often enough that the population can be viewed as "quasi-sexual" in comparison to organisms like humans, where the process of sexual reproduction, specifically fertilization, combines genes from two parents.
In sexual reproduction, new combinations of genes are the rule. Although this is not generally true for bacterial populations, for these particular hot spring bacteria, new combinations are also the rule, rather than the exception. Since DNA moves between individuals, a new generation will not be stuck with just a copy of its parental genes. Because of this level of variation, natural selection acts on the level of individual genes, not the whole genome. Transfers of DNA happen so much that bacteria can have all sorts of different combinations of genes and gene variants.
"Without deep sequencing and careful analysis, we never would have been able to detect and identify the forces at work and it will be exciting to discover if these insights extend to other microbial communities," Bhaya noted. "Microbial diversity is found everywhere from deep sea vents to the human gut or in association with plant roots. Using methods such as single cell sequencing, proteomics, and microscopy will allow exploration of this invisible and important world with great accuracy and depth."

This story is taken from Science Daily

Phages transducing antibiotic resistance detected in chicken meat

Antimicrobial resistance in bacteria poses a global threat to public health. Common antibiotics are often ineffective in treating infectious diseases because pathogens acquire resistance genes. These antimicrobial resistance genes are obtained in different ways.

"The most frequent way is the transfer via mobile genetic elements such as plasmids, or via transposons, the so-called jumping genes," explains Friederike Hilbert, scientist at the Institute of Meat Hygiene at the Vetmeduni Vienna. "Transfer of resistances via phages was thought to play a minor role so far."

Hilbert and her colleagues isolated phages from 50 chicken samples purchased from Austrian supermarkets, street markets and butchers. They found phages in 49 samples. "Phages do not pose a risk to humans because they can only infect bacteria. No other cells or organisms can be infected."

Their analysis showed that one quarter of the phages under study were able to transduce antimicrobial resistance to E. coli bacteria under laboratory conditions. They transduced resistance to kanamycin, tetracycline, ampicillin, and chloramphenicol. No phage was able to transduce resistance to an extended-spectrum beta-lactam resistance (ESBL).

"This mechanism could also be important in clinical settings, where multiresistant pathogens are on the rise. We assume that phages acquire resistance genes from already resistant bacteria and then transfer those genes to other bacteria," says Hilbert. "Our results could explain why resistances spread so rapidly among bacteria."

Catalysts for evolution

Scientists have known for a while that phages are able to transduce genes but this was considered a rare event for genes encoding resistance to antibiotics. Newer DNA analyses show, however, that phages leave their signature in bacterial genomes. This way of transfer is presumably more frequent than thought. Phages may therefore play a major role in bacterial evolution.

Phages are more robust than bacteria

Compared to bacteria, phages are significantly more resistant to disinfectants. Alcohol, in particular, is hardly active against phages. "Common disinfection methods are often inappropriate against phages," Hilbert underlines. The food industry and also hospitals may choose disinfectants that are active against bacteria, but might be ineffective against phages.

Focussing on phage therapy

Treating bacterial infections with phages has become a promising alternative combating antimicrobial-resistant pathogens where phages directly combat bacteria. Hilbert recommends to test therapeutic phages for their ability to transfer resistance genes. The combination of phages and multiresistant pathogens could otherwise result in a hazardous cocktail of phages transferring multiresistance genes."

This story is taken from Science Daily

Mining pollution alters fish genetics in southwest England

Pollution from historic mining activities in south west England has led to a reduction in genetic diversity of brown trout according to new research. The findings indicate that human activity can alter the genetic patterns of wild populations -- an important issue in modern conservation. 

The prevalence of metal contaminants in rivers across the south west of England is directly linked to mining activities dating back hundreds of years. Exposure to high concentrations of metals can be detrimental to fish health, negatively impacting their genetic diversity and population structure.
Josephine Paris, lead author and postgraduate researcher at the University of Exeter said: "Our research shows that brown trout populations have been severely affected by both historical and contemporary mining practices. The effects of both metal contamination and changes in environmental geochemistry have driven dramatic changes in the genetic architecture of these fish. In the case of the Industrial Revolution, these shifts have occurred in less than 200 years, showing the speed and magnitude at which human activity can alter the genetics of species."
To investigate the genetic impacts of metal pollution, the researchers compared DNA samples from fifteen brown trout populations from heavily-polluted and 'clean' rivers.
Genetic analysis revealed that all trout populations from metal contaminated rivers derived from a single common ancestor approximately 960 years ago, during the medieval period when tin mining in the region is first documented. Metal contamination at this time led to genetically distinct populations in different rivers.
Around 150 years ago, during the Industrial Revolution, further genetic separation occurred when rivers were again polluted with significantly increased levels of metal contaminants. During this period, trout numbers substantially declined in heavily polluted areas like the River Hayle. Those trout that remained were less genetically diverse than trout in clean rivers.
Co-author Dr Andrew King Research Fellow in Biosciences at the University of Exeter said: "Trout in the metal contaminated rivers have evolved to live in water with metal concentrations that kill metal naïve fish. The metal contaminated populations are genetically distinct from one another and we think this is a response to the unique cocktail of metals found in each river. This raises the interesting question as to whether the ability to live in contaminated water has evolved once or multiple times."
The River Camel and the River Fal are considered 'clean' rivers, although they do contain some metals due to the underlying geology and ancient mining activity. Other rivers, including the River Hayle and the Red River, are known as 'metal rivers' as they contain significantly elevated levels of metal contaminants.
The research was conducted by Josephine Paris, PhD Biosciences student, Dr. Andrew King and Dr. Jamie Stevens of the Molecular Ecology and Evolution Group at the University of Exeter. Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations is published in Evolutionary Applications.

This story is taken from Science Daily

Water fleas genetically adapt to climate change

The water flea has genetically adapted to climate change. Biologists compared 'resurrected' water fleas -- hatched from 40-year-old eggs -- with more recent specimens to reach this conclusion. 

The water flea has genetically adapted to climate change. Biologists from KU Leuven, Belgium, compared 'resurrected' water fleas -- hatched from forty-year-old eggs -- with more recent specimens. The project was coordinated by Professor Luc De Meester from the Laboratory of Aquatic Ecology, Evolution and Conservation.
The water flea Daphnia is a zooplankton organism that is typically found in shallow ponds and lakes. Under normal circumstances, water fleas reproduce asexually: they clone themselves. But in difficult living conditions -- during food shortages or heat waves, for instance -- they switch to a different type of procreation: they mate and lay dormant eggs. These eggs are in fact encapsulated embryos that are resistant to harsh conditions. A dormant egg can remain in the sediment of a pond for dozens of years and still be able to hatch.
As the dormant eggs remain viable for a long time researchers can use resurrection ecology to examine the evolution of water fleas in a changing climate. Biologist Aurora Geerts explains: "When water fleas reproduce asexually, their offspring is genetically identical to the mother. But when they mate, this results in genetic variation. The genetically fittest water fleas -- the ones that are best adapted to the environment -- survive and lay dormant eggs. When we hatch the dormant eggs of water fleas from the past and compare them with the contemporary population, we can reconstruct the evolutionary changes that occurred in that population and examine how they have adapted to the rising temperature of the water in which they live."
The biologists used dormant eggs from Felbrigg Hall, a shallow lake in England: "Both the water flea population and the changes in temperature of that lake are well-documented. Over a period of forty years the average temperature near Felbrigg Hall has risen with 1.15 degrees Celsius. In addition, the number of heat waves has tripled. This causes stress to animals that live in such shallow water. From a Felbrigg Hall sediment core we selected dormant eggs from sediment layers matching the period 1955-1965 and a more recent layer from 1995-2005. We collected eggs from both time periods and hatched them. Then we examined the heat tolerance of the resulting populations from these two time periods by scoring the temperature at which the water fleas lost motor function and fainted. The critical maximum temperature for activity for the water fleas from the recent sediment layer is half a degree more than 40 years ago."
In another experiment, the biologists examined whether current populations of the water flea Daphnia can genetically adapt to higher temperatures. "Over the course of two years we exposed a population of water fleas to two temperature treatments: ambient temperature and ambient +4°C. From the sediment of experimental units of both treatment groups we hatched dormant eggs. We then measured the heat tolerance of the water fleas under standardized laboratory conditions. For the water fleas that had been exposed to a heated environment the critical temperature for activity was on average 3.6 degrees higher than for water fleas from the control group."
The findings indicate that water flea populations can adapt quite rapidly to rising temperatures. The study is the first to show that animal populations can adapt and already have adapted to higher temperatures and increased heat wave frequencies -- two results of climate change -- by means of evolutionary changes in their heat tolerance.
The capacity for genetic adaption is, however, not enough to guarantee success, Geerts adds: "Climate change may have an impact on other factors as well. The water flea might be exposed to more enemies, less food, or an increased sensitivity to parasites. But our results show that we need to take into account the evolutionary dynamics of a species if we want to predict how it will respond to climate change."

This story is taken from Science Daily

Evolution in action: Mate competition weeds out genetically modified fish from population

Wild-type zebrafish consistently beat out genetically modified Glofish in competition for female mates, an advantage that led to the disappearance of the transgene from the fish population over time, research has found. The study, the first to demonstrate evolutionary outcomes in the laboratory, showed that mate competition trumps mate choice in determining natural selection. 

The study, the first to demonstrate evolutionary outcomes in the laboratory, showed that mate competition trumps mate choice in determining natural selection. "Mating success is actually a stronger force of evolution than survival of the fittest," said William Muir, professor of animal sciences. "If an organism can't get a mate, it can't pass its genes on. In terms of evolution, whether it survives or not doesn't matter."
Muir and Richard Howard, professor emeritus of biology, conducted a long-term study of mating success in mixed populations of wild-type zebrafish and Glofish -- zebrafish containing a transgene cloned from a sea anemone that produces a fluorescent red protein. Although female zebrafish strongly preferred the neon red males to their brown, wild-type counterparts, the females were coerced into spawning with the wild-type males who aggressively chased away their transgenic rivals.
As a result, the rate at which the red transgenic trait appeared in offspring fell rapidly over 15 generations of more than 18,500 fish and ultimately disappeared in all but one of 18 populations. "The females didn't get to choose," Muir said. "The wild-type males drove away the reds and got all the mates. That's what drove the transgene to extinction."
Except for their mating competitiveness, wild-type males and Glofish males were similar in fitness -- that is, their health, fertility and lifespan -- which was unexpected since genetically modifying an organism often decreases its ability to flourish, Muir said.
"Natural selection has had billions of years to maximize an organism's fitness for its environment," he said. "Changing its genetics in any way almost always makes an organism less fit for the wild. You've 'detuned' it."
The similarity of the wild-type zebrafish and Glofish made it possible to test mate competition and mate choice simultaneously, which few studies have done, Howard said.
"I've lectured on evolution for 25 years and never found a study that linked the mechanisms of evolution with the pattern of evolutionary outcomes," he said. "This study puts the whole story together."
The study also showed the effectiveness of a model Muir developed to assess the potential risk posed to natural populations by transgenic organisms. The model, which measures six fitness components, can be used to predict what would happen if a particular transgene were released in the wild. Its premise lies in a simple principle: If a transgene makes an organism fitter than wild types for an environment, it could pose a risk to natural populations or the ecosystem. If a transgene makes the organism less fit, the gene will be weeded out of the population over time.
"Darwin was right: Survival of the fittest works," Muir said. "If we make a transgenic organism that has reduced fitness in the wild, evolution takes over and removes it. Nature experiments with mutations all the time, and it only saves the best of the best."
Based on the model, the researchers predicted that wild-type males would chase other males and females more than Glofish males would, have greater success in securing mates and produce more offspring. The laboratory findings confirmed their predictions.
The study shows that if Glofish were released into the wild, the transgenic trait would eventually disappear as the result of sexual selection. Muir stressed that "the model does not say that even if we find no risks, we should release transgenic fish into the wild. It simply says what would likely happen if we did."
The model can be applied to genetically modified plants as well as animals and is one tool used by the U.S. Food and Drug Administration to assess potential risks posed by transgenic organisms, he said.
Glofish are the only transgenic animals approved for sale to the public by the FDA.

This story is taken from Science Daily

From the depths of a microscopic world, spontaneous cooperation

A clever combination of two different types of computer simulations enabled a group of researchers to uncover an unexpectedly cooperative group dynamic: the spontaneous emergence of resource sharing among individuals in a community. Who were the members of this friendly, digitally represented collective? Escherichia coli, rod-shaped bacteria found in the digestive systems of humans and many other animals.

The finding, initially predicted by mathematical models and then confirmed through empirical testing, was reported recently in BMC Systems Biology. William and Janet Lycan Professor of Chemistry Zan Luthey-Schulten, graduate student John Cole, and colleagues have worked for several years on computer simulations of bacterial growth. Cole was initially intrigued by the possibility of modifying the lab's Lattice Microbe software, which models how molecules such as sugars or proteins diffuse and react, with another type of computer simulation, which tracks how individual cells metabolize those molecules.
"We thought, can we marry these two approaches?" said Cole. "Let's put a whole bunch of cells in a shared environment and simulate the glucose and oxygen concentrations outside." Cole merged the two models, eventually developing an entirely new simulation code, in order to predict how bacteria within colonies access and metabolize resources as the colony expands.
Bacteria such as E. coli adapt their metabolism--what they use as fuel and how they break it down--according to what resources they have available. Just like human muscle cells, bacteria prefer to burn glucose in the presence of oxygen, but can also release some of the energy stored in glucose through a form of metabolism that does not require oxygen. Similar to lactic acid production in a tired sprinter's muscles, this metabolic pathway produces a chemical byproduct, acetate, that still contains some unharvested chemical energy.
Luthey-Schulten is a faculty member at the Carl R. Woese Institute for Genomic Biology (IGB). In the Luthey-Schulten lab's work, colony growth was simulated in 3D, which allowed Cole and others to model what would happen as the colony grew larger, making it harder for oxygen to penetrate to inside layers, or for glucose from the growth substrate to reach the top.
Allowing these resource disparities to emerge in the model revealed something unexpected and novel, yet intuitive. The model predicted that the bacteria would spontaneously begin to cooperate to make the most of their resources.
In the simulated colonies, cells at the bottom, lacking oxygen, would break down glucose into acetate. Cells at the top would take up that acetate and use their access to oxygen to complete its breakdown, extracting the remaining available energy from the original glucose substrate. Cells in the outermost ring, with access to both glucose and oxygen, exhibited the most growth and reproduction.
"As soon as I saw it, I thought, it makes perfect sense," said Cole. "It has to be going on at some level, and I'm sure it's testable."
To test the model's predictions, Luthey-Schulten, Cole and colleagues ventured into empirical work: they grew and monitored bacterial colonies in the lab, in conditions that matched those they had simulated. With microscopy support from Miyandi Sivaguru, assistant director of the IGB Core Facilities, they used a genetically engineered fluorescent dye to visually track bacterial cells that used acetate as a fuel source. The fluorescent label could be seen in the upper layers of cells in the middle of the colony, just as the simulation predicted.
One striking feature of both the simulated and real colonies in the study is that cooperative task specialization was able to quickly emerge among genetically identical or near-identical cells. The authors hope that the model can be adapted to reveal new insights into the behavior of other groups of cells, including cancer-causing tumors.

This story is taken from Science Daily

How does a honeybee queen avoid inbreeding in her colony?

Recombination, or crossing-over, occurs when sperm and egg cells are formed and segments of each chromosome pair are interchanged. This process plays an crucial role in the maintenance of genetic variation. Biologists have studied recombination in honeybees. The extreme recombination rates found in this species seem to be crucial for their survival. 

Like other social insects, honeybees live in colonies consisting mainly of closely related members of the worker caste. High genetic diversity among the workers is important for the whole colony's survival. There are several theories as to why: for example, a genetically variable workforce may be best equipped to perform the diverse tasks required in the colony, and diverse colonies may also be less susceptible to disease. But how can the queen, the colony's only fertile female, prevent inbreeding and maintain genetic variation?
The queen bee solves the problem in two ways. One is through polyandry. She mates with a score of drones and uses their sperm to fertilize the eggs randomly so that workers often have different fathers. The second is through extremely high rates of recombination.
By sequencing the entire genome of 30 African honeybees, the research team has been able to study recombination at a level of detail not previously possible. The frequency of recombination in the honeybee is higher than measured in any other animal and is more than 20 x higher than in humans.
Recombination affects how efficiently natural selection can promote favorable genetic variants. In line with this, the researchers have found that genes involved in the new adaptations to the environment in honeybees also undergo more recombination. But recombination is not entirely risk free.
"Recombination is not only beneficial for bees. When parts of chromosomes broken and exchanged, errors can sometimes occur during their repair due to a process called "GC-biased gene conversion," says Matthew Webster.
This process leads to gradual fixation of mutations that may be harmful to the honeybee. Although a similar process occurs in humans, it is more than ten times stronger in honeybees. Over time, recombination is expected to lead to a deterioration of the gene pool, a process that seems to have accelerated in bees. The extreme recombination rates -- crucial for maintaining genetically diverse honeybee colonies -- come with a high price.
"There are no free lunches. Not even for a honeybee," says Matthew Webster.

This story is taken from Science Daily

DNA that only females have

In many animal species, the chromosomes differ between the sexes. The male has a Y chromosome. In some animals, however, for example birds, it is the other way round. In birds, the females have their own sex chromosome, the W chromosome. For the first, researchers have mapped the genetic structure and evolution of the W chromosome. 

Every individual of a species has the same sorts of chromosomes, with one exception. In many species, the way the sexes differ is that males have their own sex chromosome, the Y chromosome. This contains genes which result in the development of male characters and reproductive organs. If there is no Y chromosome, the organism will be a female.
In birds, however, the situation is different. It is the females which have a unique sex chromosome -- the W chromosome.
In a study published in Nature Communications, Linnea Smeds, Hans Ellegren and their colleagues show that, surprisingly enough, a bird's W chromosome does not contain genes that lead to the development of a female.
"Sex determination in birds and other animals with a W chromosome seems instead to depend upon the number of their equivalent to the X chromosome. Two copies of it produces a male, one copy (plus a W chromosome) produces a female," says Hans Ellegren.
The W chromosome seems instead to function as some kind of buffer for females since it contains genes similar to those in the X chromosome. In order for certain genes to work, it is critical that an individual has two copies of that gene. In this way, the W chromosome can serve as a complement for females who only have one copy of the X chromosome.
Researchers have discovered that the W chromosome changes at a slower rate than any other part of the genetic material.
"This is because it is only inherited on the maternal side and fewer mutations arise in females than in males," says Hans Ellegren.
Most mutations occur during the formation of germ cells. Males produce a vastly greater number of germ cells than females and so the probability that a sperm contains a new mutation is much greater than for an egg cell.
The W chromosome is the only chromosome from the cell nucleus which is inherited on the maternal side. It shares this property with the small amount of DNA found in cell mitochondria.

This story is taken from Science Daily

How feedback from cortex helps mammals make fine distinctions about odors

Everyday tasks we may regard as 'simple' -- for example, knowing the difference between the smell of an orange and a pickle -- are actually marvels of evolutionary development, the work of eons. A neuroscience team reports results of experiments that suggest how the mammalian brain distinguishes odors -- not just dissimilar ones but, perhaps more importantly, odors that are nearly identical, such as the scents of oranges and tangerines. 

Precise discrimination of olfactory signals from the environment is nothing less than a survival skill, more so for mice, our mammalian cousins, than for us. Mice have relatively poor vision, and it is only thanks to their other senses, notably their incredible ability to identify and discriminate odors, that they can successfully hunt for food or choose a mate. Understanding how they do this, in turn, sheds light on the workings of our much more complex, but structurally related, brains.

Led by CSHL Assistant Professor Florin Albeanu, the team explored a function in the mouse brain that scientists still don't know much about. After a mouse samples a smell by sniffing, and signals from that activity are gathered and subjected to preliminary processing in the animal's olfactory bulb, the bulb sends "output" signals to the brain's higher processing center, the cerebral cortex. Albeanu's team focused on "feedback" -- the signal that the olfactory cortex, in turn, sends back to the olfactory bulb. While there are theories aplenty about the nature and purpose of this feedback signal, very little is known about it.

Even in the mouse brain, the feedback loop is a good deal more complex than just described. The olfactory bulb sends output to and receives feedback from multiple parts of the brain. Albeanu's team focused on one such feedback loop: signals sent from two principal cell types in the bulb, called mitral cells and tufted cells. These signals travel over long-distance axons to various parts of the brain, but most prominently to the piriform cortex. That's the brain's primary center for higher olfactory processing.

Some theorists have speculated that the piriform cortex works as a pattern-recognition device that compares incoming sensory inputs with representations of previously experienced odors, stored up in memory. Not only is the piriform cortex thought to do this job; it is also involved in the integration of this information with contextual information (ranging from other data about the environment to whether the animal is hungry, amorous, afraid, etc.). Further, it is theorized that based on this data, the piriform cortex sends signals back to the olfactory bulb -- feedback -- that is essentially predictive, helping the animal to make decisions based on all available information.

Albeanu's team, which included co-first authors Drs. Gonzalo Otazu and Hongggo Chae, as well as technician Martin Davis, made a series of discoveries in two related sets of experiments that support some of these theories. In one set, as they exposed awake mice to a panel of about 30 odorants, one by one, they traced the axons projecting back to the olfactory bulb from the piriform cortex -- the "wires," in effect, that carry the feedback signal -- and measured the responses of tiny button-like structures called synaptic boutons, the sites where these cortical feedback axons form connections, or synapses, in the bulb with local receiving neurons. These so-called interneurons are inhibitory.

"The idea was to image the responses of the boutons in the olfactory bulb to a set of odorants," explains Albeanu. "It's very hard to physically access the piriform cortex for optical imaging, so we used these boutons as a proxy to indicate the nature of the signal that the cortex is feeding back to the bulb."

The results were "striking," says Albeanu. First, it was clear that any given bouton responded only to a small fraction of the 30 odorants -- perhaps two or three, on average. This is what neuroscientists call a "sparse" response, and it indicates specificity. This immediately cast doubt on an existing theory suggesting that the feedback to the bulb is non-specific and acts like the volume, or "gain," control on an audio system. Rather, the response was specific and highly selective. Not only did a given bouton respond to very few odors; if it responded to one by amplifying the feedback signal (above the background level, since there is always activity in the circuit), it tended to perform that same function, amplification, on all of the odors it responded to. Conversely, those boutons that tamped down the signal coming back from the cortex tended to do that for all of the odors they responded to.

A second set of experiments enabled Albeanu's team to offer a new hypothesis of the purpose of this particular cortical feedback. By injecting mice with a drug that inactivates the piriform cortex, they were able to examine the activity of the output cells in the olfactory bulb that normally integrate the cortical feedback via inhibitory interneurons. Again a striking result: as compared with their activity profiles when receiving feedback, mitral cells in the olfactory bulb tended to have overlapping responses when the feedback was cut off. In other words, their activity profiles started to look quite similar. This suggests that without feedback from the cortex, mitral cells are no longer to supply the animal with information that can sharply distinguish odors, particularly odors that are chemically similar.

Taken together, the results lead Albeanu to propose that feedback from the cortex is highly specific, and likely used to create a useful representation of the animal's environment, "in a very specific and selective fashion that, in turn, is used to extract the identity of a given odor and to separate it from other odors," Albeanu says. The research continues now in experiments featuring animals that are actively engaged in odor discrimination in their environment, in order to obtain behavioral evidence to correlate with the results of the experiments published today.

This story is taken from Science Daily

Reprogramming of DNA observed in human germ cells for first time

A team of researchers has described for the first time in humans how the epigenome -- the suite of molecules attached to our DNA that switch our genes on and off -- is comprehensively erased in early primordial germ cells prior to the generation of egg and sperm. However, the study shows some regions of our DNA -- including those associated with conditions such as obesity and schizophrenia -- resist complete reprogramming. 

Although our genetic information -- the 'code of life' -- is written in our DNA, our genes are turned on and off by epigenetic 'switches'. For example, small methyl molecules attach to our DNA in a process known as methylation and contribute to the regulation of gene activity, which is important for normal development. Methylation may also occur spontaneously or through our interaction with the environment -- for example, periods of famine can lead to methylation of certain genes -- and some methylation patterns can be potentially damaging to our health. Almost all of this epigenetic information is, however, erased in germ cells prior to transmission to the next generation
Professor Azim Surani from the Wellcome Trust/Cancer Research UK Gurdon Institute at the University of Cambridge, explains: "Epigenetic information is important for regulating our genes, but any abnormal methylation, if passed down from generation to generation, may accumulate and be detrimental to offspring. For this reason, the information needs to be reset in every generation before further information is added to regulate development of a newly fertilised egg. It's like erasing a computer disk before you add new data."
When an egg cell is fertilized by a sperm, it begins to divide into a cluster of cells known as a blastocyst, the early stage of the embryo. Within the blastocyst, some cells are reset to their master state, becoming stem cells, which have the potential to develop into any type of cell within the body. A small number of these cells become primordial germ cells with the potential to become sperm or egg cells.
In a study funded primarily by the Wellcome Trust, Professor Surani and colleagues showed that a process of reprogramming the epigenetic information contained in these primordial germ cells is initiated around two weeks into the embryo's development and continues through to around week nine. During this period, a genetic network acts to inhibit the enzymes that maintain or programme the epigenome until the DNA is almost clear of its methylation patterns.
Crucially, however, the researchers found that this process does not clear the entire epigenome: around 5% of our DNA appears resistant to reprogramming. These 'escapee' regions of the genome contain some genes that are particularly active in neuronal cells, which may serve important functions during development. However, data analysis of human diseases suggests that such genes are associated with conditions such as schizophrenia, metabolic disorders and obesity.
Walfred Tang, a PhD student who is the first author on the study, adds: "Our study has given us a good resource of potential candidates of regions of the genome where epigenetic information is passed down not just to the next generation but potentially to future generations, too. We know that some of these regions are the same in mice, too, which may provide us with the opportunity to study their function in greater detail."
Epigenetic reprogramming also has potential consequences for the so-called 'dark matter' within our genome. As much as half of human DNA is estimated to be comprised of 'retroelements', regions of DNA that have entered our genome from foreign invaders including bacteria and plant DNA. Some of these regions can be beneficial and even drive evolution -- for example, some of the genes important to the development of the human placenta started life as invaders. However, others can have a potentially detrimental effect -- particularly if they jump about within our DNA, potentially interfering with our genes. For this reason, our bodies employ methylation as a defence mechanism to suppress the activity of these retroelements.
"Methlyation is effective at controlling potentially harmful retroelements that might harm us, but if, as we've seen, methylation patterns are erased in our germ cells, we could potentially lose the first line of our defence," says Professor Surani.
In fact, the researchers found that a notable fraction of the retroelements in our genome are 'escapees' and retain their methylation patterns -- particularly those retroelements that have entered our genome in our more recent evolutionary history. This suggests that our body's defence mechanism may be keeping some epigenetic information intact to protect us from potentially detrimental effects.

This story is taken from Science Daily

High levels of moral reasoning correspond with increased gray matter in brain

Individuals with a higher level of moral reasoning skills showed increased gray matter in the areas of the brain implicated in complex social behavior, decision making, and conflict processing as compared to subjects at a lower level of moral reasoning, according to new research. 

Moral development research pioneered by psychologist Lawrence Kohlberg in the mid-20th century shows that people progress through different stages of moral reasoning as their cognitive abilities mature. Neuroscience has recently reinvigorated moral psychology by introducing new methods for studying moral decision-making. However, no study to date has quantified brain structures supporting individual stages of moral reasoning.

"To investigate this question, we employed a sample of MBA students ages 24 to 33, past the age at which structural brain maturation is complete, and tested their moral reasoning, then looked at the level of gray matter in the brains of a subset of subjects," said senior author Hengyi Rao, PhD, a research assistant professor of Cognitive Neuroimaging in Neurology and Psychiatry in the Perelman School of Medicine.

"MBA students were ideal candidates for this work, as the Wharton curriculum addresses issues of moral decision-making and reasoning," explained Diana Robertson, PhD, a professor of legal studies and business ethics at the Wharton School and an author of the study. "We aimed to investigate whether the stage of moral reasoning is reflected in structural brain architecture."

A total of 67 MBA students were administered the Defining Issue Test to determine which pattern of thought or behavior, known as cognitive schema, each student used when reasoning about moral issues. In it, students were presented with complex moral dilemmas such as medical assisted suicide and asked them to choose the relevance of each of 12 given rationales. Based on the results, subjects were then assigned to one of seven schema types which represent increasing levels of moral development. Students then underwent MRI scanning to investigate differences in gray matter volume between students who reached the post-conventional level of moral reasoning compared to those who have not reached that level yet.

Subjects also underwent personality testing and were placed into one of the following categories: neuroticism, extraversion, openness to experience, conscientiousness, and agreeableness. Analysis showed higher scores in openness to experience and lower scores in neuroticism for participants at the more advanced levels of moral development.

With regard to brain structure, the team observed increased gray matter in the prefrontal cortex in subjects who reached the post-conventional level of moral reasoning compared to those who are still at a pre-conventional and conventional level. In other words, gray matter volume was correlated with the subject's degree of post-conventional thinking.

"This research adds an investigation of individual differences in moral reasoning to the expanding landscape of moral neuroscience," Rao said. "The current findings provide initial evidence for brain structural difference based on the stages of moral reasoning proposed by Lawrence Kohlberg decades ago. However, further research will be needed to determine whether these changes are the cause or the effect of higher levels of moral reasoning."

This story is taken from Science Daily

Study pinpoints what part genes play in the age of first-time moms, family size

Researchers have analyzed the genomes of thousands of women in the UK and the Netherlands to measure the extent to which a woman's genes play a role for when she has her first baby and how many children she will have. Significantly, they have found that some women are genetically predisposed to have children earlier than others, and conclude that they have passed down their reproductive advantage to the next generation. 

The research was carried out by an international team working on the Sociogenome project, led by the University of Oxford and funded by the European Research Council. The researchers exploited the latest advances in molecular and quantitative genetics taking existing datasets of 4,300 unrelated women in the Netherlands from the Lifelines Cohort Study. They combined these results with data relating to 2,400 women from TwinsUK, the country's largest adult twin registry (from which they randomly selected only one twin for analysis).
The researchers found that genes account for about 15 per cent of the differences between modern women when they have their first baby, and 10 per cent in the differences in the number of children they have. They also discovered an overlap between these genetic effects that the study says partly explains why women who have children earlier also have a higher number of children.
Previous similar studies have relied on datasets relating to twins or within families, but this is the first time that researchers have used molecular genetic information of unrelated women including the population-based Lifelines Study. By combining the genetic results of both datasets from this large sample, they found that natural selection is not just an historical process. Modern societies are still evolving today, with early fertility patterns being an inherited reproductive advantage, says the paper.
Project leader Professor Melinda Mills, from the Department of Sociology at the University of Oxford and Nuffield College, said: 'In evolutionary and genetic terms, this suggests that younger generations today should be inclined to have children at an earlier age than women in the past. However, what we actually observe is that the reverse is happening. Social and environmental factors mean women in modern societies are delaying starting families, knowing that there is the risk of becoming infertile if they leave it too late. This research tells us there are genetic differences between women which could be significant for women making decisions about when to have their first baby.'
Lead author Felix Tropf, from the University of Groningen in the Netherlands, said: 'In the second half of the 20th century, women across many societies delayed starting a family. Although genes play a significant part, it seems wider social changes, such as an expansion of women in further education and work, as well as the availability of effective contraception, are having a stronger effect on determining when women in modern societies have children.'

This story is taken from Science Daily

Programming DNA to reverse antibiotic resistance in bacteria

New research introduces a promising new tool to combat the rapid, extensive spread of antibiotic resistance around the world. It nukes antibiotic resistance in selected bacteria, and renders other bacteria more sensitive to antibiotics. The research, if ultimately applied to pathogens on hospital surfaces or medical personnel's hands, could turn the tide on untreatable, often lethal bacterial infections. 

New Tel Aviv University research published in PNAS introduces a promising new tool: a two-pronged system to combat this dangerous situation. It nukes antibiotic resistance in selected bacteria, and renders other bacteria more sensitive to antibiotics. The research, led by Prof. Udi Qimron of the Department of Clinical Microbiology and Immunology at TAU's Sackler Faculty of Medicine, is based on bacterial viruses called phages, which transfer "edited" DNA into resistant bacteria to kill off resistant strains and make others more sensitive to antibiotics.
According to the researchers, the system, if ultimately applied to pathogens on hospital surfaces or medical personnel's hands, could turn the tide on untreatable, often lethal bacterial infections. "Since there are only a few pathogens in hospitals that cause most of the antibiotic-resistance infections, we wish to specifically design appropriate sensitization treatments for each one of them," Prof. Qimron says. "We will have to choose suitable combinations of DNA-delivering phages that would deliver the DNA into pathogens, and the suitable combination of 'killing' phages that could select the re-sensitized pathogens."
Reprogramming the system
"Antibiotic-resistant pathogens constitute an increasing threat because antibiotics are designed to select resistant pathogens over sensitive ones," Prof. Qimron says. "The injected DNA does two things: It eliminates the genes that cause resistance to antibiotics, and it confers protection against lethal phages.
"We managed to devise a way to restore antibiotic sensitivity to drug-resistant bacteria, and also prevent the transfer of genes that create that resistance among bacteria," he continues.
Earlier research by Prof. Qimron revealed that bacteria could be sensitized to certain antibiotics -- and that specific chemical agents could "choose" those bacteria more susceptible to antibiotics. His strategy harnesses the CRISPR-Cas system -- a bacterial DNA-reprogramming system Prof. Qimron pioneered -- as a tool to expand on established principles.
According to the researchers, "selective pressure" exerted by antibiotics renders most bacteria resistant to them -- hence the epidemic of lethal resistant infections in hospitals. No counter-selection pressure for sensitization of antibiotics is currently available. Prof. Qimron's strategy actually combats this pressure -- selecting for the population of pathogens exhibiting antibiotic sensitivity.
"We believe that this strategy, in addition to disinfection, could significantly render infections once again treatable by antibiotics," said Prof. Qimron.
Prof. Qimron and his team are now poised to apply the CRISPR/phage system on pseudomonas aeruginosa -- one of the world's most prevalent antibiotic-resistant pathogens involved in hospital-acquired infections -- and to test whether bacterial sensitization works in a more complex microbial environment: the mouse cage.

This story is taken from Science Daily

Your viral infection history in a single drop of blood

New technology makes it possible to test for current and past infections with any known human virus by analyzing a single drop of a person's blood. The method, called VirScan, is an efficient alternative to existing diagnostics that test for specific viruses one at a time. 

  With VirScan, scientists can run a single test to determine which viruses have infected an individual, rather than limiting their analysis to particular viruses. That unbiased approach could uncover unexpected factors affecting individual patients' health, and also expands opportunities to analyze and compare viral infections in large populations. The comprehensive analysis can be performed for about $25 per blood sample.

Stephen Elledge, an HHMI investigator at Brigham and Women's Hospital, led the development of VirScan. "We've developed a screening methodology to basically look back in time in people's [blood] sera and see what viruses they have experienced," he says. "Instead of testing for one individual virus at a time, which is labor intensive, we can assay all of these at once. It's one-stop shopping."
Elledge and his colleagues have already used VirScan to screen the blood of 569 people in the United States, South Africa, Thailand, and Peru. The scientists described the new technology and reported their findings in the June 5, 2015, issue of the journal Science.
VirScan works by screening the blood for antibodies against any of the 206 species of viruses known to infect humans. The immune system ramps up production of pathogen-specific antibodies when it encounters a virus for the first time, and it can continue to produce those antibodies for years or decades after it clears an infection. That means VirScan not only identifies viral infections that the immune system is actively fighting, but also provides a history of an individual's past infections.
To develop the new test, Elledge and his colleagues synthesized more than 93,000 short pieces of DNA encoding different segments of viral proteins. They introduced those pieces of DNA into bacteria-infecting viruses called bacteriophage. Each bacteriophage manufactured one of the protein segments -- known as a peptide -- and displayed the peptide on its surface. As a group, the bacteriophage displayed all of the protein sequences found in the more than 1,000 known strains of human viruses.
Antibodies in the blood find their viral targets by recognizing unique features known as epitopes that are embedded in proteins on the virus surface. To perform the VirScan analysis, all of the peptide-displaying bacteriophage are allowed to mingle with a blood sample. Antiviral antibodies in the blood find and bind to their target epitopes within the displayed peptides. The scientists then retrieve the antibodies and wash away everything except for the few bacteriophage that cling to them. By sequencing the DNA of those bacteriophage, they can identify which viral protein pieces were grabbed onto by antibodies in the blood sample. That tells the scientists which viruses a person's immune system has previously encountered, either through infection or through vaccination. Elledge estimates it would take about 2-3 days to process 100 samples, assuming sequencing is working optimally. He is optimistic the speed of the assay will increase with further development.
To test the method, the team used it to analyze blood samples from patients known to be infected with particular viruses, including HIV and hepatitis C. "It turns out that it works really well," Elledge says. "We were in the sensitivity range of 95 to 100 percent for those, and the specificity was good -- we didn't falsely identify people who were negative. That gave us confidence that we could detect other viruses, and when we did see them we would know they were real."
Elledge and his colleagues used VirScan to analyze the antibodies in 569 people from four countries, examining about 100 million potential antibody/epitope interactions. They found that on average, each person had antibodies to ten different species of viruses. As expected, antibodies against certain viruses were common among adults but not in children, suggesting that children had not yet been exposed to those viruses. Individuals residing South Africa, Peru, and Thailand, tended to have antibodies against more viruses than people in the United States. The researchers also found that people infected with HIV had antibodies against many more viruses than did people without HIV.
Elledge says the team was surprised to find that antibody responses against specific viruses were surprisingly similar between individuals, with different people's antibodies recognizing identical amino acids in the viral peptides. "In this paper alone we identified more antibody/peptide interactions to viral proteins than had been identified in the previous history of all viral exploration," he says. The surprising reproducibility of those interactions allowed the team to refine their analysis and improve the sensitivity of VirScan, and Elledge says the method will continue to improve as his team analyzes more samples. Their findings on viral epitopes may also have important implications for vaccine design.
Elledge says the approach his team has developed is not limited to antiviral antibodies. His own lab is also using it to look for antibodies that attack a body's own tissue in certain autoimmune diseases that are associated with cancer. A similar approach could also be used to screen for antibodies against other types of pathogens.

This story is taken from  Science Daily

Largest turtle breeding colony in the Atlantic discovered

A new study has revealed that the Central African country of Gabon is providing an invaluable nesting ground for a vulnerable species of sea turtle considered a regional conservation priority. 

A huge ground survey covering nearly 600 km of Gabon's coastline has uncovered the largest breeding colony of olive ridley turtles in the Atlantic. The study, published in the journal Biological Conservation, is the first to combine existing monitoring data with a back-to-basics coastal survey of the area. The results suggest that Gabon hosts the most important rookery for this species in the Atlantic, with estimates indicating that there could be up to 9,800 turtle nests per year compared with around 3,300 in French Guiana and 3,000 in Brazil.

Olive ridley turtles are one of the smallest of the sea turtles and are named for the greenish colour of their shell and skin. Although considered the most abundant of the marine turtles, there has been a net decline in the global numbers of the species, such that they are currently listed as 'vulnerable' by the International Union for Conservation of Nature (IUCN).

Although a considerable proportion of nesting occurs within protected areas in Gabon, a range of illegal activities and external pressures continue to exist highlighting the need for continued conservation efforts.

Dr Kristian Metcalfe, lead author from the Centre for Ecology and Conservation (CEC) at the University of Exeter who undertook the coastal survey with colleagues, said: "Conservation efforts for sea turtles can be hampered by their migratory life cycles, which carry them across jurisdictional boundaries and international waters. That makes this first population assessment which covered extensive areas of Gabon's coast outside of monitored regions all the more valuable and worthwhile, and demonstrates the importance of focusing beyond intensively monitored beaches."

Co-author Professor Brendan Godley from the CEC stated: "There have been increasing calls for improved sea turtle data at a local and regional scale to help inform conservation assessments. Our study goes some way to providing the data needed and will help us understand sea turtle distribution, density, population trends and threats as well as allowing the people of Gabon to manage their marine resources more sustainably."

Co-author Dr Matthew Witt from the Environment and Sustainability Institute (ESI) at the University of Exeter added: "These findings further emphasize the regional and global importance of Gabon's nesting sea turtle populations and places the country in a better position to support and implement measures to protect them."

This story is taken from Science Daily

Eukaryotes: A new timetable of evolution

The first single-celled organisms with a nucleus originated more than a billion years later than biogeochemical evidence had previously indicated. In contrast to prokaryotes such as bacteria, eukaryotes have a nucleus. Some researchers thought they had discovered molecular remnants of living organisms in rock samples up to 2.8 billion years old. However, as the current study shows, these molecular traces were introduced by contamination. 

Amoeba are more closely related to humans than to bacteria, at least in the tree of life. Like mammals, they belong to the realm of the eukaryotes, while bacteria are prokaryotes. The first eukaryotes are thus indeed the primeval ancestors of all higher life forms including humans. To this extent, evolution made a big leap towards complex life forms when eukaryotic cells appeared. The so-called symbiogenesis, which caused two or more single-celled bacteria to merge into a new organism with a nucleus and organelles, was the essential prerequisite that allowed most living creatures that surround us today to evolve.
To understand how higher life forms developed, evolutionary biologists want to know when and under what conditions the first eukaryotes entered the scene. An international team, in which researchers from Christian Hallmann's Group at the Max Planck Institute for Biogeochemistry were involved, is now supplying crucial arguments to the scientific debate surrounding these questions.

A gap between fossils and chemical traces

The oldest microfossils that are widely acknowledged as the remains of eukaryotes were found in ca. 1.5 billion-year-old rocks in northern Australia. Researchers have analyzed these fossils morphologically in micropaleontogical studies and identified them as the remains of microalgae. In alternative attempts to trace the origin of higher life forms, scientists analyzed certain lipid molecules (steroids) contained in the cell walls of eukaryotic organisms. Not only can they serve as highly specific markers for certain groups of organisms, they can also survive in sediments for extremely long periods of time given the right conditions. "By analyzing such molecules, so-called biomarkers, we can reconstruct early life on Earth on a molecular level," says Christian Hallmann, Leader of the Max Planck Research Group 'Organic Paleobiogeochemistry'.
Since 2012 Hallmann's team has been working on increasing our understanding of how environmental conditions developed and the diversity of life appeared in the period from when Earth was created until animal life first appeared (i.e. during the Precambrian). "Our understanding of this period, which is of great evolutionary interest, is benefiting enormously from this molecular approach," Hallmann explains. The paleontologist and his staff have now analyzed rock samples up to 2.7 billion years old for traces of molecules.
Steroid molecules can be preserved as steranes in old sediments, in other words the petrified beds of prehistoric seas and lakes. And since during the last 15 years an increasing number of scientists had repeatedly identified such molecular traces in samples of sediments from 2.5 to 2.8 billion years old, they concluded that eukaryotic algae already existed in this period, i.e. during the Late Archean. Thus, a gap of more than a billion years appeared between the earliest deposits of these biomarkers and the oldest fossilized microalgae.

Ultra-clean sampling aimed at clarifying the question of contamination

In addition, the discovery of a large variety of steroids pointed to a seemingly-modern pattern representing various algae species. "At first there was speculation that it might suggest that algae had split into different species at a very early date," says Christian Hallmann. "But suspicion mounted that the samples in these studies might have become contaminated in spite of extensive precautionary measures." The problem was that the Archean sample material either had not been taken under special conditions or had been stored for several years under conditions that were not ideal. "The question of contamination gradually split our fellow scientists into two conflicting camps," Hallmann continues.
Working with Katherine French from the Massachusetts Institute of Technology (MIT), Hallmann therefore developed a method for taking ultra-clean samples from the oldest rocks that had been classified as containing steroids. Together with Roger Buick from the University of Washington, the scientists drilled and collected rock samples over the course of several weeks in the remote Australian outback during the "Agouron Institute Drilling Projects (AIDP)" in 2012, and in the process took unprecedented precautionary measures to prevent contamination.

Not even a picogram of eukaryotic steroids
French, Hallmann and other colleagues split open these drill cores and analyzed them in several independent laboratories -- with astonishingly uniform results. "My biggest fear was having to discover in the laboratory that the samples had become contaminated despite our excessive endeavours," Hallmann continues. "Then the whole effort would have been useless." However, the samples were extremely clean -- so clean in fact that the highly sensitive mass spectrometers in the various labs were unable to detect even picogram quantities of indigenous eukaryotic steroids. The suspicion that earlier samples might have been contaminated was confirmed.
At the same time, the researchers found relatively large amounts of so-called diamondoids and polyaromatic hydrocarbons in the rock. Hallmann calls this the 'exhaust signature' as these molecules also occur in the exhaust gases of combustion engines and they point to organic material that has been modified at high temperatures. "The entire organic material in these samples was modified by pressure and temperature during the course of billions of years, and no biomarker molecules could have survived. We are thus unable to draw any conclusions on the original biological signature of the material," says Hallmann.
At any rate, the steroid molecules, which were supposedly 2.7 billion years old, can no longer serve as evidence that eukaryotes originated much earlier than indicated by the fossil record. The microfossils, which are about 1.5 billion years old, must therefore currently be deemed the oldest evidence of eukaryotic life on Earth -- an insight that is expected to have major consequences, not only in the geosciences.

Biomarkers remain an important tool in Precambrian paleontology
French and Hallmann's results not only help to clarify when eukaryotes originated, they also aid in the solution of a further puzzle: since all eukaryotes require oxygen, the development of oxygen-producing (oxygenic) photosynthesis must have preceded the evolutionary transition to the eukaryotes. The consequences of this biochemical innovation, known as the "great oxidation event," changed the entire planet as the atmosphere became gradually enriched with oxygen. This event is clearly dated to between 2.5 and 2.4 billion years ago. Until now, it had been hard to explain how the eukaryotes could have originated several 100 million years earlier given that they were inherently dependent on access to molecular oxygen.
"Using a well-designed technique and a large-scale international collaborative process, we were able to answer one of the major questions in molecular geobiology," says Hallmann. In spite of these new insights, biomarkers in old rocks remain an important tool for paleontological investigations of the Precambrian, not least because sedimentary steroids and other biomarkers can be much more specific than microfossils. In contrast to the studied Archean rocks, late-Precambrian sedimentary basins on Earth contain a wide variety of rocks whose organic material is relatively well preserved and can be examined for biomarkers. "With the gained knowledge that eukaryotes appeared later, we can now work on the true early evolution of algae in a new context and with greatly enhanced prospects of achieving success."

This story is taken from Science Daily