Number of fungal species has been greatly overestimated

The good news for the Estonian mycophile is that when it comes to mycorrhizal fungi, which include almost all edible and poisonous mushrooms, the forests of our climate zone are the richest in species.

A study led by the researchers of the University of Tartu Natural History Museum discovered that the most species-rich fungal communities are in tropical rainforests. The estimated global species richness of fungi, 1.5-5.1 million species, however, seems to be a vast overestimation, according to their data.

"Together with 35 research institutions we collected approximately 15,000 soil samples from various areas across the world. We then sequenced the DNA in the collected samples, using the new generation sequencing method. When analysing the soil samples, we found more than 45,000 fungal species. To our knowledge, this is the largest dataset of biodiversity studies published so far," said Leho Tedersoo, Senior Research Fellow of the University of Tartu Natural History Museum and the manager of the project.

"The coordination of the activities of all partners and obtaining all the required permits for getting the samples meant a lot of paperwork. In some countries we could not collect samples just because we could not get the permits. For generalisations, however, the amount of the collected material is more than enough," said Tedersoo.

As the main findings, the study concluded that the species richness patterns of fungi in general follow these of plants and animals -- i.e. the species richness is the highest in tropical rainforests and general rules of biogeography apply. In the past, it was commonly held that the latter do not apply to microorganisms -- that all forms are present everywhere depending on the substrate. The study found that the number of fungal species in the world has been greatly overestimated.

"We discovered that endemism -- the phenomenon that particular species live only in a rather limited area -- is also very common among fungi," explained Tedersoo. Tedersoo added that there are also many species that are spread across the world, such as mould and animal pathogens. "Although the spread of plant and animal species in the temperate climate zone of the northern hemisphere is limited to continents, many fungal species are equally spread in Asia, North America and Europe. This indicates that fungi have a more efficient spreading mechanism: microscopic spores," said Tedersoo.

"The research findings will not save the world, but help the researchers understand the global biological processes much better. As the species richness and spread of fungi mostly depend on precipitation, temperature and vegetation, it can be assumed that climate change strongly affects mycobiota in dry and cool regions. The good news for the Estonian mycophile is that when it comes to mycorrhizal fungi, which include almost all edible and poisonous mushrooms, the forests of our climate zone are the richest in species. The age-old Abruka limetree forest holds the record," said Tedersoo.

In the future, the working group of ecology of biological interactions is planning to focus on detecting functional difference in soil organisms in different ecosystems of the world, to show how these organisms have adapted to different climatic and soil-formation processes and to historical-biogeographical factors.

"Such analyses require computational power and cloud services, which are available in the PlutoF system and at the High Performance Computing Center of the University of Tartu," said Tedersoo. "Huge work has been done by my colleagues Mohammad Bahram, Sergei Põlme, Urmas Kõljalg and Kessy Abarenkov. These days, analyses of such scale cannot even be conducted by a single researcher or a small working group."

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Scientists question tropical protected areas' role under climate change

Prothoe franck (marked in pink to allow to its dispersal to be studied), is a forest dependent butterfly that may be at risk from climate change in lowland forest habitats.

New research led by University of York scientists highlights how poor connectivity of protected area (PA) networks in Southeast Asia may prevent lowland species from responding to climate change.

Tropical species are shifting to higher elevations in response to rising temperatures, but there has been only limited research into the effectiveness of current protected area networks in facilitating such movements in the face of climate change.

However, the new study, published in the journal Biological Conservation, focuses on the connectivity of the protected area network on the highly biologically diverse island of Borneo. The island is facing severe pressure due to deforestation and cultivation of oil palm plantations, resulting in an important biodiversity conservation role for protected areas in this region.

The research paper analyses future changes in the spatial distribution of climate within protected areas, and also uses population modelling to examine their connectivity. The results suggest that low elevation protected areas are particularly vulnerable to climate change, and that management to improve their linkage as terrain increases in elevation should be a conservation priority.

Lead author Sarah Scriven, a PhD student from the Department of Biology at York, said: "This study gave me an opportunity to learn valuable new skills such as the manipulation of land cover and climate data using GIS (geographic information system) software, as well as modelling the dispersal of species -- such as forest-dependant butterflies -- through fragmented landscapes. I will combine these new research skills with field-work in Sabah, Malaysian Borneo, to address the overall theme of my PhD -- which is to examine the resilience of biodiversity to climate change within tropical agricultural landscapes."

The study shows that analogue climates will shift out of more than 61 per cent of protected areas resulting in many species needing to move to cooler areas if they are to track climate changes. The study also reveals that many low-lying protected areas are isolated and not well connected to cooler forested areas at higher elevation.

Co-author Dr Colin McClean, from the Environment Department at York, said: "We show that the majority of PAs on Borneo will fail to retain analogue climate conditions in future, and these PAs are primarily located in lowland areas. This is worrying because there has been huge expansion of oil palm plantations in tropical lowlands in recent decades, not just in Borneo, but all over Southeast Asia."

Co-author Dr Jenny Hodgson, now of the University of Liverpool but formerly in the Department of Biology at York, who developed the population model used in the study, said: "Our results are concerning because biodiversity is known to peak in low-lying forests, and in Borneo these forests contain exceptionally high numbers of endemic species. Large-scale oil palm plantations will likely act as barriers to species moving between PAs."

Project leader Professor Jane Hill, Sarah Scriven's PhD supervisor, added: "Our new research highlights the isolation of low-lying PAs on Borneo. Management to improve linkage of PAs along elevation gradients should be a conservation priority."

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Female mice do not avoid mating with unhealthy males

Mating choice is not based solely on odor.

Female mice are attracted more strongly to the odour of healthy males than unhealthy males. This had already been shown in an earlier study by researchers from the Konrad Lorenz Institute of Ethology at the Vetmeduni Vienna. Now the team of behavioural scientists went one step further -- and tested a common assumption that more attractive males have better mating success than other males.

Females also mate with unhealthy males

Sarah Zala and Dustin Penn investigated whether females would also choose to mate with healthy over infected male if given a choice. In the laboratory and in large enclosures, the females were allowed to freely choose between two males, one healthy and another challenged with a mild infection, which they previously found to alter male odour.

The majority of females, about 86 percent, were initially more attracted to the healthy males. However, unhealthy males were also chosen as mating partners. "That surprised us. We assumed that the females would opt for the healthy males. Not only would this minimise the chance of becoming infected themselves, but choosing a healthy, disease-resistant partner would also be advantageous for their offspring," first author Zala explains.

Polyandry not unusual for female mice

A genetic analysis of the offspring revealed that about 30 percent of the litters had two fathers, the healthy male and the unhealthy one.

"Many females apparently mate with both males, whether these are healthy or not," Zala says. "We suspect that the females do this to protect their young. A male that was rejected as a mating partner may commit infanticide in order to get another chance at siring offspring."

"The females recognise whether males are healthy or unhealthy. We saw this quite clearly. But why they still mate with the unhealthy male remains unclear," says Dustin Penn.

In the future, Zala and Penn intend to study more closely the effect of an infection on the odour of the animals.

Odour preference seems irrelevant for mate choice

"Until now, scientists generally assumed that females choose their mates depending on their males' scent or other secondary sexual traits. Our study shows that this isn't necessarily the case," says Zala. The situation could be different in the wild. As females recognise healthy males quite well based on odour, and are more attracted to them, they may be more likely to find healthy males in the wild. In the end, odour preference could still be an important factor determining sexual selection.

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Hidden meaning and 'speed limits' found within genetic code

Case Western Reserve scientists have discovered that speed matters when it comes to how messenger RNA (mRNA) deciphers critical information within the genetic code -- the complex chain of instructions critical to sustaining life. The investigators' findings, which appear in the March 12 journal Cell, give scientists critical new information in determining how best to engage cells to treat illness -- and, ultimately, keep them from emerging in the first place.

"Our discovery is that the genetic code is more complex than we knew," said senior researcher Jeff Coller, PhD, associate professor, Division of General Medical Sciences, and associate director, The Center for RNA Molecular Biology, Case Western Reserve University School of Medicine. "With this information, researchers can manipulate the genetic code to achieve more predictable outcomes in an exquisite fashion."

The genetic code is a system of instructions embedded within DNA. The code tells a cell how to generate proteins that control cellular functions. mRNA transmits the instructions from DNA to ribosomes. Ribosomes translate the information contained within the mRNA and produce the instructed protein. The genetic code comprises 61 words, called "codons," and a single codon, a sequence of three nucleotides, instructs the ribosome how to build proteins.

The code not only dictates what amino acids are incorporated into proteins, it also tells the cell how fast they should be incorporated. With this information, researchers can manipulate the genetic code to achieve predictable protein levels in an exquisite fashion."

The most significant breakthrough in the Case Western Reserve work is that all of the words, or codons, in the genetic code are deciphered at different rates; some are deciphered rapidly while others are deciphered slowly. The speed of how mRNA decodes its information is the sum of all the codons it contains. This imposed speed limit then ultimately affects the amount of protein produced. Sometimes faster is better to express a high level of protein. Sometimes slower is better to limit the amount protein. Importantly, codons are redundant -- many of these words mean the same thing.

Coller and colleagues found that each of the codons is recognized differently by a ribosome. Some codons are recognized faster than others, but these differences in speed are tiny. Over the entire span of an mRNA, however, each tiny difference in speed is powerfully additive.

"Many codons mean the same thing, but they influence decoding rate differently. Because of this, we can change an mRNA without changing its protein sequence and cause it to be highly expressed or poorly expressed and anywhere in between," he said. "We can literally dial up or down protein levels any way we want now that we know this information."

During their research, investigators measured the mRNA decay rate for every transcript within the cell. They were seeking answers for why different RNAs had different stabilities. With statistical analysis, investigators compared the half-lives of mRNAs to the codons used within these messages. A strong correlation emerged between codon identity and mRNA message stability. They ultimately linked these observations back to the process of mRNA translation.

"mRNA translation and mRNA decay are intimately connected. This can be very beneficial to scientists. If you would like a gene to be expressed really well, you simply change the protein sequence to be derived by all optimal codons. This will both stabilize the mRNA and cause it to be translated more efficiently," Coller said. "If you need an mRNA to express at a low level, you fill it with non-optimal codons. The mRNA will be poorly translated and thus unstable. Evolution has used codon optimization to shape the expression of the proteome. Genes of similar function use similar codons; therefore, they are expressed at similar levels."

His discovery has a variety of practical implications for medicine. From a bioengineering perspective, molecular biology techniques can be applied to manipulate the gene to contain ideal codons and obtain the gene expression pattern that is most beneficial to the application. From a human physiological standpoint, it's possible to learn the speed limit for each and every mRNA and then determine if this changes in specific pathologies such as cancer. Currently, it is unknown whether codons convey different speeds in disease states. A future direction for research will be to link codon speeds to specific illnesses. The potential is also there to develop drugs that can manipulate higher or lower gene expression by changing the decoding rate.

Codon activity also may also provide important clues about the source of many illnesses that have not been linked to specific gene mutations. Altering codon-dependent translation rates has the potential to change protein function profoundly, and no primary mutation will be detected. Rather the problem is not the gene itself, but the factors that influence decoding rates. Codon-dependent speed limits may underlie the cause of whole classes of disease states. For example, a recent study suggests that in more than 450 different cancer samples, factors influencing codon-dependent speed limits might be changing.

"The sky is the limit," Coller said. "Since this finding is so new, we have no idea what the potential is. The next step is to determine if changes in decoding speed can be an underlying mechanism that alters gene expression in human disease."

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Nature's inbuilt immune defense could protect industrial bacteria from viruses

Findings from a new study that set out to investigate the evolution of immune defences could boost the development of industrial bacteria that are immune to specific viral infections. The study is published today in the journal Current Biology.

Bacteria have many industrial uses including the production of cheese and yoghurt, paper making, biogas and the synthetic production of hormones like insulin. Viral infections of these bacterial cultures can halt production processes resulting in significant financial cost.

Dr Edze Westra from the Environment and Sustainability Institute at the University of Exeter's Penryn Campus in Cornwall said: "Our study indicates that it is the risk of infection that determines the type of immune defence used. This naturally occurring mechanism can be used to our advantage to equip industrial bacteria with immunity against viral attack."

In a series of experiments researchers from the University of Exeter exposed bacteria to phages -- viruses that infect bacteria. They discovered that when the bacteria were exposed to high numbers of the same strain of phage they evolved a permanent immune response by modifying their cell walls. This was an irreversible defence mechanism that had a negative impact on the long term health of the bacteria.

When the bacteria were exposed to low numbers of the same phage, a temporary defence was induced that used an immune response known as a CRISPR. Although costly when in use, in the absence of viruses the CRISPR response can lie dormant until required. The low overhead cost of this immune response has little impact on the long term health of the bacteria making it ideal for use in commercial applications.

Working in a similar way to a vaccine, bacteria could be 'pre-loaded' with CRISPR immune responses for multiple different phages. This is better for the health of the bacteria and results in higher product yields as well as protecting the culture in the event of infection with a range of viruses.

CRISPR functions by integrating genetic information from the virus into the bacterial DNA, forming a genetic database of viral sequences that is used as a memory to identify viruses during infection. If a viral infection then threatens the bacterial cell, the CRISPR immune system can thwart the attack by destroying the genome of the invading virus.

The research indicates that parasite exposure is likely to be a key factor in driving the evolution of permanent versus inducible -- or temporary -- defences in nature. This suggests that organisms living together in large populations, or parasite-rich conditions, are more likely to evolve permanent defences, whereas low parasite conditions select for inducible defences.

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'Warhead' molecule to hunt down deadly bacteria

Targeting deadly, drug-resistant bacteria poses a serious challenge to researchers looking for antibiotics that can kill pathogens without causing collateral damage in human cells. A team of Boston College chemists details a new approach using a "warhead" molecule to attack bacteria -- and spare healthy human cells -- by targeting a pair of lipids found on the surface of deadly germs, according to a report today in the journal Nature Communications.

The new strategy required the researchers to develop a novel type of "warhead molecule" capable of selectively targeting bacteria, overcoming biological conditions that interfere with bonding to pathogens and avoiding healthy human cells, said Boston College Associate Professor of Chemistry Jianmin Gao, the lead author of the report.

The BC team found answers to those challenges in the covalent chemistry of lipids, Gao said.

"In contrast to other efforts focused on the charge-to-charge attraction between molecules, we are using a completely different mechanism to target bacterial cells," said Gao. "Our method exploits the covalent chemistry of lipids -- where the lipids react with synthetic molecules to form new chemical structures based on the formation of new covalent bonds."

Pathogenic bacteria that are resistant to conventional antibiotics pose increasingly serious threats to public health. Researchers in medicinal chemistry, particularly those who seek to develop new antibiotics, are constantly looking for new ways to identify and differentiate bacterial pathogens from host cells within the human body.

Gao said bacterial cells are known to display a different set of lipids in their membranes. Prior research has focused on the use of positively charged peptides to target negatively charged lipids on the surface of bacterial cells. The approach has seen limited success as the charge-charge attraction between the attacking molecules and bacteria is prone to weakening by the presence of salt and other molecules, said Gao.

The researchers developed a novel, unnatural amino acid that serves as a suitable molecular warhead to target bacterial pathogens. Gao and his group sent the warhead molecule after bacterial lipids known as amine-presenting lipids -- specifically phosphatidylethanolamine (PE) and lysyl phosphatidylglycerol (Lys-PG) -- which can be selectively derivatized to form iminoboronates, a covalent bond forming process that allows the selective recognition and labeling of bacterial cells.

In addition, because amine-presenting lipids are scarce on the surface of mammalian cells, they are able to seek out and label bacterial cells with a high degree of selectivity, Gao said. Furthermore, iminoboronate formation can be reversed under physiologic conditions, giving the new method a high degree of control and allowing the warhead molecules to self-correct if unintended targets are reached.

Gao said a large number of bacterial species present PE and Lys-PG on their surfaces, making the covalent labeling strategy applicable to many applications in the diagnosis of bacterial infections and the delivery of antibiotic therapies.

"For the short term, we hope this work will inspire other people to consider using covalent chemistry for interrogating biological systems," Gao said. "Going into the future, we are excited to explore the potential of our chemistry for imaging bacterial infections. We are also working hard to apply our current findings to facilitate the targeted delivery of potent antibiotics to bacterial cells only."

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Why do cells rush to heal a wound? Mysteries of wound healing unlocked

These are leader cells, shown fluorescing green in this photomicrograph, pull follower cells in their wake as they move to cover and heal a wound.

Researchers at the University of Arizona have discovered what causes and regulates collective cell migration, one of the most universal but least understood biological processes in all living organisms.

The findings, published in the March 13, 2015, edition of Nature Communications, shed light on the mechanisms of cell migration, particularly in the wound-healing process. The results represent a major advancement for regenerative medicine, in which biomedical engineers and other researchers manipulate cells' form and function to create new tissues, and even organs, to repair, restore or replace those damaged by injury or disease.

"The results significantly increase our understanding of how tissue regeneration is regulated and advance our ability to guide these processes," said Pak Kin Wong, UA associate professor of mechanical and aerospace engineering and lead investigator of the research.

"In recent years, researchers have gained a better understanding of the molecular machinery of cell migration, but not what directs it to happen in the first place," he said. "What, exactly, is orchestrating this system common to all living organisms?"

Leaders of the Pack

The answer, it turns out, involves delicate interactions between biomechanical stress, or force, which living cells exert on one another, and biochemical signaling.

The UA researchers discovered that when mechanical force disappears -- for example at a wound site where cells have been destroyed, leaving empty, cell-free space -- a protein molecule, known as DII4, coordinates nearby cells to migrate to a wound site and collectively cover it with new tissue. What's more, they found, this process causes identical cells to specialize into leader and follower cells. Researchers had previously assumed leader cells formed randomly.

Wong's team observed that when cells collectively migrate toward a wound, leader cells expressing a form of messenger RNA, or mRNA, genetic code specific to the DII4 protein emerge at the front of the pack, or migrating tip. The leader cells, in turn, send signals to follower cells, which do not express the genetic messenger. This elaborate autoregulatory system remains activated until new tissue has covered a wound.

The same migration processes for wound healing and tissue development also apply to cancer spreading, the researchers noted. The combination of mechanical force and genetic signaling stimulates cancer cells to collectively migrate and invade healthy tissue.

Biologists have known of the existence of leader cells and the DII4 protein for some years and have suspected they might be important in collective cell migration. But precisely how leader cells formed, what controlled their behavior, and their genetic makeup were all mysteries -- until now.


Broad Medical Applications

"Knowing the genetic makeup of leader cells and understanding their formation and behavior gives us the ability to alter cell migration," Wong said.

With this new knowledge, researchers can re-create, at the cellular and molecular levels, the chain of events that brings about the formation of human tissue. Bioengineers now have the information they need to direct normal cells to heal damaged tissue, or prevent cancer cells from invading healthy tissue.

The UA team's findings have major implications for people with a variety of diseases and conditions. For example, the discoveries may lead to better treatments for non-healing diabetic wounds, the No. 1 cause of lower limb amputations in the United States; for plaque buildup in arteries, a major cause of heart disease; and for slowing or even stopping the spread of cancer, which is what makes it so deadly.

The research also has the potential to speed up development of bioengineered tissues and organs that can be successfully transplanted in humans.

About the Study

In the UA Systematic Bioengineering Laboratory, which Wong directs, researchers used a combination of single-cell gene expression analysis, computational modeling and time-lapse microscopy to track leader cell formation and behavior in vitro in human breast cancer cells and in vivo in mice epithelial cells under a confocal microscope.

Their work included manipulating leader cells through pharmacological, laser and other means to see how they would react.

"Amazingly, when we directed a laser at individual leader cells and destroyed them, new ones quickly emerged at the migrating tip to take their place," said Wong, who likened the mysteries of cell migration and leader cell formation to the processes in nature that cause geese to fly in V-formation or ants to build a colony.

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Giant sea creature hints at early arthropod evolution

Artist's rendering of Aegirocassis benmoulae. (Screenshot from video available at: 

 

 

 

http://youtu.be/vzvCH2td-AM

Newly discovered fossils of a giant, extinct sea creature show it had modified legs, gills on its back, and a filter system for feeding -- providing key evidence about the early evolution of arthropods.

The new animal, named Aegirocassis benmoulae in honor of its discoverer, Mohamed Ben Moula, attained a size of at least seven feet, ranking it among the biggest arthropods that ever lived. It was found in southeastern Morocco and dates back some 480 million years.

"Aegirocassis is a truly remarkable looking creature," said Yale University paleontologist Derek Briggs, co-author of a Nature paper describing the animal. "We were excited to discover that it shows features that have not been observed in older Cambrian anomalocaridids -- not one but two sets of swimming flaps along the trunk, representing a stage in the evolution of the two-branched limb, characteristic of modern arthropods such as shrimps."

Briggs is the G. Evelyn Hutchinson Professor of Geology and Geophysics at Yale and curator of invertebrate paleontology at the Yale Peabody Museum of Natural History. First author Peter Van Roy, an associate research scientist at Yale, led the research; Allison Daley of the University of Oxford is co-author.

Since their first appearance in the fossil record 530 million years ago, arthropods have been the most species-rich and morphologically diverse animal group on Earth. They include such familiar creatures as horseshoe crabs, scorpions, spiders, lobsters, butterflies, ants, and beetles. Their success is due in large part to the way their bodies are constructed: They have a hard exoskeleton that is molted during growth, and their bodies and legs are made up of multiple segments. Each segment can be modified separately for different purposes, allowing arthropods to adapt to every environment and mode of life.

Modern arthropod legs, in their most basic form, have two branches. Each is highly modified to cater to a specific function on that leg, such as locomotion, sensing its surroundings, respiration, or copulation; or it has been lost altogether. Understanding how these double-branched limbs evolved has been a major question for scientists.

A long-extinct group of arthropods, the anomalocaridids, is considered central to the answer. The youngest known anomalocaridids are 480 million years old, and all of them looked quite alien: They had a head with a pair of grasping appendages and a circular mouth surrounded by toothed plates. Their elongate, segmented bodies carried lateral flaps that they used for swimming. Until now, it was believed that anomalocaridids had only one set of flaps per trunk segment, and that they may have lost their walking legs completely.

But the recent discovery of Aegirocassis benmoulae tells another story. The new animal shows that anomalocaridids in fact had two separate sets of flaps per segment. The upper flaps were equivalent to the upper limb branch of modern arthropods, while the lower flaps represent modified walking limbs, adapted for swimming. Furthermore, a re-examination of older anomalocaridids showed that these flaps also were present in other species, but had been overlooked. These findings show that anomalocaridids represent a stage before the fusion of the upper and lower branches into the double-branched limb of modern arthopods.

"It was while cleaning the fossil that I noticed the second, dorsal set of flaps," said Van Roy, who spent hundreds of hours working on the specimens. "It's fair to say I was in shock at the discovery, and its implications. It once and for all resolves the debate on where anomalocaridids belong in the arthropod tree, and clears up one of the most problematic aspects of their anatomy."

Aegirocassis benmoulae is also remarkable from an ecological standpoint, note the researchers. While almost all other anomalocaridids were active predators that grabbed their prey with their spiny head limbs, the Moroccan fossil has head appendages that are modified into an intricate filter-feeding apparatus. This means that the animal could harvest plankton from the oceans.

"Giant filter-feeding sharks and whales arose at the time of a major plankton radiation, and Aegirocassis represents a much, much older example of this -- apparently overarching -- trend," Van Roy said.

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Some Genes 'Foreign' in Origin and Not from Our Ancestors

Abstract illustration depicting DNA (stock image).

Many animals, including humans, acquired essential 'foreign' genes from microorganisms co-habiting their environment in ancient times, according to research published in the open access journal Genome Biology. The study challenges conventional views that animal evolution relies solely on genes passed down through ancestral lines, suggesting that, at least in some lineages, the process is still ongoing.

The transfer of genes between organisms living in the same environment is known as horizontal gene transfer (HGT). It is well known in single-celled organisms and thought to be an important process that explains how quickly bacteria evolve, for example, resistance to antibiotics.

HGT is thought to play an important role in the evolution of some animals, including nematode worms which have acquired genes from microorganisms and plants, and some beetles that gained bacterial genes to produce enzymes for digesting coffee berries. However, the idea that HGT occurs in more complex animals, such as humans, rather than them solely gaining genes directly from ancestors, has been widely debated and contested.

Lead author Alastair Crisp from the University of Cambridge, UK, said: "This is the first study to show how widely horizontal gene transfer (HGT) occurs in animals, including humans, giving rise to tens or hundreds of active 'foreign' genes. Surprisingly, far from being a rare occurrence, it appears that HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing, meaning that we may need to re-evaluate how we think about evolution."

The researchers studied the genomes of 12 species of Drosophila or fruit fly, four species of nematode worm, and 10 species of primate, including humans. They calculated how well each of their genes aligns to similar genes in other species to estimate how likely they were to be foreign in origin. By comparing with other groups of species, they were able to estimate how long ago the genes were likely to have been acquired.

A number of genes, including the ABO blood group gene, were confirmed as having been acquired by vertebrates through HGT. The majority of the other genes were related to enzymes involved in metabolism.

In humans, they confirmed 17 previously-reported genes acquired from HGT, and identified 128 additional foreign genes in the human genome that have not previously been reported.

Some of those genes were involved in lipid metabolism, including the breakdown of fatty acids and the formation of glycolipids. Others were involved in immune responses, including the inflammatory response, immune cell signalling, and antimicrobial responses, while further gene categories include amino-acid metabolism, protein modification and antioxidant activities.

The team were able to identify the likely class of organisms the transferred genes came from. Bacteria and protists, another class of microorganisms, were the most common donors in all species studied. They also identified HGT from viruses, which was responsible for up to 50 more foreign genes in primates.

Some genes were identified as having originated from fungi. This explains why some previous studies, which only focused on bacteria as the source of HGT, originally rejected the idea that these genes were 'foreign' in origin.

The majority of HGT in primates was found to be ancient, occurring sometime between the common ancestor of Chordata and the common ancestor of the primates.

The authors say that their analysis probably underestimates the true extent of HGT in animals and that direct HGT between complex multicellular organisms is also plausible, and already known in some host-parasite relationships.

The study also has potential impacts on genome sequencing more generally. Genome projects frequently remove bacterial sequences from results on the assumption that they are contamination. While screening for contamination is necessary, the potential for bacterial sequences being a genuine part of an animal's genome originating from HGT should not be ignored, say the authors.

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Carnivorous plant packs big wonders into tiny genome

Light micrograph of the bladder of Utricularia gibba, the humped bladderwort plant (color added).

Great, wonderful, wacky things can come in small genomic packages.

That's one lesson to be learned from the carnivorous bladderwort, a plant whose tiny genome turns out to be a jewel box full of evolutionary treasures.

Called Utricularia gibba by scientists, the bladderwort is a marvel of nature. It lives in an aquatic environment. It has no recognizable roots. It boasts floating, thread-like branches, along with miniature traps that use vacuum pressure to capture prey.

A new study in the scientific journal Molecular Biology and Evolution breaks down the plant's genetic makeup, and finds a fascinating story.

According to the research, the bladderwort houses more genes than several well-known plant species, such as grape, coffee or papaya -- despite having a much smaller genome.

This incredibly compact architecture results from a history of "rampant" DNA deletion in which the plant added and then eliminated genetic material at a very fast pace, says University at Buffalo Professor of Biological Sciences Victor Albert, who led the study.

"The story is that we can see that throughout its history, the bladderwort has habitually gained and shed oodles of DNA," he says.

"With a shrunken genome," he adds, "we might expect to see what I would call a minimal DNA complement: a plant that has relatively few genes -- only the ones needed to make a simple plant. But that's not what we see."

A unique and elaborate genetic architecture

In contrast to the minimalist plant theory, Albert and his colleagues found that U. gibba has more genes than some plants with larger genomes, including grape, as already noted, and Arabidopsis, a commonly studied flower.

A comparison with the grape genome shows U. gibba's genetic opulence clearly: The bladderwort genome, holding roughly 80 million base pairs of DNA, is six times smaller than the grape's. And yet, the bladderwort is the species that has more genes: some 28,500 of them, compared to about 26,300 for the grape.

U. gibba is particularly rich in genes that may facilitate carnivory -- specifically, those that enable the plant to create enzymes similar to papain, which helps break down meat fibers. The bladderwort is also rich in genes linked to the biosynthesis of cell walls, an important task for aquatic species that must keep water at bay.

"When you have the kind of rampant DNA deletion that we see in the bladderwort, genes that are less important or redundant are easily lost," Albert says. "The genes that remain -- and their functions -- are the ones that were able to withstand this deletion pressure, so the selective advantage of having these genes must be pretty high.

"Accordingly, we found a number of genetic enhancements, like the meat-dissolving enzymes, that make Utricularia distinct from other species."

Much of the DNA the bladderwort deleted over time was noncoding "junk DNA" that contains no genes, Albert says.

High gene turnover

The study included partners from UB, the Universitat de Barcelona in Spain, the Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) in Mexico and the Instituto de Ecología in Mexico.

To determine how the bladderwort evolved its current genetic structure, the team compared the plant to four related species. What they uncovered was a pattern of rapid DNA alteration.

As Albert explains, "When you look at the bladderwort's history, it's shedding genes all the time, but it's also gaining them at an appreciable enough rate, permitting it to stay alive and produce appropriate adaptations for its unique environmental niche."

In the realm of DNA gain, the study found that U. gibba has undergone three duplication events in which its entire genome was replicated, giving it redundant copies of every gene.

This fast-paced gene gain was balanced out by swift deletion. Evidence for this phenomenon comes from the fact that the plant has a tiny genome despite its history of genetic duplication. In addition, the plant houses a high percentage of genes that don't have close relatives within the genome, which suggests the plant quickly deleted redundant DNA acquired through duplication events.

The study builds on the work of Albert and other team members, who reported in the journal Nature in 2013 that the bladderwort's genome was comprised almost entirely of useful, functional genes and their controlling elements, in contrast to species like humans, whose genomes are more than 90 percent "junk DNA."

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Retracing the roots of fungal symbioses

Mycorrhizal fungi include some of the most conspicuous forest mushrooms, such as the iconic fly agaric (Amanita muscaria), of the fungi sequenced for this project.

With apologies to the poet John Donne, and based on recent work from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, it can be said that no plant is an island, entire of itself. Unseen by the human eye, plants interact with many species of fungi and other microbes in the surrounding environment, and these exchanges can impact the plant's health and tolerance to stressors such as drought or disease, as well as the global carbon cycle.

Mycorrhizal fungi live in the roots of host plants, where they exchange sugars that plants produce by photosynthesis for mineral nutrients that fungi absorb from the soil. They include some of the most conspicuous forest mushrooms, including the iconic, flaming red "fly agaric," Amanita muscaria, and are of interest to bioenergy researchers, because they play roles in maintaining the health of candidate feedstock crop trees. Recent studies indicate that mycorrhizal fungi also play a significant role in belowground carbon sequestration, which may mitigate the effects of anthropogenic CO2 emissions.

To understand the basis for fungal symbiotic relationships with plants, a team of DOE JGI researchers led by Igor Grigoriev and longtime collaborators at the French National Institute for Agricultural Research (INRA) and Clark University conducted the first broad, comparative phylogenomic analysis of mycorrhizal fungi, drawing on 49 fungal genomes, 18 of which were sequenced for this study. The 18 new fungal sequences included 13 mycorrhizal genomes, from ectomycorrhizal fungi that penetrate the host roots, and including species that comingle with orchid and heathland (which include blueberry, heather, and heath) plant roots. In the February 23, 2015 online edition of Nature Genetics, these researchers describe how the comparative analyses of these genomes allowed them to track the evolution of mycorrhizal fungi. The results help researchers understand how plants and fungi developed symbiotic relationships, and how the mutualistic association provides host plants with beneficial traits for environmental adaptation.

Starting with previously sequenced mycorrhizal fungi

"Mycorrhizal symbioses are highly complex, but analyses of the 49 genomes indicate that they have evolved independently in many fungal lineages," said INRA's Francis Martin, one of the study's senior authors. To understand the genetic shifts underlying the repeated origins of mycorrhizal lifestyles, the researchers focused on enzymes that degrade plant cell walls from 16 gene families associated with plant cell wall degradation. They took their cue from the first sequenced ectomycorrhizal fungus, Laccaria bicolor and the first sequenced arbuscular mycorrhizal fungus Rhizophagus irregularis- all work done at the DOE JGI-which illuminates the origins and evolution of these enzymes, knowledge to be applied in collaboration for improving biomass breakdown for biofuels production.

Through molecular clock analyses, which combine genome-scale molecular data with fossil calibrations, the team could work backwards to estimate when saprotrophic and mutualistic lineages last shared common ancestors based on the amount of divergence.

The analyses of the fungal genomes and fossils suggested that in comparison to brown rot fungi and white rot fungi that evolved over 300 million years ago, ectomycorrhizal fungi emerged fairly recently from several species and then spread out across lineages less than 200 million years ago. The team also found that up to 40 percent of the symbiosis-induced genes were restricted to a single mycorrhizal species.

Fungi evolving to break down plant cell walls

David Hibbett of Clark University, another of the study's senior authors, compared the work to a previous collaboration with the DOE JGI detailed in Science to trace the evolution of white rot fungi, which are capable of breaking down cellulose, hemicellulose and lignin in plants. Prior to the emergence of white rot fungi hundreds of millions of years ago, fungi were not capable of breaking down lignin, and the undecayed plant mass became the basis of large coal deposits.

"Together these studies tell a story about how mushroom-forming fungi evolved a complex mechanism for breakdown of plant cell walls in 'white rot' and then cast it aside following the evolution of mycorrhizal associations, as well as the alternative decay mechanism of 'brown rot,'" Hibbett said. "The other major part of the story is that in mycorrhizal lineages there is a huge turnover in genes that are upregulated in the symbiosis-many of these have no homologs in even closely related species, suggesting that the evolution of the symbiosis is associated with massive genetic innovation."

Martin chimed in: "Many of these genes are likely used to control plant immunity during the massive colonization of root tissues by the fungus."

DOE JGI's Igor Grigoriev also pointed out, "This first large-scale study of mycorrhizal genomics is also the first step in both broader and deeper exploration of mycorrhizal diversity, their interactions with host plans, and roles in forest ecosystems using genomics tools, which are the focus areas for the JGI Fungal Genomics Program."

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Bacteria network for food

Electron micrograph of genetically modified Acinetobacter baylyi and Escherichia coli strains. The bacteria exchange amino acids via nanotubes (i.e. tube-like connections between cells).

It is well-known that bacteria can support each others' growth and exchange nutrients. Scientists at the Max Planck Institute for Chemical Ecology in Jena, Germany, and their colleagues at the universities of Jena, Kaiserslautern, and Heidelberg, however, have now discovered a new way of how bacteria can achieve this nutritional exchange. They found that some bacteria can form nanotubular structures between single cells that enable a direct exchange of nutrients (Nature Communications, February 2015).

Bacteria usually live in species-rich communities and frequently exchange nutrients and other metabolites. Until now, it was unclear whether microorganisms exchange metabolites exclusively by releasing them into the surrounding environment or whether they also use direct connections between cells for this purpose. Scientists from the Research Group Experimental Ecology and Evolution at the Max Planck Institute for Chemical Ecology in Jena, Germany addressed this question using the soil bacterium Acinetobacter baylyi and the gut microbe Escherichia coli. By experimentally deleting bacterial genes from the genome of both species, the scientists generated mutants that were no longer able to produce certain amino acids, yet produced increased amounts of others.

In co-culture, both bacterial strains were able to cross-feed each other, thereby compensating the experimentally induced deficiencies (see also our press release "Division of Labor in the Test Tube − Bacteria grow faster if they feed each other," December 2, 2013). However, separating the two bacterial strains with a filter that allowed free passage of amino acids, yet prevented a direct contact between cells, abolished growth of both strains. "This experiment showed that a direct contact between cells was required for the nutrient exchange to occur," explains Samay Pande, who recently obtained his PhD at the Max Planck Institute in Jena on this research project and now started a postdoc at the ETH Zürich.

Observing the co-culture under the electron microscope revealed structures that formed between bacterial strains, which functioned as nanotubes and enabled the exchange of nutrients between cells. Especially remarkable, however, was the fact that only the gut microbe Escherichia coli was capable of forming these structures and connecting to Acinetobacter baylyi or other E. coli cells. "The major difference between both species is certainly that E. coli is able to actively move in liquid media, whereas A. baylyi is immotile. It may thus be possible that swimming is required for E. coli to find suitable partners and connect to them via nanotubes," explains Christian Kost, head of the Research Group Experimental Ecology and Evolution, which is funded by the Volkswagen Foundation.

"A lack of amino acids triggered the formation of nanotubes. Deleting a gene, which is involved in the production of a certain amino acid, caused the resulting bacteria to connect to other bacterial cells and − in this way − compensate their nutritional deficiency. However, nanotubes did not form when the required amino acids were supplemented to the growth medium, indicating that the formation of these structures obviously depends on how 'hungry' a cell is," the scientist summarizes the results.

Cells that specialize on particular biochemical processes and thereby divide their labor can be advantageous for bacterial communities: Resources can be used more economically, thus enhancing growth and efficiency. Whether the formation of nanotubes exclusively serves the mutual exchange of nutrients or whether some bacterial species also parasitize other bacterial cells in this way will be subject to further investigation. Moreover, it remains unclear whether bacteria can actively choose the cells to which they attach. After all, such tubular connections also pose a potential risk, because the partner on the other side of the tube could also provide harmful substances.

"To me, the most exciting question that remains to be answered is whether bacteria are in fact unicellular and relatively simply structured organisms or whether we are actually looking at some other type of multicellularity, in which bacteria increase their complexity by attaching to each other and combining their biochemical abilities," Christian Kost summarizes. His research focuses mainly on the question why organisms cooperate with each other. Using bacterial communities as experimentally tractable model systems will help to explain why so many organisms have developed a cooperative lifestyle in the course of their evolution.

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Yellow Sugarcane Aphid Detected in Continental Europe

Researchers from the UAB and CREAF and from the University of León have discovered this species in Tarragona and Girona, which probably arrived from Northern Africa. It is also the first time that this species is found in Continental Europe.

Aphids are a kind of insects typically living on the aerial part of plants, feeding on the sap that flows through the phloem of plants with a specialized buccal apparatus. That is why they often behave as a pest in agricultural crops.

Recently, Carlos Hernández-Castellano, student of the MSc in Terrestrial Ecology at the Universitat Autònoma de Barcelona and research collaborator of the Centre for Ecological Research and Forestry Applications, and Nicolás Pérez Hidalgo, researcher from the University of León, discovered a new aphid species for the European Continent, in La Selva del Camp (province of Tarragona) and Blanes (province of Girona) (NE Spain).

This aphid, called Sipha flava, is native to North America, although it has achieved to expand throughout South and Central America. In these regions it is known as "the yellow sugarcane aphid," and is an important pest of this crop, where it feeds on the plant and acts as a virus vector, leading to yield reduction.

The researchers contemplate the possibility that the species has reached Continental Europe from the Southern Iberian Peninsula as a result of sugarcane crop expansion in northern Africa.

"This crop is rather marginal in European Continent, so Sipha flava is not expected to become a sugarcane pest in this zone. However, we know that it feeds on several species from the same family, in this case grasses, and it is unknown to what extent the aphid could represent a threat to these kinds of crops in Europe, such as rice or corn," Carlos Hernández-Castellano explains. Therefore, a distribution map of this species in Europe is needed in order to evaluate its potential pest behaviour, implementing the principle of precaution."

In addition to the new species for the European Continent, researchers also discovered the first case in Eurasia and North Africa of an aphid feeding on a plant from the genus Hyparrhenia (also from the grass family), and also contributed with the first evidences that this aphid is attended by ants -- ants and aphids tend to establish mutualistic relationships, in which ants offer protection in exchange for honeydew excreted by the aphids.

This discovery, researchers say, highlights the increasing threat of invasive species, a booming phenomenon caused by globalisation, leading not only to agricultural issues but also rising as the second cause of biodiversity loss in the world, just after habitat destruction in importance.

Therefore they point out that, although the finding supposes an increase in the diversity knowledge of this aphid genera -- to date just 10 species of this genus were known in Europe, and only 3 in the Iberian Peninsula -- the alert message is clear.

The discovery was made during a sampling campaign which aimed to study the insect trophic web of an organic citrus grove. The work was carried out in the context of Fauna Iberica Project, which aims to catalogue and to establish the distribution of the whole animal diversity in the Iberian Peninsula in order to guarantee its conservation.

The report is available online at: http://redia.it/images/stories/pdf2014/Redia_97_2014_16%20Hernandez%20%20et%20al__.pdf

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New products from bark to replace fossil compounds: Adhesives and insulating foams from softwood bark tannins

In collaboration with its partners, VTT developed tannin extraction from softwood bark as part of an ERA-NET project. At least 130 kg of crude tannin powder can be produced from one tonne of dry wood bark, still leaving 87% of the original bark mass available for incineration. In Finland, tannin could replace, in particular, fossil-based phenols in adhesives used in the wood products industry.

Hundreds of tonnes of tannin is produced from wood materials and wood bark for the needs of leather, beverage and animal feed industry in South America and South Africa in particular. However, the supply of the main sources of tannin, acacia and quebracho trees, is not sufficient to satisfy the increasing industrial demand for tannin.

In industrial use, tannin could be used to replace fossil chemicals in adhesives and insulating foams. In Finland, softwood bark tannins would be well suited for adhesive production for the manufacturing of wood products at sawmills. It could also enhance the fire resistance of insulating foams.

As part of the international ERA-NET project, VTT Technical Research Centre of Finland Ltd developed, in collaboration with its partners, a tannin extraction process from bark material generated as a by-product in the paper and wood industry to give added value to the fraction currently used for incineration.

Extraction and drying produce 130 kg of tannin powder from one tonne of wood bark

The extraction process is quite simple: tannin can be extracted from bark using hot water, after which the extract is dried into a powder. Drying the water extract into powder may not be necessary if the tannin is extracted near the site where glued wood products are manufactured. One tonne of dry wood bark yields at least 130 kg of tannin powder, leaving 87% of the original bark mass available for incineration.

The tannin extracted from present raw material sources is relatively pure. Extract from spruce bark, however, also contains other compounds, carbohydrates in particular, which limits the use of crude tannin. Yet, it may be possible to develop extraction and extract purification technologies for different end uses. The market price per kilo of tannin extracted from present raw material sources is approximately 1-2 euros. The market price per kilo of phenol is has varied recently from 0.8 to 1.4 euros.

VTT part of the three-year BioFoamBark project (2012−2014) was financed by Tekes -- the Finnish Funding Agency for Innovation , Savanaho Ltd, Finnish Wood Research Oy and Chemigate Ltd. Other project partners were University of Freiburg, University of Ljubljana, Université de Lorraine, University of Santiago de Compostela, Fraunhofer Institute of Solar Energy Systems ISE, Nova-Institut GmbH and Ledoga Srl.

Multi-purpose tannin

One of tannin's special properties is its ability to precipitate proteins and for this reason it has been used for tanning leather for thousands of years. This natural polyphenol is also known as a natural or added ingredient in red wine, where it clarifies the liquid and improves its shelf life and taste. Tannin is also added to certain feed products. For example, it enhances cattle's ability to take advantage of proteins contained in feed in its metabolic processes.

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Virus-cutting enzyme helps bacteria remember a threat

Microbial memory: CRISPR systems allow bacteria to adapt to new viral threats. Above, Staphylococcus aureus microbes lacking a CRISPR system are killed off by the bacteria-attacking virus ?NM4. This plate approximates the concentration of virus particles used in the recent experiments.

Bacteria may not have brains, but they do have memories, at least when it comes to viruses that attack them. Many bacteria have a molecular immune system which allows these microbes to capture and retain pieces of viral DNA that they have encountered in the past, in order to recognize and destroy it when it shows up again.

Research at Rockefeller University described in Nature offers new insight into the mysterious process by which this system works to encode viral DNA in a microbe's genome for later use as guides for virus-cutting enzymes.

"Microbes, like vertebrates, have immune systems capable of adapting to new threats. Cas9, one enzyme employed by these systems, uses immunological memories to guide cuts to viral genetic code. However, very little is known about how these memories are acquired in the first place," says Assistant Professor Luciano Marraffini, head of the Laboratory of Bacteriology. "Our work shows that Cas9 also directs the formation of these memories among certain bacteria."

These memories are embedded in the bacterial equivalent of an adaptive immune system capable of discerning helpful from harmful viruses called a CRISPR (clustered regularly interspaced short palindromic repeats) system. It works by altering the bacterium's genome, adding short viral sequences called spacers in between the repeating DNA sequences. These spacers form the memories of past invaders. They serve as guides for enzymes encoded by CRISPR-associated genes (Cas), which seek out and destroy those same viruses should they attempt to infect the bacterium again.

Cas9's ability to make precision cuts within a genome -- viral or otherwise -- has caught the attention of researchers who now use it to alter cells' genetics for experimental or therapeutic purposes. But it is still not well understood just how this CRISPR system works in its native bacteria.

Some evidence suggested that other Cas enzymes managed the memory-making process on their own, without Cas9. But because of the way Cas9 goes about identifying the site at which to make a cut, the researchers, including co-first authors Robert Heler, a graduate student, and Poulami Samai, a postdoc in the lab, suspected a role for Cas9 in memory making.

In addition to matching its CRISPR guide sequence up with the DNA of the virus, Cas9 needs to find a second cue nearby: a PAM (protospacer adjacent motif) sequence in the viral DNA. This is a crucial step, since it is the absence of a PAM sequence that prevents Cas9 from attacking the bacterium's own memory-containing DNA.

"Because Cas9 must recognize a PAM sequence before cutting the viral DNA, it made sense to us that Cas9 would also recognize the PAM sequence when the system is forming a memory of its first encounter with a virus," Heler says. "This is a new and unexpected role for Cas9."

To test their hypothesis, Heler swapped the Cas9 enzymes between the immune systems of Streptococcus pyogenes and Streptococcus thermophilus, each of which recognizes a different PAM sequence. As a result, the PAM sequences followed, swapping between the two bugs -- evidence that Cas9 is responsible for identifying the PAM during memory formation. In another experiment, he altered the part of Cas9 that binds to the PAM sequence, and found the microbes then began acquiring the target viral sequences randomly, making them unusable.

Samai, meanwhile, looked at the relationship between Cas9 and three other Cas enzymes: Cas1, Cas2 and Csn2. Components of the same CRISPR system, these enzymes were already suspected to play a role in memory making without help from Cas9.

Samai expressed these enzymes together, then tagged each one and attempted to purify it. But each time, the other three came out as well. "This indicates there is some kind of interaction between the four; most likely they form a complex during the acquisition of memory," she says.

"Because of its importance to biotechnology, Cas9's has attracted a great deal of interest for its action targeting and cleaving viral genomes. Our work reveals an overlooked role for Cas9: forming the memories that make adaptive immunity possible for bacteria," Marraffini says.

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Newborn neurons in adult brain may help us adapt to environment

Neurons (stock image). "New neurons may serve as a means to fine-tune the hippocampus to the predicted environment," Opendak says. "In particular, seeking out rewarding experiences or avoiding stressful experiences may help each individual optimize his or her own brain.

The discovery that the human brain continues to produce new neurons in adulthood challenged a major dogma in the field of neuroscience, but the role of these neurons in behavior and cognition is still not clear. In a review article published by Cell Press February 21st in Trends in Cognitive Sciences, Maya Opendak and Elizabeth Gould of Princeton University synthesize the vast literature on this topic, reviewing environmental factors that influence the birth of new neurons in the adult hippocampus, a region of the brain that plays an important role in memory and learning.

The authors discuss how the birth of such neurons may help animals and humans adapt to their current environment and circumstances in a complex and changing world. They advocate for testing these ideas using naturalistic designs, such as allowing laboratory rodents to live in more natural social burrow settings and observing how circumstances such as social status influence the rate at which new neurons are born.

"New neurons may serve as a means to fine-tune the hippocampus to the predicted environment," Opendak says. "In particular, seeking out rewarding experiences or avoiding stressful experiences may help each individual optimize his or her own brain. However, more naturalistic experimental conditions may be a necessary step toward understanding the adaptive significance of neurons born in the adult brain."

In recent years, it has become increasingly clear that environmental influences have a profound effect on the adult brain in a wide range of mammalian species. Stressful experiences, such as restraint, social defeat, exposure to predator odors, inescapable foot shock, and sleep deprivation, have been shown to decrease the number of new neurons in the hippocampus. By contrast, more rewarding experiences, such as physical exercise and mating, tend to increase the production of new neurons in the hippocampus.

The birth of new neurons in adulthood may have important behavioral and cognitive consequences. Stress-induced suppression of adult neurogenesis has been associated with impaired performance on hippocampus-dependent cognitive tasks, such as spatial navigation learning and object memory. Stressful experiences have also been shown to increase anxiety-like behaviors that are associated with the hippocampus. In contrast, rewarding experiences are associated with reduced anxiety-like behavior and improved performance on cognitive tasks involving the hippocampus.

Although scientists generally agree that our day-to-day actions change our brains even in adulthood, there is some disagreement on the adaptive significance of new neurons. For instance, the literature presents mixed findings on whether new neurons generated under a specific experimental condition are geared toward the recognition of that particular experience or if they provide a more naive pool of new neurons that enable environmental adaptation in the future.

Gould and her collaborators recently proposed that stress-induced decreases in new neuron formation might improve the chances of survival by increasing anxiety and inhibiting exploration, thereby prioritizing safety and avoidant behavior at the expense of performing optimally on cognitive tasks. On the other hand, reward-induced increases in new neuron number may reduce anxiety and facilitate exploration and learning, leading to greater reproductive success.

"Because the past is often the best predictor of the future, a stress-modeled brain may facilitate adaptive responses to life in a stressful environment, whereas a reward-modeled brain may do the same but for life in a low-stress, high-reward environment," says Gould, a professor of psychology and neuroscience at Princeton University.

However, when aversive experiences far outnumber rewarding ones in both quantity and intensity, the system may reach a breaking point and produce a maladaptive outcome. For example, repeated stress produces continued reduction in the birth of new neurons, and ultimately the emergence of heightened anxiety and depressive-like symptoms.

"Such a scenario could represent processes that are engaged under pathological conditions and may be somewhat akin to what humans experience when exposed to repeated traumatic stress," Opendak says.

Because many studies that investigate adult neurogenesis use controlled laboratory conditions, the relevance of the findings to real-world circumstances remains unclear. The use of a visible burrow system--a structure consisting of tubes, chambers, and an open field--has allowed researchers to recreate the conditions that allow for the production of dominance hierarchies that rats naturally form in the wild, replicating the stressors, rewards, and cognitive processes that accompany this social lifestyle.

"This more realistic setting has revealed individual differences in adult neurogenesis, with more new neurons produced in dominant versus subordinate male rats," Gould says. "Taking findings from laboratory animals to the next level by exploring complex social interactions in settings that maximize individual variability, a hallmark of the human experience, is likely to be especially illuminating."

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Breastfeeding, other factors help shape immune system early in life

Henry Ford Hospital researchers say that breastfeeding and other factors influence a baby's immune system development and susceptibility to allergies and asthma by what's in their gut.

The striking findings from a series of studies further advance the so-called hygiene hypothesis theory that early childhood exposure to microorganisms affects the immune system's development and onset of allergies, says Christine Cole Johnson, Ph.D., MPH, chair of Henry Ford's Department of Public Health Sciences and principal research investigator.

The gut microbiome is the collection of microorganisms in the gastrointestional, or GI, tract, and the human body has billions of these microbes. The GI tract contains what scientists often call a bacterial ecosystem. The gut microbiome is known to play an important role in immune system development, and is thought to contribute to a host of diseases like obesity, autoimmune diseases, circulating disorders and pediatric allergies and infection.

"For years now, we've always thought that a sterile environment was not good for babies. Our research shows why. Exposure to these microorganisms, or bacteria, in the first few months after birth actually help stimulate the immune system," Dr. Johnson says.

"The immune system is designed to be exposed to bacteria on a grand scale. If you minimize those exposures, the immune system won't develop optimally."

The studies are being presented at the annual meeting of the American Academy of Allergy, Asthma & Immunology in Houston.

The findings come from Henry Ford's long-running Wayne County Health, Environment, Allergy and Asthma Longitudinal Study (WHEALS), funded by the National Institute of Allergy and Infectious Diseases, that is exploring the role of environmental factors and measuring biological markers to understand how allergies and asthma develop early in life.

In six separate studies, researchers sought to evaluate whether breastfeeding and maternal and birth factors had any effect on a baby's gut microbiome and allergic and asthma outcomes. Using data collected from the WHEALS birth cohort, researchers analyzed stool samples from infants taken at one month and six months after birth. They also looked at whether the gut microbiome impacted the development of regulatory T-cells, or Treg, which are known to regulate the immune system. Highlights:

• Breastfed babies at one month and six months had distinct microbiome compositions compared to non-breastfed babies. These distinct compositions may influence immune system development. • Breastfed babies at one month were at decreased risk of developing allergies to pets. • Asthmatic children who had nighttime coughing or flare-ups had a distinct microbiome composition during the first year of life. • For the first time, gut microbiome composition was shown to be associated with increasing Treg cells.

Researchers found that a baby's gut microbiome patterns vary by:
• A mother's race/ethnicity.
• A baby's gestational age at birth.
• Prenatal and postnatal exposure to tobacco smoke.
• Caesarean section versus vaginal delivery.
• Presence of pets in the home.

Dr. Johnson and her team, which includes researchers at George Regents University, University of California-San Francisco and University of Michigan, have been at the forefront of research investigating how allergies develop in early life and the role of environmental factors. Henry Ford's landmark 2002 study found exposure to dogs or cats in the first year of a baby's life reduced their risk for allergies.

"The research is telling us that exposure to a higher and more diverse burden of environmental bacteria and specific patterns of gut bacteria appear to boost the immune system's protection against allergies and asthma," Dr. Johnson says.

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Popular YouTube videos drown viewers with positive portrayals of drunkenness

The 70 most popular videos depicting drunkenness on YouTube account for more than 330 million views, with little portrayal of the negative outcomes of excessive alcohol consumption, according to an analysis led by the University of Pittsburgh Center for Research on Media, Technology, and Health (CRMTH).

The popularity of such videos on YouTube could be an opportunity for public health interventions aimed at educating teenagers and young adults of the negative consequences of intoxication, the researchers suggest in an article published in today's issue of the journal Alcoholism: Clinical and Experimental Research.

"There has been little research examining Internet-based, alcohol-related messaging," said lead author Brian A. Primack, M.D., Ph.D., director of CRMTH and assistant vice chancellor for health and society in Pitt's Schools of the Health Sciences. "While we know that some viewers may be savvy enough to skeptically view music videos or advertisements portraying intoxication as fun, those same viewers may be less cynical when viewing user-generated YouTube videos portraying humorous and socially rewarding escapades of a group of intoxicated peers."

Dr. Primack's team mined YouTube for five terms synonymous with alcohol intoxication -- drunk, buzzed, hammered, tipsy and trashed -- winnowing their findings down to the most relevant.

There were a total of 333,246,875 views for all 70 videos combined.

• Humor was juxtaposed with alcohol use in 79 percent of the videos.
• Motor vehicle use was present in 24 percent.
• Although 86 percent of the videos showed active intoxication, only 7 percent contained references to alcohol dependence.
• An average of 23.2 "likes" were registered for every "dislike."
• While 89 percent of the videos involved males, only 49 percent involved females.
• A specific brand of alcohol was referenced in 44 percent of the videos.

"This is the first comprehensive attempt to analyze YouTube data on intoxication, and these statistics should be valuable in guiding interventions," said Dr. Primack, also a practicing physician. "For example, we know that men tend to report more frequent binge drinking than women and that alcohol use is perceived as more socially acceptable for men. Because they are portrayed more frequently in YouTube videos, it may be useful to target men with future interventions debunking alcohol-related myths propagated on social media."

Dr. Primack found it concerning that nearly half the videos contained specific brand references. While this could indicate industry influence, the researchers did not note any clear indication of intentional advertising. Past research has linked exposure to brand references in popular media to encouraging alcohol consumption.

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A lower IQ has been linked to greater and riskier drinking among young adult men

Although several studies have shown an association between intelligence and various health-related outcomes, the research on cognitive abilities and alcohol-related problems has been inconsistent. A new study of the association between IQ-test results and drinking, measured as both total intake and pattern of use, has found that a lower IQ is clearly associated with greater and riskier drinking among young adult men, although their poor performance on the IQ-test may also be linked to other disadvantages.

Results will be published in the March 2015 online-only issue of Alcoholism: Clinical & Experimental Research.

"Previous results in this area have been inconsistent," said Sara Sjölund, a doctoral student at the Karolinska Institutet in Stockholm, Sweden as well as corresponding author for the study. "In two studies where the CAGE questionnaire -- a method of screening for alcoholism -- was used, a higher cognitive ability was found to be associated with a higher risk for drinking problems. Conversely, less risk has been found when looking at outcomes such as, for example, International Classification of Diseases diagnoses of alcoholism, alcohol abuse, and dependence."

"In this study of a general population, intelligence probably comes before the behavior, in this case, alcohol consumption and a pattern of drinking in late adolescence," said Daniel Falkstedt, assistant professor in the department of public health sciences at Karolinska Institutet. "It could be the other way around for a minority of individuals, that is, when exposure to alcohol has led to cognitive impairment, but this is less likely to be found among young persons of course."

Sjölund and her colleagues analyzed data collected from 49,321 Swedish males born during 1949 to 1951 and who were conscripted for Swedish military service from 1969 to 1971. IQ results were available from tests performed at conscription, and questionnaires also given at conscription provided data on total alcohol intake (consumed grams of alcohol/week) and pattern of drinking, as well as medical, childhood and adolescent conditions, and tobacco use. Adjustments were made for socio-economic position as a child, psychiatric symptoms and emotional stability, and the father's alcohol habits.

"We found that lower results on IQ tests in Swedish adolescent men are associated with a higher consumption of alcohol, measured in both terms of total intake and binge drinking," said Sjölund. "It may be that a higher IQ results in healthier lifestyle choices. Suggested explanations for the association between IQ and different health outcomes, could be childhood conditions, which could influence both IQ and health, or that a socio-economic position as an adult mediates the association."

"By taking into account as little as four measured characteristics of the men, including their backgrounds," added Falkstedt, "the authors seem to be able to explain a large part of the association between IQ and heavy drinking. I think this may be a main message of this large cohort study: poor performance on IQ tests tend to go along with other disadvantages, for instance, poorer social background and emotional problems, which may explain the association with risky alcohol consumption. In reality, other differences of importance are likely to exist among the men, which could further explain the IQ-alcohol association."

Both Sjölund and Falkstedt noted that results may vary among cultures and countries.

"I think that large parts of the association between IQ and alcohol consumption may be indirect and mediated by experiences in everyday life and differences in social situations," said Falkstedt. "It is not necessarily about making intelligent or unintelligent choices. For instance, in countries with weak social-safety nets and high alcohol consumption among low-wage workers and the unemployed, I assume the association could be stronger than in economically more-equal countries, perhaps also among the young."

"I hope that our findings add to the general understanding of drinking behaviours and what factors that may influence them," said Sjölund. "However, we must be very careful in making any attempt to generalize our results to women, since their level of consumption and patterns of drinking likely differ in comparison with men."

"I think a higher intelligence may give some advantage in relation to lifestyle choices," noted Falkstedt. "However, I think it is very important to remember that intelligence differences already existing in childhood and adolescence may put people at an advantage or disadvantage and may generate subsequent differences in experiences, and accumulation of such experiences over many years. Therefore, another important explanation of 'bad choices' among lower-IQ individuals may be feelings of inadequacy and frustration, I think. A number of studies have shown that a lower IQ in childhood or adolescence is associated with an increased risk of suicide over many years in adulthood."

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Caribbean coral findings may influence Barrier Reef studies

Corals may be better equipped to tolerate climate change than previously believed, according to research led by Griffith University's Dr Emma Kennedy.

Working with scientists from the University of Exeter in the UK, Dr Kennedy says the findings -- published in the journal Coral Reefs -- relate to an extensive study of Caribbean corals, but could influence future analysis of Australia's Great Barrier Reef.

Using a high-resolution molecular screening technique called Real Time-PCR, the researchers confirmed that the partnership between Symbiodinium D -- a symbiotic algae associated with resistance to coral bleaching -- and Caribbean corals is more common than had been supposed.

"Corals rely on a relationship with algae in order to get energy via photosynthesis," says Dr Kennedy, a Postdoctoral Research Fellow in the School of Environment's Australian Rivers Institute.

"However, under stressful conditions such as increased temperatures, this relationship can be disrupted, resulting in a loss of the algae in an event known as bleaching. In an extreme event, this can lead to coral death.

"Our study focused on populations of the Mountain Star coral, Orbicella annularis, a widespread and prominent reef species in the Caribbean.

"Understanding its ability to weather the pressures of a changing climate, in particular rising sea temperatures, is a key question for conservationists."

Symbiodinium D was found to be present in low abundances at almost every location the researchers tested, from Tobago to the Bahamas. As well as being geographically widespread, it was also more common in individuals, found on average in more than 30 per cent of the corals in each location.

Dr Kennedy says previous studies have shown that if Orbicella annularis contains just a small amount of Symbiodinium D it can sometimes respond better to stress events -- such as heatwaves -- and is more likely to avoid coral bleaching.

A 2007 research paper (Mieog et al. 2007, Coral Reefs) reported the presence of Symbiodinium D in 71 per cent of coral colonies tested on the Great Barrier Reef.

Having completed her PhD at the University of Exeter, Dr Kennedy's latest research involves assessing the responses of coralline algae to ocean acidification and warming. It aims to determine whether coralline algae can be used to track the impacts of climate change in the Great Barrier Reef.

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