Understanding, improving body's fight against pathogens

Significant reductions in the number of plasma cells in the spleen and bone marrow were observed in the absence of DOK3. Each dot in the figure represents one plasma cell detected. Credit: Image courtesy of A*Star Agency for Science, Technology and Research

Scientists from A*STAR's Bioprocessing Technology Institute (BTI) have uncovered the crucial role of two signalling molecules, DOK3 and SHP1, in the development and production of plasma cells. These discoveries, published in two journals PNAS and Nature Communications, advance the understanding of plasma cells and the antibody response, and may lead to optimisation of vaccine development and improved treatment for patients with autoimmune diseases such as lupus and tumours such as multiple myeloma.

While they exist in small populations in humans, the large amounts of antibodies secreted by plasma cells make them key to the body's immune system and its ability to defend itself against pathogens, such as bacteria and viruses. Proper maintenance of a pool of plasma cells is also critical for the establishment of lifelong immunity elicited by vaccination.

Dysregulation of plasma cell production and maintenance could lead to autoimmune diseases and multiple myeloma. Autoimmune diseases occur when the immune system does not distinguish between healthy tissue and antigens, which are found in pathogens. This results in expansion of plasma cells which produce excessive amounts of antibodies leading to destruction of one's own healthy tissue. The discoveries by scientists in BTI's Immunology Group have improved understanding of the mechanism by which plasma cells are developed from a major class of white blood cells called B cells.

For the first time, the molecule DOK3 was found to play an important role in formation of plasma cells. While calcium signalling typically controls a wide range of cellular processes that allow cells to adapt to changing environments, it was found to inhibit the expression of the membrane proteins essential for plasma cell formation. These membrane proteins include PDL1 and PDL2, and represent some of the key targets for the development of immunotherapy by pharmaceutical companies. DOK3 was able to promote the production of plasma cells by reducing the effects of calcium signalling on these membrane proteins. The absence of DOK3 would thus result in defective plasma cell formation.

In another study, BTI scientists discovered the importance of SHP1 signalling to the long term survival of plasma cells. While the molecule SHP1 has a proven role in prevention of autoimmune diseases, it was found that the absence of SHP1 would result in the failure of plasma cells to migrate from the spleen where they are generated to the bone marrow, a survival niche where they are able to survive for much longer periods. This could result in a reduction of the body's immune response and thus, an increased susceptibility to infections and diseases. The scientists in this study also successfully rectified the defective immune response caused by an absence of SHP1 by applying antibody injections, which might advance the development of therapeutics. On the other hand, targeting SHP1 might be a strategy to treat multiple myeloma where the accumulation of cancerous plasma cells in the bone marrow survival niches is undesirable.

Findings hold potential for improved treatment

The discovery of these new targets for modulating the antibody response allows the development of novel therapeutic strategies for patients with autoimmune diseases and cancer.Understanding the mechanism that governs plasma cell differentiation is also critical for the optimal design of vaccines and adjuvants, which are added to vaccines to boost the body's immune response.

Prof Lam Kong Peng, Executive Director of BTI, said, "These findings allow better understanding of plasma cells and their role in the immune system. The identification of these targets not only paves the way for development of therapeutics for those with autoimmune diseases and multiple myeloma, but also impacts the development of immunological agents for combating infections."

Source: A*Star Agency for Science, Technology and Research

Source of most cases of invasive bladder cancer identified

Philip Beachy and his team found a single type of cell in mice that gives rise to invasive bladder cancers. Credit: Steve Fisch

A single type of cell in the lining of the bladder is responsible for most cases of invasive bladder cancer, according to researchers at the Stanford University School of Medicine.

Their study, conducted in mice, is the first to pinpoint the normal cell type that can give rise to invasive bladder cancers. It's also the first to show that most bladder cancers and their associated precancerous lesions arise from just one cell, and explains why many human bladder cancers recur after therapy.

"We've learned that, at an intermediate stage during cancer progression, a single cancer stem cell and its progeny can quickly and completely replace the entire bladder lining," said Philip Beachy, PhD, professor of biochemistry and of developmental biology. "All of these cells have already taken several steps along the path to becoming an aggressive tumor. Thus, even when invasive carcinomas are successfully removed through surgery, this corrupted lining remains in place and has a high probability of progression."

Although the cancer stem cells, and the precancerous lesions they form in the bladder lining, universally express an important signaling protein called sonic hedgehog, the cells of subsequent invasive cancers invariably do not -- a critical switch that appears vital for invasion and metastasis. This switch may explain certain confusing aspects of previous studies on the cellular origins of bladder cancer in humans. It also pinpoints a possible weak link in cancer progression that could be targeted by therapies.

"This could be a game changer in terms of therapeutic and diagnostic approaches," said Michael Hsieh, MD, PhD, assistant professor of urology and a co-author of the study. "Until now, it's not been clear whether bladder cancers arise as the result of cancerous mutations in many cells in the bladder lining as the result of ongoing exposure to toxins excreted in the urine, or if it's due instead to a defect in one cell or cell type. If we can better understand how bladder cancers begin and progress, we may be able to target the cancer stem cell, or to find molecular markers to enable earlier diagnosis and disease monitoring."

Beachy is the senior author of the study, which will be published online April 20 in Nature Cell Biology. He is the Ernest and Amelia Gallo Professor in the School of Medicine and a member of the Stanford Cancer Institute and the Stanford Institute for Stem Cell Biology and Regenerative Medicine. He is also a Howard Hughes Medical Institute investigator. Kunyoo Shin, PhD, an instructor at the institute, is the lead author.

Bladder cancer is the fourth most common cancer in men and the ninth most common in women. Smoking is a significant risk factor. There are two main types of the disease: one that invades the muscle around the bladder and metastasizes to other organs, and another that remains confined to the bladder lining. Unlike the more-treatable, noninvasive cancer -- which comprises about 70 percent of bladder cancers -- the invasive form is largely incurable. It is expensive and difficult to treat, and the high likelihood of recurrence requires ongoing monitoring after treatment.

In 2011, Shin and Beachy and their colleagues identified a cell type in the bladder that is capable of completely replacing the lining of the organ after infection or damage. The fact that it could give rise to multiple cell types (even forming small, multilayered, bladder-like spheres when cultured in vitro), and also self-renew, showed that it was a bladder stem cell. 

They found that the cell, which came from the basal layer of the bladder epithelium, used a protein called sonic hedgehog to "talk" to other cells in the bladder and stimulate proliferation and specialization into other cell types. (Beachy identified the first hedgehog protein in fruit flies in 1992; the hedgehog signaling pathway has since been shown to play a vital role in embryonic development and in many types of cancers.)

Many animal models of cancer rely on prior knowledge or hunches as to what genes or cell types are involved. Researchers may genetically alter an animal, or a certain cell type, to induce the overexpression of a gene known to be involved in tumorigenesis, for example, or block the expression of a gene that inhibits cancer development.

Although prior work suggested that basal cells may play a role in bladder cancer, the researchers chose an unbiased approach when developing their mouse model that more closely mimicked what happens in humans: They put a chemical compound called N-butyl-N-4-hydroxybutyl nitrosamine, or BBN, in the mice's drinking water and watched the animals over a period of months.

Nitrosamines are carcinogens found in cigarette smoke; BBN is a form of the chemical that is specifically activated in the bladder. After four months, many of the animals had developed precancerous lesions, or carcinomas in situ, in their bladders that very closely resemble those seen in human patients. By six months, all of the animals had developed invasive bladder cancers.

With their model in place, the researchers then conducted two main experiments in the mice: In the first experiment, they looked to see what would happen in animals exposed to BBN when the sonic-hedgehog-expressing cells were marked with a distinctive fluorescent color. In the second, they used genetic techniques to selectively kill those same cells in animals prior to exposure with BBN.

In the first case, they saw something startling: After just a few months of BBN exposure, nearly the entire lining of the bladder was labeled with the fluorescent green marker that indicated the cells had arisen from the sonic-hedgehog-expressing basal stem cells. When transplanted into other mice, those labeled cells were able to give rise to bladder cancers, but cells not expressing sonic hedgehog did not.

In the second case, no tumors grew in the animals in which the stem cells had been selectively killed -- although the bladder architecture became severely compromised in the absence of stem cells to regenerate cells lost during the normal course of bladder function.

"So now we have two lines of evidence indicating that the bladder stem cells are solely responsible for tumorigenesis," Shin said. "When we mark the bladder stem cells, the tumors are also marked. When we remove, or ablate, the stem cells, no tumors arise after BBN treatment."

Next the researchers tackled the question of whether bladder cancers arise as the result of genetic changes to one or more of these bladder stem cells. To do so, they used a genetically engineered mouse with cells that fluoresce green, but which can be triggered to randomly fluoresce one of three other colors: red, blue or yellow. Known as a "rainbow mouse," the animal allows researchers to more precisely determine the origin of groups of cells. If all cells in a tumor are red, for example, it is much more likely that they originated from a single cell.

"After four months of BBN treatment," Beachy said, "we'd most often see just one color dominating the entire epithelium. This clearly indicates that a single cell has taken over the lining of the entire bladder, elbowing out its neighbors in a way that's not been seen in other organs."

Further studies showed that, surprisingly, none of the cells in the most advanced, invasive carcinomas in the BNN-treated animals expressed sonic hedgehog -- despite the fact that only sonic-hedgehog-expressing cells are able to give rise to the earlier stages of bladder cancer. One obvious implication of the lack of sonic hedgehog expression in these cells is that the hedgehog pathway somehow inhibits steps required for tissue invasion or metastasis.

"We know that the hedgehog pathway is widely used throughout the animal kingdom to tightly regulate cellular and tissue differentiation," Hsieh said. "So its loss could make sense in this context because cancer is essentially a loss of normal regulation."

"One really important lesson from this study," Beachy said, "is the idea that, by the time you get to a full-blown tumor, the properties of the cells in that tumor may have changed quite significantly from the cell type that gives rise to the tumors. This can complicate understanding how human tumors arise, because even if you identify the tumor-propagating cells within a mature tumor, conclusions about the origins of a cancer based on properties of these cells may be inaccurate."

Source: Stanford University Medical Center

Multiple allergic reactions traced to single protein

This is a mast cell. Credit: Priyanka Pundir/University of Alberta

Johns Hopkins and University of Alberta researchers have identified a single protein as the root of painful and dangerous allergic reactions to a range of medications and other substances. If a new drug can be found that targets the problematic protein, they say, it could help smooth treatment for patients with conditions ranging from prostate cancer to diabetes to HIV. Their results appear in the journal Nature on Dec. 17.

Previous studies traced reactions such as pain, itching and rashes at the injection sites of many drugs to part of the immune system known as mast cells. When specialized receptors on the outside of mast cells detect warning signals known as antibodies, they spring into action, releasing histamine and other substances that spark inflammation and draw other immune cells into the area. Those antibodies are produced by other immune cells in response to bacteria, viruses or other perceived threats. However, "although many of these injection site reactions look like an allergic response, the strange thing about them is that no antibodies are produced," says Xinzhong Dong, Ph.D., an associate professor of neuroscience in the Institute for Basic Biomedical Sciences at the Johns Hopkins University School of Medicine.

To zero in on the cause of the reactions, Benjamin McNeil, Ph.D., a postdoctoral fellow in Dong's laboratory, first set out to find which mast cell receptor -- or receptors -- responded to the drugs in mice. Previous studies had identified a human receptor likely to be at fault in the allergic reactions; McNeil found a receptor in mice that, like the human receptor, is found only in mast cells. He then tested that receptor by putting it into lab-grown cells and found that they did react to medications that provoke mast cell response. He found similar results for the human receptor that previous studies had indicated was a likely culprit.

"It's fortunate that all of the drugs turn out to trigger a single receptor -- it makes that receptor an attractive drug target," McNeil says.

To find out whether eliminating the receptor really would eliminate the allergic reactions, the research team also disabled the gene for the suspect receptor in mice. These "knockout" mice did not have any of the drug allergy symptoms that their genetically normal counterparts displayed.

The researchers are now working to find compounds that could safely block the culprit receptor in humans, known as MRGPRX2. Such a drug would not prevent true allergic reactions, which produce antibodies, but only the pseudoallergic reactions triggered by MRGPRX2. Still, it could improve the lives of many patients, says McNeil, by lessening the drug side effects they currently endure. Medications that trigger MRGPRX2 include cancer drugs cetrorelix, leuprolide and octreotide; HIV drug sermorelin; fluoroquinolone antibiotics; and neuromuscular blocking drugs used to paralyze muscles during surgeries.

Dong's research group is also looking into the possibility that MRGPRX2 could be behind immune conditions such as rosacea and psoriasis that don't stem from medication use.

Source: Johns Hopkins Medicine

Sharing that crowded holiday flight with countless hitchhiking dust mites

Predicted structure of the group 1 allergen protein from an American house dust mite. Arrow points to the location of a novel mutation discovered by the University of Michigan-led team.
Credit: Rubaba Hamid

As if holiday travel isn't stressful enough. Now University of Michigan researchers say we're likely sharing that already overcrowded airline cabin with countless tiny creatures including house dust mites.

"What people might not realize when they board a plane is that they can share the flight with a myriad of microscopic passengers-- including house dust mites--that take advantage of humanity's technological progress for their own benefit," said U-M biologist Pavel Klimov.

"House dust mites can easily travel on an airline passenger's clothes, skin, food and baggage," said Klimov, an assistant research scientist in the U-M Department of Ecology and Evolutionary Biology. "Like humans, they use air travel to visit new places, where they establish new populations, expand their ranges and interact with other organisms through various means."

Air travel likely explains some of the findings of a new genetic study conducted by Klimov and U-M visiting scholar Rubaba Hamid that looked at the connections between house dust mite populations in the United States and South Asia.

They found genetic mutations shared by mites in the U.S. and Pakistan that demonstrate the eight-legged creatures' propensity for intercontinental dispersal, according to a research paper scheduled for online publication Dec. 10 in the journal PLOS ONE.

"What we found suggests that mite populations are indeed linked through migration across continents, though geographic differences still can be detected," Hamid said. "Every time a mite successfully migrates to a new place, it brings its own genetic signature that can be detected in the resident population a long time after the migration event."

The study focused on two medically important mite species, the American and European house dust mite. Both species have global distributions, though the former is more abundant in the U.S.

Ancestors of the two species probably separated from each other nearly 81 million years ago--long before the origin of humans--when they inhabited bird nests. Today, house dust mites are blamed for causing allergic reactions in more than 65 million people worldwide and thrive in the mattresses, sofas and carpets of even the cleanest homes.

Hamid, Klimov and their colleagues examined genetic variation in the group 1 allergen gene from samples of the two mite species collected in the U.S. and Pakistan. The group 1 allergen gene encodes for the most important allergy-causing protein in house dust mites.

An inactive form of this protein is used in clinics worldwide as part of the standard skin-prick test for allergies. Though the test can be inaccurate if it does not include local genetic variants of the allergy-causing protein, geographical variation in group 1 allergen proteins has not been extensively studied in the U.S., Klimov said.

"We need to have a better idea about the diversity of allergenic proteins around the world, and particularly in the United States," he said.

In genetic sequences from American house dust mites (Dermatophagoides farinae), the 
researchers observed mutations at 14 positions along the length of the group 1 allergen gene.

All but one of the mutations are "silent," meaning they occur at the DNA level without changing the amino acid structure of the protein. Only mutations at the protein level have medical significance because they can change allergenic properties.

"The most unexpected result was the finding that a previously unknown mutation occurred at the active site of the protein at position 197," Klimov said. "This was a rare mutation, found in only a single population of house dust mite in South Asia.

"Our analysis indicates that this mutation might alter the enzyme activity of the protein. But allergenic properties, immune response and cross-reactivity of the protein are unknown at this time," he said. "Follow-up experiments to elucidate these issues are underway in our lab."

Source: University of Michigan

Poisonous cure: Toxic fungi may hold secrets to tackling deadly diseases

Take two poisonous mushrooms, and call me in the morning, said no doctor ever. Credit: Photo by G.L. Kohuth

Take two poisonous mushrooms, and call me in the morning. While no doctor would ever write this prescription, toxic fungi may hold the secrets to tackling deadly diseases.

A team of Michigan State University scientists has discovered an enzyme that is the key to the lethal potency of poisonous mushrooms. The results, published in the current issue of the journal Chemistry and Biology, reveal the enzyme's ability to create the mushroom's molecules that harbor missile-like proficiency in attacking and annihilating a single vulnerable target in the human liver.

The team revealed how the enzyme contributes to the manufacture of chemical compounds known as cyclic peptides, a favorite type of molecule that pharmaceutical companies use to create new drugs. These findings could lead to single-minded medicines with zero side effects, said Jonathan Walton, professor of plant biology and co-lead author.

"Mushrooms are prolific chemical factories, yet only a few of their peptides are poisonous," he said. "These toxins survive the high temperatures of cooking and the acids of digestion, and yet they're readily absorbed by the bloodstream and go directly to their intended target. These are the exact qualities needed for an effective medicine."

Walton published the paper with fellow MSU scientists Hong Luo, Sung-Yong Hong, R. Michael Sgambelluri and Evan Angelos. Working with the mushroom species Amanita, Walton and his teammates disassembled one of its poisonous peptides, which can be compared to a laser-guided missile with a nuclear warhead.

By removing the molecular equivalent of the deadly warhead, they now have a sturdy, precise delivery system that can supply medicine -- rather than poison -- to a single target. By taking a laser, rather than a shotgun approach, scientists could develop medicines capable of curing disease without the patient suffering any side effects.

The enzyme the team discovered is called POPB, and it converts toxins from their initial linear shape into cyclic peptides, fortress-like molecular circles comprising eight amino acids.

Harnessing the distinct properties of POPB will allow scientist to create billions of variant molecules, which can be tested against many different medical targets such as pathogenic bacteria and cancer.

"We've found some variables that are key," said Walton, an AgBioResearch scientist. "By making more variants, we can add or replace molecules that may or may not work. To date we've created a library of a hundred or so, and we eventually plan to create millions."

The challenge of the next stage of research, though, is testing the variants against diseases such as cancer. The bottleneck lies in the screening process. While Walton's team has discovered a missile capable of carrying a million different potential medicines, as of yet the payload that will be effective remains a mystery.

Source: Michigan State University

Mother's diet affects the 'silencing' of her child's genes

An infant from the Gambia. Credit: Felicia Webb

A mother's diet before conception can permanently affect how her child's genes function, according to a study published in Nature Communications.

The first such evidence of the effect in humans opens up the possibility that a mother's diet before pregnancy could permanently affect many aspects of her children's lifelong health.

Researchers from the MRC International Nutrition Group, based at the London School of Hygiene & Tropical Medicine and MRC Unit, The Gambia, utilized a unique 'experiment of nature' in rural Gambia, where the population's dependence on own grown foods and a markedly seasonal climate impose a large difference in people's dietary patterns between rainy and dry seasons.

Through a selection process involving over 2,000 women, the researchers enrolled pregnant women who conceived at the peak of the rainy season (84 women) and the peak of the dry season (83 women). By measuring the concentrations of nutrients in their blood, and later analysing blood and hair follicle samples from their 2-8 month old infants, they found that a mother's diet before conception had a significant effect on the properties of her child's DNA.

While a child's genes are inherited directly from their parents, how these genes are expressed is controlled through 'epigenetic' modifications to the DNA. One such modification involves tagging gene regions with chemical compounds called methyl groups and results in silencing the genes. The addition of these compounds requires key nutrients including folate, vitamins B2, B6 and B12, choline and methionine.

Experiments in animals have already shown that environmental influences before conception can lead to epigenetic changes that affect the offspring. A 2003 study found that a female mouse's diet can change her offspring's coat colour by permanently modifying DNA methylation.1 But until this latest research, funded by the Wellcome Trust and the MRC, it was unknown whether such effects also occur in humans.

Senior author Dr Branwen Hennig, Senior Investigator Scientist at the MRC Gambia Unit and the London School of Hygiene & Tropical Medicine, said: "Our results represent the first demonstration in humans that a mother's nutritional well-being at the time of conception can change how her child's genes will be interpreted, with a life-long impact."

The researchers found that infants from rainy season conceptions had consistently higher rates of methyl groups present in all six genes they studied, and that these were linked to various nutrient levels in the mother's blood. Strong associations were found with two compounds in particular (homocysteine and cysteine), and the mothers' body mass index (BMI) had an additional influence. However, although these epigenetic effects were observed, their functional consequences remain unknown.

Professor Andrew Prentice, Professor of International Nutrition at the London School of Hygiene & Tropical Medicine, and head of the Nutrition Theme at the MRC Unit, The Gambia, said: "Our on-going research is yielding strong indications that the methylation machinery can be disrupted by nutrient deficiencies and that this can lead to disease. Our ultimate goal is to define an optimal diet for mothers-to-be that would prevent defects in the methylation process. Pre-conceptional folic acid is already used to prevent defects in embryos. Now our research is pointing towards the need for a cocktail of nutrients, which could come from the diet or from supplements."

Dr Rob Waterland of Baylor College of Medicine in Houston, who conducted the epigenetic analyses said: "We selected these gene regions because our earlier studies in mice had shown that establishment of DNA methylation at metastable epialleles is particularly sensitive to maternal nutrition in early pregnancy."

The authors note that their study was limited by including only one blood sampling point during early pregnancy, but estimates of pre-conception nutrient concentrations were calculated using results from non-pregnant women sampled throughout a whole calendar year. The authors also plan to increase the sample size in further studies.

Source: London School of Hygiene & Tropical Medicine

Revolutionizing genome engineering

Streptococcus pyogenes is one of the bacteria in which the HZI scientists have studied the CRISPR-Cas system. Credit: © HZI / M. Rohde

Genome engineering with the RNA-guided CRISPR-Cas9 system in animals and plants is changing biology. It is easier to use and more efficient than other genetic engineering tools, thus it is already being applied in laboratories all over the world just a few years after its discovery. This rapid adoption and the history of the system are the core topics of a review published in the journal Science. The review was written by the discoverers of the system Prof. Emmanuelle Charpentier, who works at the Helmholtz Centre for Infection Research (HZI) and is also affiliated to the Hannover Medical School and Umeå University, and Prof. Jennifer Doudna from the University of California, Berkeley, USA.

Many diseases result from a change of an individual's DNA -- the letter code that genes consist of. The defined order of the letters within a gene usually codes for a protein. Proteins are the workforce of our body and responsible for almost all processes needed to keep us running. When a gene is altered, its protein product may lose its normal function and disorders can result. "Making site-specific changes to the genome therefore is an interesting approach to preventing or treating those diseases," says Prof Emmanuelle Charpentier, head of the HZI research department "Regulation in Infection Biology." Due to this, ever since the discovery of the DNA structure, researchers have been looking for a way to alternate the genetic code.

First techniques like zinc finger nucleases and synthetic nucleases called TALENs were a starting point but turned out to be expensive and difficult to handle for a beginner. "The existing technologies are dependent on proteins as address labels and customizing new proteins for any new change to introduce in the DNA is a cumbersome process," says Charpentier. In 2012, while working at Umeå University, she described what is now revolutionising genetic engineering: the CRISPR-Cas9 system.

It is based on the immune system of bacteria and archaea but is also of value in the laboratory. CRISPR is short for Clustered Regularly Interspaced Palindromic Repeats, whereas Cas simply stands for the CRISPR-associated protein. "Initially we identified a novel RNA, namely tracrRNA, associated to the CRISPR-Cas9 system, which we published in 2011 in Nature. We were excited when Krzysztof Chylinski from my laboratory subsequently confirmed a long term thinking: Cas9 is an enzyme that functions with two RNAs," says Charpentier.

Together the system has the ability to detect specific sequences of letters within the genetic code and to cut DNA at a specific point. In this process the Cas9 protein functions as the scissors and an RNA snippet as the address label ensuring that the cut happens in the right place. In collaboration with Martin Jinek and Jennifer Doudna, the system could be simplified to use it as a universal technology. Now the user would just have to replace the sequence of this RNA to target virtually any sequence in the genome.

After describing the general abilities of CRISPR-Cas9 in 2012 it was shown in early 2013 that it works as efficiently in human cells as it does in bacteria. Ever since, there has been a real hype around the topic and researchers from all over the world have suggested new areas in which the new tool can be used. The possible applications extend from developing new therapies for genetic disorders caused by gene mutations to changing the pace and course of agricultural research in the future all the way to a possible new method for fighting the AIDS virus HIV.

"The CRISPR-Cas9 system has already breached boundaries and made genetic engineering much more versatile, efficient and easy," Charpentier says. "There really does not seem to be a limit in the applications."

Source: Helmholtz Centre for Infection Research

Squid supplies blueprint for printable thermoplastics

This is a whimsical image of a squid creating 3-D printed devices. Credit: Adriás Bago

Squid, what is it good for? You can eat it and you can make ink or dye from it, and now a Penn State team of researchers is using it to make a thermoplastic that can be used in 3-D printing.

"Most of the companies looking into this type of material have focused on synthetic plastics," said Melik C. Demirel, professor of engineering science and mechanics. "Synthetic plastics are not rapidly deployable for field applications, and more importantly, they are not eco-friendly."

Demirel and his team looked at the protein complex that exists in the squid ring teeth (SRT). The naturally made material is a thermoplastic, but obtaining it requires a large amount of effort and many squid.

"We have the genetic sequence for six squid collected around the world, but we started with the European common squid," said Demirel, who with his team collected the cephalopods.

The researchers looked at the genetic sequence for the protein complex molecule and tried synthesizing a variety of proteins from the complex. Some were not thermoplastics, but others show stable thermal response, for example, the smallest known molecular weight SRT protein was a thermoplastic. The results of their work were published in today's (Dec. 17) issue of Advanced Functional Materials and illustrates the cover.

Most plastics are currently manufactured from fossil fuel sources like crude oil. Some high-end plastics are made from synthetic oils. Thermoplastics are polymer materials that can melt, be formed and then solidify as the same material without degrading materials properties.

This particular thermoplastic can be fabricated either as a thermoplastic, heated and extruded or molded, or the plastic can be dissolved in a simple solvent like acetic acid and used in film casting. The material can also be used in 3D printing machines as the source material to create complicated geometric structures.

To manufacture this small, synthetic SRT molecule, the researchers used recombinant techniques. They inserted SRT protein genes into E. coli, so that this common, harmless bacteria could produce the plastic molecules as part of their normal activity and the thermoplastic was then removed from the media where the E. coli lived. Wayne Curtis, professor of chemical engineering and Demirel collaborating on this project together with their students worked on this aspect of the project.

"The next generation of materials will be governed by molecular composition -- sequence, structure and properties," said Demirel.

The thermoplastic the researchers created is semi-crystalline and can be rigid or soft. It has a very high tensile strength and is a wet adhesive; it will stick to things even if it is wet.

This thermoplastic protein has a variety of tunable properties, which can be adjusted to individual requirements of manufacturing. Because it is a protein, it can be used for medical or cosmetic applications.

"Direct extraction or recombinant expression of protein based thermoplastics opens up new avenues for materials fabrication and synthesis, which will eventually be competitive with the high-end synthetic oil based plastics," the researchers report.

Source: Penn State

Reshaping the horse through millennia: Sequencing reveals genes selected by humans in domestication

A man catches domestic Mongolian horses with a lasso in Khomiin Tal, Mongolia. Credit: Copyright: Ludovic Orlando.

Whole genome sequencing of modern and ancient horses unveils the genes that have been selected by humans in the process of domestication through the latest 5,500 years, but also reveals the cost of this domestication. A new study led by the Centre for GeoGenetics at the University of Copenhagen, in collaboration with scientists from 11 international universities, reports that a significant part of the genetic variation in modern domesticated horses could be attributed to interbreeding with the descendants of a now extinct population of wild horses. This population was distinct from the only surviving wild horse population, that of the Przewalski's horses. The study has been published in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

The domestication of the horse some 5,500 years ago ultimately revolutionized human civilization and societies. Horses facilitated transportation as well as the circulation of ideas, languages and religions. Horses also revolutionized warfare with the advent of chariotry and mounted cavalry and beyond the battlefield horses greatly stimulated agriculture. However, the domestication of the horse and the subsequent encroachment of human civilization also resulted in the near extinction of wild horses.

The only surviving wild horse population, the Przewalski's horses from Mongolia, descends from mere 13 individuals, preserved only through a massive conservation effort. As a consequence of this massive loss of genetic diversity, the effects of horse domestication through times have been difficult to unravel on a molecular level. Says Dr. Ludovic Orlando, Associate Professor at the Centre for GeoGenetics, who led this work

"The classical way to evaluate the evolutionary impact of domestication consists of comparing the genetic information present amongst wild animals and their living domesticates. This approach is ill suited to horses as the only surviving population of wild horses has experienced a massive demographic decline in the 20th century. We therefore decided to sequence the genome of ancient horses that lived prior to domestication to directly assess how pre-domesticated horses looked like genetically."

Recent advances in ancient DNA research have opened the door for reconstructing the genomes of ancient individuals. In 2013, Ludovic Orlando and his team succeeded in decoding the genome of a ~700,000 year-old horse, which represents the oldest genome sequenced to date. This time, the researchers focused on much more recent horse specimens, dating from ~16,000 and ~43,000 years ago. These were carefully selected to unambiguously predate the beginning of domestication, some 5,500 years ago. The bone fossils were excavated in the Taymyr Peninsula, Russia, where arctic conditions favor the preservation of DNA.

The human reshaping of the horse

While the horse contributed to reshaping human civilization, humans in turn reshaped the horse to fit their diverse needs and the diverse environments they lived in. This transformation left specific signatures in the genomes of modern horses, which the ancient genomes helped reveal. The scientists were able to detect a set of 125 candidate genes involved in a wide range of physical and behavioral traits, by comparing the genomes of the two ancient horses with those of the Przewalski's horse and five breeds of domesticated horses. Says Dr. Dan Chang, post-doctoral researcher at the UCSC Paleogenomics Lab and co-leading author of the study:

"Our selection scans identified genes that were already known to evolve under strong selection in horses. This provided a nice validation of our approach."

Dr. Beth Shapiro, head of the UCSC Paleogenomics Lab continues: "We provide the most extensive list of gene candidates that have been favored by humans following the domestication of horses. This list is fascinating as it includes a number of genes involved in the development of muscle and bones. This probably reveals the genes that helped utilizing horses for transportation."

And Dr. Ludovic Orlando from the Centre for GeoGenetics at the University of Copenhagen concludes: "Perhaps even more exciting as it represents the hallmark of animal domestication, we identify genes controlling animal behavior and the response to fear. These genes could have been the key for turning wild animals into more docile domesticated forms."

The 'cost of domestication' in horses

However, the reshaping of the horse genome during their domestication also had significant negative impacts. This was apparent in the increasing levels of inbreeding found amongst domesticates, but also through an enhanced accumulation of deleterious mutations in their genomes relative to the ancient wild horses. This finding supports an earlier theory coined 'the cost of domestication', which predicted increasing genetic loads in domesticates compared to their wild ancestors. Says Professor Laurent Excoffier, University of Bern and group leader at the Swiss Institute for Bioinformatics:

"Domestication is generally associated with repeated demographic crashes. Yet, mutations that negatively impact genes are not eliminated by selection and can even increase in frequency when populations are small. Domestication thus generally comes at a cost, as deleterious mutations can accumulate in the genome. This had already been shown for rice and dogs. Horses now provide another example of this phenomenon."

This is something that was only detectable in the horse in comparison to the ancient genomes, as Przewalski's horses were found to show a proportion of deleterious mutations similar to domesticated horses. Says Hákon Jónsson, PhD-student at the Centre for GeoGenetics, co-leading author of the study: "The recent near extinction of the Przewalski's horse population resulted in the persistence of deleterious mutations in the population, following the same mechanism that once led to the accumulation of deleterious mutations in the genomes of domesticated horses. What is striking is that a similar order of magnitude 
was reached even though this occurred in a much shorter time scale than domestication."

An ancient contribution to the present

In addition, comparison of the ancient and modern genomes revealed that the ancient individuals contributed a significant amount of genetic variation to the modern population of domesticated horses, but not to the Przewalski's horses. This suggests that restocking from a wild population descendant from the ancient horses occurred during the domestication processes that ultimately led to the modern domesticated horses. Mikkel Schubert, PhD- student at the Centre for GeoGenetics, co-leading author of the study concludes:

"This confirms previous findings that wild horses were used to restock the population of domesticated horses during the domestication process. However, as we sequenced whole genomes, we can estimate how much of the modern horse genome has been contributed through this process. Our estimate suggests that at least 13%, and potentially up to as much as 60%, of the modern horse genome has been acquired by restocking from the extinct wild population. That we identified the population that contributed to this process demonstrates that it is possible to identify the ancestral genetic sources that ultimately gave rise to our domesticated horses."

Source: Faculty of Science - University of Copenhagen

A clear, molecular view of how human color vision evolved

Mountain Gorilla - Bwindi Uganda. “Gorillas and chimpanzees have human color vision,” Yokoyama says. “Or perhaps we should say that humans have gorilla and chimpanzee vision.” Credit: © Alexander / Fotolia

Many genetic mutations in visual pigments, spread over millions of years, were required for humans to evolve from a primitive mammal with a dim, shadowy view of the world into a greater ape able to see all the colors in a rainbow.

Now, after more than two decades of painstaking research, scientists have finished a detailed and complete picture of the evolution of human color vision. PLOS Genetics published the final pieces of this picture: The process for how humans switched from ultraviolet (UV) vision to violet vision, or the ability to see blue light.

"We have now traced all of the evolutionary pathways, going back 90 million years, that led to human color vision," says lead author Shozo Yokoyama, a biologist at Emory University. 

"We've clarified these molecular pathways at the chemical level, the genetic level and the functional level."

Co-authors of the PLOS Genetics paper include Emory biologists Jinyi Xing, Yang Liu and Davide Faggionato; Syracuse University biologist William Starmer; and Ahmet Altun, a chemist and former post-doc at Emory who is now at Fatih University in Istanbul, Turkey.

Yokoyama and various collaborators over the years have teased out secrets of the adaptive evolution of vision in humans and other vertebrates by studying ancestral molecules. The lengthy process involves first estimating and synthesizing ancestral proteins and pigments of a species, then conducting experiments on them. The technique combines microbiology with theoretical computation, biophysics, quantum chemistry and genetic engineering.

Five classes of opsin genes encode visual pigments for dim-light and color vision. Bits and pieces of the opsin genes change and vision adapts as the environment of a species changes.

Around 90 million years ago, our primitive mammalian ancestors were nocturnal and had UV-sensitive and red-sensitive color, giving them a bi-chromatic view of the world. By around 30 million years ago, our ancestors had evolved four classes of opsin genes, giving them the ability to see the full-color spectrum of visible light, except for UV.

"Gorillas and chimpanzees have human color vision," Yokoyama says. "Or perhaps we should say that humans have gorilla and chimpanzee vision."

For the PLOS Genetics paper, the researchers focused on the seven genetic mutations involved in losing UV vision and achieving the current function of a blue-sensitive pigment. 

They traced this progression from 90-to-30 million years ago.

The researchers identified 5,040 possible pathways for the amino acid changes required to bring about the genetic changes. "We did experiments for every one of these 5,040 possibilities," Yokoyama says. "We found that of the seven genetic changes required, each of them individually has no effect. It is only when several of the changes combine in a particular order that the evolutionary pathway can be completed."

In other words, just as an animal's external environment drives natural selection, so do changes in the animal's molecular environment.

In previous research, Yokoyama showed how the scabbardfish, which today spends much of its life at depths of 25 to 100 meters, needed just one genetic mutation to switch from UV to blue-light vision. Human ancestors, however, needed seven changes and these changes were spread over millions of years. "The evolution for our ancestors' vision was very slow, compared to this fish, probably because their environment changed much more slowly," 
Yokoyama says.

About 80 percent of the 5,040 pathways the researchers traced stopped in the middle, because a protein became non-functional. Chemist Ahmet Altun solved the mystery of why the protein got knocked out. It needs water to function, and if one mutation occurs before the other, it blocks the two water channels extending through the vision pigment's membrane.

"The remaining 20 percent of the pathways remained possible pathways, but our ancestors used only one," Yokoyama says. "We identified that path."

In 1990, Yokoyama identified the three specific amino acid changes that led to human ancestors developing a green-sensitive pigment. In 2008, he led an effort to construct the most extensive evolutionary tree for dim-light vision, including animals from eels to humans. At key branches of the tree, Yokoyama's lab engineered ancestral gene functions, in order to connect changes in the living environment to the molecular changes.

The PLOS Genetics paper completes the project for the evolution of human color vision. "We have no more ambiguities, down to the level of the expression of amino acids, for the mechanisms involved in this evolutionary pathway," Yokoyama says.

Source: Emory Health Sciences