January 20, 2016 § Leave a comment
Many of us can attest to the rejuvenating effects of a manicure or a pedicure. The same applies to mice, as recently determined by Stanford University School of Medicine researchers. The investigators report that a simple pedicure can treat ulcerative dermatitis, a ubiquitous and often fatal condition among laboratory mice.
UD affects up to 21 percent of lab mice. Its specific cause remains unknown, although strong evidence suggests that it is behavior-related. Deep, itchy lesions often appear first on the neck. These lesions spread as the mouse scratches itself. UD is currently the most common cause of unplanned euthanasia among lab mice.
In a PLoS ONE paper, Sean Adams’ group described nail trimming as an alternative to the laborious and ineffective application of daily ointment to treat UD. This method was the first of several anecdotally-reported strategies that the researchers planned to explore. A pedicure, they found, reduces animal suffering, saves time and money, and boosts the integrity of mouse studies by reducing the need for medical intervention. Fewer euthanized mice means fewer mice needed per study.
The investigators then carried out a study. In one 14-day trial, 93.3 percent of mice were cured of UD with a pedicure compared with 25.4 percent of mice treated with daily ointment. The nail-trimmed mice received a one-time dose of topical treatment to prevent bacterial growth and soothe inflammation. These mice resisted scratching even after their nails grew back. “By intervening in the itch-scratch cycle, we are giving the animals the time that they need to recover, and also perhaps for that behavior to ramp down,” says Joseph Garner at Stanford University, a coauthor on the study.
The researchers later devised a plastic restraint, a modified conical tube, to keep the mice still while their nails are trimmed. With training, this process can take as little as 30 seconds. The researchers have been distributing these tubes when they present their findings at conferences, hoping to encourage more labs to adopt this humane and economical practice.
“There was a lot of serendipity and luck involved,” says Garner. “We never expected that we would find a solution that works in such a high percentage of mice, that it would be so simple, or that we would find it on the first try.”
Alexandra Taylor (firstname.lastname@example.org) is a staff science writer at ASBMB and a master’s candidate in science and medical writing at Johns Hopkins University.
January 11, 2016 § 1 Comment
Mammals, there’s a new enzyme in town. In a paper just published in the Proceedings of the National Academy of Sciences, scientists report the discovery of a new enzyme called glycerol-3-phosphate phosphatase. The enzyme plays a critical role in metabolism by overseeing the levels of different fuels in the body.
Metabolism has been a heavily trodden field of study ever since the dawn of molecular biology. These days, “it is extremely rare that a novel enzyme is discovered at the heart of intermediary metabolism in all mammalian tissues,” says S.R. Murthy Madiraju at the Montreal Diabetes Research Center, one of the corresponding authors on the paper.
Madiraju, along with Marc Prentki at the Montreal Diabetes Research Center and others, found the enzyme while grappling with a puzzle. They were studying pancreatic beta cells that produce insulin to control blood glucose levels. These cells get stressed when barraged with metabolic fuel from the diet, such as glucose and fatty acids. When that happens, the cells make and get rid of glycerol as a way of dealing with the excessive fuel supply.
Initially researchers thought the glycerol came from the breakdown of fats. But when Madiraju, Prentki and colleagues inhibited fat breakdown, the cells kept making glycerol. This suggested there was another glycerol source.
Microorganisms, plants and some fish have an enzyme that turns a molecule called glycerol-3-phosphate into glycerol. Mammals were thought not to have the enzyme.
But the investigators set out to check if mammals really and truly didn’t have a glycerol-3-phosphate phosphatase. It turns out they do. Madiraju, Prentki and colleagues confirmed the presence of the enzyme both in cell and animal models.
In discovering a mammalian glycerol-3-phosphate phosphatase, “we have to re-adjust our thinking that fat breakdown is not the only way by which mammalian cells generate glycerol, as has been believed so far!” says Prentki.
Glycerol-3-phosphate, the molecule on which the enzyme works, is made from glucose and gets incorporated into fats. It lies at the heart of glucose and lipid metabolism. With the discovery of an enzyme that can directly break down glycerol-3-phosphate, researchers now have a new player to contend with in understanding how the body maintains energy levels under normal circumstances and what goes wrong in different metabolic diseases.
The investigators say that they believe that, because of its critical metabolic role, glycerol-3-phosphate phosphatase will be a new target for treating chronic conditions such as obesity and type 2 diabetes as well as some cancers.
December 14, 2015 § Leave a comment
Much like Legos, proteins can come together in a number of ways to create complex structures. The various ways make it hard to organize protein complexes into categories.
But now, in a paper just out in Science, researchers describe an approach to classify protein complexes that creates a periodic table, like the periodic table that’s used in chemistry to organize elements. “We’re bringing a lot of order into the messy world of protein complexes,” explained Sebastian Ahnert at the University of Cambridge who is the first author on the paper in a press release.
Many proteins spend much of their time interacting with other proteins and assembling into complexes in order to carry out their functions. But the interactions and functions are specific, much like in the way different Lego bricks can latch onto each other only in certain ways. The underlying principles of protein interactions and assembly are not yet fully understood. But by organizing the different ways protein comes together into a table, Ahnert, along with Sarah Teichmann at the European Molecular Biology Laboratory–European Bioinformatics Institute, Joseph Marsh at the University of Edinburgh and others, wanted to see if some of the fundamental steps in protein complex evolution would become apparent.
They did. The investigators organized complexes based on simple rules so that they could find the most basic structures. “In the end, we discovered that three possible steps of interface evolution, combined in very specific ways, give rise to almost all known structures of protein complexes,” says Ahnert.
The investigators say that the fact that almost all known protein complexes could be arranged into a periodic table is revealing and will help understand how protein complexes come about. “Most heteromeric protein complexes—ones with more than one protein type—consist of identical repeated units of several protein types,” says Ahnert. “Because of this, heteromeric protein complexes can, in fact, be viewed as simpler, homomeric protein complexes—ones that only consist of a single type of protein—if we think of these repeated units as larger ‘single proteins.’”
(For an interactive version of the periodic table for proteins, go here)
October 22, 2015 § Leave a comment
Pollen, which consists of grains with the plant male gametes tucked inside, dries as it matures to increase its chances of survival. When carried over to neighboring plants, for example by insects or wind, pollen comes into contact with fluid in the female organ of a plant and then swells rapidly.
This swelling process a sensitive procedure; a pollen grain can die if it is not carefully rehydrated. Until now, the mechanism regulating this fluid uptake was unknown. Researchers writing in the journal Science today report that they have discovered an ion channel that helps pollen grains sense and respond to changes in internal water pressure.
Elizabeth Haswell at Washington University in St. Louis has been studying mechanical signals in plants for more than a decade. In the paper just published, she and her colleagues describe the discovery of ion channels on pollen membranes that monitor and respond to osmotic changes.
If the fluid content inside a membrane becomes too great, pores open to allow ions to leave. Water follows, relieving the pressure. The mechanosensitive ion channel, known as MSL8, senses pressure and makes adjustments as necessary. An incorrect amount of this protein deceases the pollen’s ability to fertilize.
By using RNA analysis, Haswell’s team determined that MSL8 transcripts are found in floral tissue but not in leaf or root tissue. They then fluorescently marked the proteins to show that the proteins were present on the plasma membranes of mature pollen grains.
After rehydrating, pollen grows a tube to carry its sperm cell to the eggs. Haswell and colleagues found that pollen without MSL8 germinated more effectively but generated so much pressure that the tube burst, impairing fertilization. Conversely, pollen that overexpressed MSL8 did not generate enough pressure for the pollen tube to break through the cell wall, rendering the pollen infertile.
This delicate osmotic balance demonstrates mechanical signals aiding in the developmental process. Researchers previously established that bacteria use stretch-activated channels to relieve internal pressure in response to environmental stress signals. The findings by Haswell and colleagues now indicate a previously unknown use for mechanically gated ion channels: reproduction. To cope with “the uncertain and potentially severe conditions of [the] pollen journey, pollen has developed some equally severe compensatory mechanisms, including this fascinating desiccation and rehydration process,” Haswell says. Other strategies include multiple nuclei and a tough cell wall.
While the function of MSL8 seems clear, the mechanism by which it operates — directly, by releasing osmolytes, or indirectly, through regulatory pathways — will be a target for further study. Haswell’s team also is interested in several related ion channels and in studying how membranes survive the dehydration/rehydration process.
This blog post was written by Alexandra Taylor who is a science writing intern at the American Society for Biochemistry and Molecular Biology.
September 29, 2015 § 1 Comment
Each year in the U.K., about 2 percent of horses die from grass sickness. No one knows what causes the disease, but it does occur almost exclusively in grass-fed animals, including ponies and donkeys. A similar disease is thought to afflict dogs, cats, rabbits, hares, llamas, and possibly sheep.
In an attempt to understand what happens at the molecular level of equine grass sickness, researchers recently reported in the journal Molecular & Cellular Proteomics their analysis of tissue samples taken from horses stricken with the disease. They found misfolded and dysregulated proteins in the tissues that resembled those found in human neurodegenerative conditions, such as Alzheimer disease, Parkinson disease and Huntington disease.
Animals with grass sickness usually suffer gut paralysis. The animals roll, sweat, drool and have trouble swallowing. Animals acutely afflicted with the disease usually have to be euthanized.
The disease is known to attack the neurons, but the causative agent is not known. To get a look at what goes on at the molecular level, Thomas Wishart at The Roslin Institute in Scotland, teamed up with Bruce McGorum at the University of Edinburgh’s veterinary school. The investigators applied proteomic techniques to samples taken from horses that came down with grass sickness.
“We do know which tissues are most consistently affected” by the disease, says Wishart. “We considered that a proteomic analysis would provide a snapshot of the molecular processes in play within those samples at that point in time.”
He points out that the work described in the MCP paper “is the first application of modern proteomic tools and in-silico analytical techniques to equine neuronal tissues and to an inherent neurodegenerative disease of large animals that is not a model of human disease.”
The investigators found that the expression levels of 506 proteins were changed in the ganglia taken from horses felled by grass sickness. Moreover, some of the proteins were misfolded, aggregated or in the wrong places. The proteins included amyloid precursor protein, the microtubule associated protein tau and several components of the ubiquitin proteasome system. These proteins have been implicated in human neurodegenerative disorders.
Finding this similarity between human and horse neurodegenerative diseases, says Wishart, suggests the aggregated or misregulated proteins are “more likely to be end-stage regulators or late consequences rather than initiators of the degenerative cascades.”
As equine grass sickness can be hard to diagnose in some horses, a next step for the investigators is to see if they can come up with a noninvasive diagnostic test.
July 29, 2015 § 1 Comment
Frustration has its perks. In a paper just out in Nature, researchers describe making an artificial ribosome because they couldn’t get normal ribosomes to do what they wanted. In creating this artificial ribosome, called Ribo-T, the investigators unwittingly turned conventional molecular biology wisdom on its head: Unlike regular ribosomes, Ribo-T doesn’t need to fall apart and come together again to support protein synthesis.
Alexander Mankin from the University of Illinois at Chicago says his group and that of Michael Jewett at the Northwestern University were trying to teach normal ribosomes new tricks, like getting it to translate “difficult-to-make” proteins or to take in unnatural amino acids to make special polymers. “We were frustrated with our inability to test or alter the functions of the ribosome,” says Mankin.
Trying to tweak the existing ribosomal RNA, which does much of the work of protein synthesis in the ribosome, didn’t go anywhere. Changes to it killed the cell.
So Mankin, Jewett and their teams considered making a portion of the ribosome that would be able to guide the ribosome into making the special polymers. But the problem is that the ribosome, made up of two subunits, falls apart and comes together in every cycle of protein synthesis. How would they stop the re-engineered portion of the ribosome from being swapped out by the normal subunit?
That’s when the idea of a tether came in. But “dissociation of ribosomal subunits was believed to be a prerequisite for efficient translation, and it was unclear whether ribosome with the tethered subunits would be functional,” says Mankin. Still, the investigators decided to give it a shot.
After many tries, one design worked: the Ribo-T. Mankin, Jewett and colleagues engineered a ribosomal RNA that combined sequences from the two subunits of the ribosome into a single unit. Short RNA linkers separated the two subunit RNAs in the contiguous stretch of nucleic acid.
And Ribo-T worked even better than anticipated. Not only did Ribo-T make proteins in a test tube, it also made proteins in bacterial cells that lacked naturally occurring ribosomes and keep the cells alive. Mankin still sounds surprised: “We have created probably the first-ever-on-Earth organism which lived with the ribosome where two subunits are combined into a single entity.”
He adds that Ribo-T could pave the way to exploring properties of the ribosome and to make a independent protein-synthesis system in cells that does not interfere with the ribosomes that take care of expression the rest of the cellular proteins. But, for now, the investigators are focusing on what sparked off the whole project in the first place: Getting Ribo-T to carry out the tasks that are difficult for normal ribosomes to do.
June 19, 2015 § Leave a comment
Sometimes the end doesn’t justify the means. In a recent paper in the Journal of Lipid Research, investigators describe how spinning high-density lipoproteins fast, a typical way to isolate them quickly, damages them. The finding suggests that the current understanding of the hydrodynamic properties and composition of HDL “is incorrect,” states William Munroe at the University of California, Los Angeles.
HDL, known as the “good cholesterol,” is an important lipoprotein in diagnosing cardiovascular disease. Its abundance in the bloodstream is considered to be a sign of good cardiovascular health because HDL carries away cholesterol.
Ever since the discovery in 1949 that lipoproteins can be separated and isolated in an ultracentrifuge, spinning lipoproteins like HDL at speeds 40,000 rpm or greater has been the norm. Samples often get spun at speeds of 65,000 to 120,000 rpm within 48 hours to hasten the isolation process.
But there have been whispers in the lipid community that the high speeds damage the molecules. So a trio of researchers at UCLA, led by Verne Schumaker, decided to see how speed affects HDL. “The phenomenon of HDL potentially exhibiting sensitivity to the ultracentrifuge speed is sometimes mentioned between lipoprotein researchers,” says Munroe, who is the first author on the paper. “However, there was little in the literature describing this phenomenon.”
In their JLR paper, Munroe, Schumaker and Martin Phillips showed that damage to HDL began as soon as the ultracentrifuge speed hit 30,000 rpm. Using mouse plasma samples, the investigators demonstrated that the damage got worse as the rotor went faster. Proteins, which are integral to the lipoproteins, got ripped out of the protein-lipid complexes, leaving few intact particles. “With enough gravitational force or time, this protein-deficient HDL undergoes further damage to lose lipid,” notes Munroe.
To try to circumvent the damage, the investigators tested out an alternative method for isolating HDL. They poured a potassium bromide density gradient over their sample. Next, they spun the gradient with the sample at a low speed of 15,000 rpm. Admittedly, the isolation took longer at 96 hours, but at least the amount of HDL that rose to the top of gradient was significantly higher than when using the conventional method.
Based on their findings, the investigators now want “to identify HDL-associated proteins that previous identification studies may have missed because certain proteins may have been completely lost from the recovered HDL particle during its isolation by ultracentrifugation,” says Munroe. “This may give insight into additional roles the HDL may participate in besides reverse cholesterol transport.”
June 18, 2015 § Leave a comment
Some scientists credit schoolteachers or graduate-school and postdoctoral advisers as their career role models. Henrik Dohlman at the University of North Carolina stays within his family. He credits his father.
“I really look up to him,” he says of Claes Dohlman. “He’s not only done great things professionally, he’s a very kind man.”
“Great things professionally” is a fair description. Claes Dohlman is a well-known figure in vision research. Inducted into the American Society of Cataract and Refractive Surgery’s Hall of Fame in 2004 and the recipient in 2007 of the American Academy of Ophthalmology’s highest honor, the Laureate’s Award, the elder Dohlman who is an emeritus professor at Harvard University, is considered the founder of modern corneal science. His research into corneal physiology established the basis for current clinical practice with dry eye disease, corneal burns, wound healing and corneal transplantation.
Although he retired from university administration in 1989, Claes Dohlman has stayed on as a scientist. At 92, he is the director of Boston Keratoprosthesis Research and Development, which is part of Massachusetts Eye and Ear, where he created and works to perfect a device he is now famous for: an artificial cornea known as the “Boston keratoprosthesis.” The artificial cornea can be used on patients who can’t rely on standard human corneal transplants, such as chemical-burn victims. A prosthetic that resembles a collar button, it is made of medical-grade plastic and titanium. Since cleared by the FDA in 1992, over 10,000 patients have had the device inserted in their eyes.
The older Dohlman turned his full attention to the device in the 1990s, once he retired from being the chair of Harvard’s ophthalmology department, director of his ophthalmology laboratory, and a chief at Massachusetts Eye and Ear.
With a hint of understatement, the younger Dohlman says of his father, “He has a lot of energy.”
From Sweden to the U.S.
Science and medicine surrounded Claes Dohlman as he grew up in Sweden. His father was the chairman of the ear, nose, and throat department at the University of Lund. “It was hinted that there was only one worthwhile profession to consider and that was academic medicine,” remembers Dohlman. “All my friends were heading for medicine so I followed the path of least resistance.”
Dohlman got an M.D. and finished a residency in ophthalmology at the University of Lund’s Eye Clinic. Drawn by the work of Jonas Friedenwald at Johns Hopkins University on the histochemistry and biochemistry of corneal wound healing, Dohlman did a fellowship with him in the early 1950s in Baltimore, Md. He returned to Sweden to get a Ph.D. in biochemistry from the Karolinska Institute.
A famous retina surgeon in Boston, Charles Schepens, noticed Dohlman’s work. He offered Dohlman a fellowship at Harvard. Having been in the U.S. for the Hopkins fellowship, Dohlman says, he knew that “the possibilities, professionally, were so much greater.”
So in 1958, Dohlman and his wife, Carin, moved to the U.S. with three children. Two years later, Henrik became their fourth child and the first to be born in the U.S. Two more children followed.
The little professor
Henrik Dohlman displayed traits of an academic at a young age. “He was a little professor from the start,” says his father. “He was always very curious, always eager to lecture people on how things really are and copiously read all kinds of literature.”
He also had a willingness to experiment. Claes Dohlman describes a moment in 1968 when he and Carin opened the front door of their home to a sales representative from a hearing-aid company. All of the adults were confused. The sales representative insisted that a Henrik Dohlman had contacted the company. The parents couldn’t figure out why a hearing-aid sales representative wanted to see an 8-year-old boy.
The confusion cleared when the child admitted to finding an advertisement that offered free testing of a hearing aid.
“I had this image that it would give me super powers, and I would hear what people were saying at great distances,” says Henrik Dohlman, still sounding sheepish almost five decades after the incident. “So I filled out the card, and then the salesman showed up. When he discovered that the person he was about to try to sell a hearing aid to was an 8-year-old boy with perfect hearing, he stomped off.”
The younger Dohlman recalls his childhood home in Arlington, Mass., as filled with joyful chaos of a large and close-knit family. “When my father came from work, we all swarmed to greet him and he would be tackled by his kids,” he says. “Dinnertime was masses of spaghetti and conversation.”
But Henrik Dohlman got hints from a young age that his father also was a well-known figure in the community. “Every time I would pass the principal of my elementary school, he’d tousle my hair and say, ‘How’s the son of the famous Dr. Dohlman?’ I figured if my principal knew who he was, then my father must be prominent.”
Education was critical in the Dohlman family. Among the six, two are M.D.s and the rest are Ph.D.s. Henrik Dohlman says his father is very proud of the fact that all his children hold advanced degrees. “If I can say one thing about my parents, it is that they were exceedingly generous financially,” says Dohlman. “They put six kids through college and then graduate or medical school. It’s something I took for granted when I was growing up. But once I got to college and grad school, I realized what a gift that was, to have no financial barriers to completing my education. That’s my inheritance.”
Henrik Dohlman was the only one to go into the life sciences. His other Ph.D.-toting siblings are economists. He credits his mother for turning him onto biology even though she holds a degree in political science. Carin Dohlman also grew up in Sweden, where, as her son notes, all schoolchildren are taught to appreciate the natural world and revere the 18th-century botanist and zoologist Carl Linnaeus who laid the foundations for modern species nomenclature and ecology. Carin Dohlman shared her love and wonder of nature with Henrik.
Identity of his own
Despite earning a Ph.D. in biochemistry like his dad, Henrik Dohlman, who is also an associate editor for the Journal of Biological Chemistry, is quick to point out that he was always intent on making his way through science as independently as possible. His research portfolio at UNC focuses on understanding the fundamental properties of yeast G protein-coupled receptors, a far cry from clinical corneal research.
Ironically, the first project Henrik Dohlman was involved in as a graduate student landed him in his father’s territory. The younger Dohlman was in the laboratory of Robert Lefkowitz at Duke University in the 1980s. At the time, the laboratory was focused on cloning the β-adrenergic receptor, the first hormone-based G protein-coupled receptor identified and cloned. The work later led to Lefkowitz’s Nobel Prize in chemistry in 2012, shared with Brian Kobilka at Stanford University.
“I thought I was working in an area that had nothing to do with vision research,” says Henrik Dohlman. “But the first thing we noticed about this receptor was it was clearly homologous to rhodopsin, the light receptor.”
Because of the striking similarities between the two systems, Henrik Dohlman’s first scientific conference was the annual meeting of the Association for Research in Vision and Ophthalmology. “It was not only one of my first public presentations, but it was a public presentation in front of about 500 of my father’s friends and colleagues, with my father in the front row,” recounts the younger Dohlman.
Perhaps realizing how unprepared his son was for his first presentation at a national scientific meeting, the older Dohlman pulled him aside and asked to see the slides and hear the talk before the event. “It was a very painful experience for both of us,” recalls his son. “The talk that came out in the end bore no resemblance to what I’d prepared. It was the first and last time I’ve given a scientific presentation with my father in the audience.”
But the younger Dohlman acknowledges that the pain of having his father redo his first public presentation for him was well worth it. “I’m a much better public speaker because of it!” he says with a laugh.
“Just shrug it off”
Besides teaching him the value of a good talk, Claes Dohlman has influenced Henrik in two other critical ways. “Probably the most important one was that I saw from an early age that he really loved his work,” says his son. “That’s not a bad way to go through life.”
Claes Dohlman also modeled what it is to be a good laboratory manager. “He’s always had a positive outlook. He rarely loses his temper. He tries to be generous in assigning credit. He does not get distracted by office politics or idle gossip,” says the younger Dohlman.
When it comes to research, Claes Dohlman knows how to roll with the punches. Something his son says he’s still working on. “There are many failures in this business. There are a lot of setbacks, and there’s no escaping that. You can drive yourself crazy if you let it get under your skin. The best that you can do is brush it off and move onto the next challenge,” says Henrik Dohlman. “I hear my father’s voice in my head saying, ‘Just shrug it off.’”
May 19, 2015 § Leave a comment
On October 14, 2010, construction workers excavating a site for a reservoir dam near Snowmass Village in Colorado stumbled across bones. The bones belonged to a woolly mammoth. More careful digging revealed close to 5,000 bones from different Ice Age animals. Camels, mastodons, and bison were among them. In a recent paper from the journal Molecular & Cellular Proteomics, researchers reported the analysis of proteins found in the bones of an extinct species of giant bison from the site. From their analysis, they described an unexpected feature of ancient collagen.
The bones at the Snowmass Village fossil site (which is also known as the Ziegler reservoir site) were remarkably well-preserved. The high altitude of the site, which was a lake in the Ice Age, kept it at relatively cool temperatures over the past 130,000 to 150,000 years. The cooler temperatures probably contributed to the preservation the buried materials; even some of the ancient plant material buried at the site was still green at the time of the discovery.
Kirk Hansen at the University of Colorado, Denver, heard of the Snowmass Village discovery in 2010 “while listening to public radio on my way into work.” Hansen is a protein biochemist whose expertise is in the extracellular matrix. He called the Denver Museum of Nature & Science, which was directing the excavation of the bones, to see if he could help with analyzing samples.
Hansen’s laboratory carries out mass spectrometry analyses and he was aware of existing mass spectrometry work on fossilized proteins. Some studies have suggested that red blood cells can be preserved in ancient bones, but the validity of these interpretations have been questioned. Skeptics also have wondered about inadvertent contamination of ancient samples with modern proteins.
But, Hansen says, “I thought that the methods we were developing to improve characterization of proteins from the extracellular matrix could be used on these well-preserved samples.” Hansen knew he would get good quality samples from the Snowmass Village site when, he says, “one of the scientists described the smell of the bone fossils as ‘very organic. ’”
Mindful of the issue of contamination, Hansen and colleagues were careful with the samples given to them by the museum. The samples were skull bones from an extinct species of giant-horned bison from the Pleistocene era called Bison latifrons. “We took extra precautions by using new chromatography columns and ensuring the samples were placed in only new vials,” he says.
The investigators carried out mass spectrometry on the proteins left in the bison bones. The biggest challenge was in the data analysis. Some of the proteins had degraded, as expected of old proteins, giving a “laddering” effect in the peptides, and numerous peptides were changed by post-translational modifications.
But the investigators sorted through the data and identified extracellular matrix proteins and plasma proteins. Thirty-three of the ancient bison proteins mapped over to modern bovine proteins, showing the evolutionary kinship.
In particular, Hansen and colleagues sequenced in detail the collagen from the bison samples. The extracellular matrix protein, which forms a fibrous ropelike structure, bore modifications seen in other studies of ancient collagen, such as proline hydroxylation.
But one modification was new and unexpected—hydroxylysine glucosylgalactosylation. “This was the first discovery of a preserved glycan, to the best of my knowledge,” says Hansen. “Finding it in a sample that is over 100,000 years old was surprising.”
Bioarcheologist Matthew Collins at the University of York in the U.K., who specializes in studying ancient collagen, is most impressed with the finding of the hydroxylysine glucosylgalactosylated residue. Glycosylation is a key structural feature of collagen, crosslinking chains together to stablilize its ropelike structure. But it was assumed the seemingly labile glycosylated residues would not withstand the test of time.
“You’d imagine, over this period of time, you would have lost the sugars. That’s one of the reasons why we never bothered to look for them: We didn’t expect to find them. This work elegantly shows that I was wrong!” says Collins. “We’re now going back and looking at our samples for glycosylated residues.”
As Hansen and colleagues were working on the bison samples, data came from a young Siberian woolly mammoth called Lyuba. Her proteins bore similar modifications to those of the bison proteins. “Finding these modifications in modern tissue samples usually requires some form of enrichment,” says Hansen. But, with these two fossils, “the modifications were relatively easy to find.” He says the discoveries suggest that collagen with hydroxylysine glucosylgalactosylation might be enriched over time because it creates a stable complex.
Hansen and his team’s next aim is to study the relationships between collagen modifications and collagen fiber architecture. The ramifications of the work will go beyond the study of ancient proteins. As Hansen explains, “Once we make progress in this area, we will have a better understanding of the microenvironment’s role in tumor progression and the ability to rationally design biomaterials for tissue engineering applications.”
April 23, 2015 § 3 Comments
Universal blood is an appealing notion because it could be transfused into anyone regardless of blood type. Researchers have been kicking around the idea of using enzymes to create universal blood since the early 1980s, “but a major limitation has always been the efficiency of the enzymes,” says Stephen Withers at the University of British Columbia. “Impractically large amounts of enzyme were needed.”
Now in a paper just out in the Journal of the American Chemical Society, Withers, David Kwan, Jay Kizhakkedathu at the Centre for Blood Research and others describe the development of an improved enzyme that takes us a step closer to having universal and others describe the development of an improved enzyme that takes us a step closer to having universal blood.
Blood comes in four major types: A, B, AB and O. The difference between them lies in the sugar structures that festoon the surface of red blood cells. Both blood type A and B have the same core sugar structure as blood type O, but differ in an additional sugar at the tip of the sugar structure. Type A has an N-acetylgalactosamine residue. Type B has a galactose residue. Type AB has a mix of both residues. The moiety carrying the additional residue can be tacked onto the core structure in various ways, giving rise to subtypes of A and B blood.
The additional residue presents trouble during blood transfusions: It can trigger life-threatening immune responses. Type A people can’t take type B blood; type B people can’t take in type A blood. Type AB can take A or B. Only type O blood can be freely shared without the fear of immune responses.
The idea from the 1980s has been to use enzymes to remove the moieties with the terminal N-acetylgalactosamine or the galactose residues to leave the core sugar structure on red blood cells, just like in type O blood. But to date, sugar hydrolases have not been sufficiently efficient to make the idea practical.
So Withers’ group, which had some success in engineering different classes of sugar enzymes, tackled the creation of more efficient sugar hydrolases by directed evolution. In directed evolution, researchers carry out iterative rounds of mutations on a gene to ultimately produce a protein that performs better than the original gene product.
Kwan, Withers and the rest of the team carried out directed evolution on the family 98 glycoside hydrolase from a strain of Streptococcus pneumoniae. Kwan explains that the structure of the enzyme is known, which helped the investigators design their variants.
Kwan adds that the enzyme also is good at cleaving most A and B subtypes with the exception of a few A subtypes. The investigators decided to engineer the enzyme so it had better activity against those A subtypes. By directed evolution, the investigators got an engineered enzyme with a 170-fold greater efficiency than the original enzyme.
However, the engineered enzyme still doesn’t remove every single moiety with the N-acetylgalactosamine. Withers says that the immune system is sensitive enough to small amounts of the moiety to start an immune response. He says, “Before our enzyme can be used clinically, further improvements by directed evolution will be necessary to effect complete removal” of all moieties with the terminal N-acetylgalactosamine residues.
The investigators are now looking to tackle the remaining subtypes of type A blood that the S. pneumoniae hydrolase struggles to cut. Withers says, “Given our success so far, we are optimistic that this will work.”