FDA Issues Final Rule on Safety and Effectiveness of Antibacterial Soaps
Washing with plain soap and running water remains one of the most important steps consumers can take to avoid getting sick and to prevent spreading germs to others. If soap and water are not available and a consumer uses a hand sanitizer instead, the U.S. Centers for Disease Control and Prevention (CDC) recommends that it be an alcohol-based hand sanitizer that contains at least 60 percent alcohol.
The FDA issued a final rule establishing that over-the-counter (OTC) consumer antiseptic wash products containing certain active ingredients can no longer be marketed. Companies will no longer be able to market antibacterial washes with these ingredients because manufacturers did not demonstrate that the ingredients are both safe for long-term daily use and more effective than plain soap and water in preventing illness and the spread of certain infections. Some manufacturers have already started removing these ingredients from their products.
This final rule applies to consumer antiseptic wash products containing one or more of 19 specific active ingredients, including the most commonly used ingredients – triclosan and triclocarban. These products are intended for use with water, and are rinsed off after use. This rule does not affect consumer hand sanitizers or wipes, or antibacterial products used in health care settings. The agency issued a proposed rule in 2013 after some data suggested that long-term exposure to certain active ingredients used in antibacterial products – for example, triclosan (liquid soaps) and triclocarban (bar soaps) – could pose health risks, such as bacterial resistance or hormonal effects. Under the proposed rule, manufacturers were required to provide the agency with additional data on the safety and effectiveness of certain ingredients used in over-the-counter consumer antibacterial washes if they wanted to continue marketing antibacterial products containing those ingredients. This included data from clinical studies demonstrating that these products were superior to non-antibacterial washes in preventing human illness or reducing infection.
Antibacterial hand and body wash manufacturers did not provide the necessary data to establish safety and effectiveness for the 19 active ingredients addressed in this final rulemaking. For these ingredients, either no additional data were submitted or the data and information that were submitted were not sufficient for the agency to find that these ingredients are Generally Recognized as Safe and Effective (GRAS/GRAE). In response to comments submitted by industry, the FDA has deferred rulemaking for one year on three additional ingredients used in consumer wash products – benzalkonium chloride, benzethonium chloride and chloroxylenol (PCMX) – to allow for the development and submission of new safety and effectiveness data for these ingredients. Consumer antibacterial washes containing these specific ingredients may be marketed during this time while data are being collected.
Since the FDA’s proposed rulemaking in 2013, manufacturers already started phasing out the use of certain active ingredients in antibacterial washes, including triclosan and triclocarban. Manufacturers will have one year to comply with the rulemaking by removing products from the market or reformulating (removing antibacterial active ingredients) these products.
Tender Fresh Veggie Salad with Tuna Sauce
Easy to make, simple healthy ingredients, and oh-h how tasty! This is an appetizer that’s so-o good, you don’t want an entre, you just want to make an entire meal of this delicious recipe. It took me a while to get the ingredients and the amounts, just right. Try it; you’ll love it! ©Joyce Hays, Target Health Inc.
Not only is this individual salad attractive, but it is truly delicious and was fun to create. We have been enjoying peak corn, right off the cob with no cooking necessary, for all of August, that’s how sweet it is this year. This healthy eating section will carry, during September, recipes in which fresh cob corn, is one of the key ingredients. ©Joyce Hays, Target Health Inc.
You can use one endive leaf or two. When you use two, it looks like a canoe filled with colorful crunchy veggies. Enjoy! © Joyce Hays, Target Health Inc.
(Recipe for two people)
2 fresh corn on cob, all kernels scraped from cob
1 celery stalk, from the heart of the celery, very finely chopped
4 radishes, thinly sliced
1/3 cup chopped fresh cilantro
1/2 apple, chopped into small pieces
1 hardboiled egg, use white only, chop into small pieces
1/2 black olive per person, sliced thinly, for garnish
Flat leaf parsley, chopped, for garnish
1 fat fresh asparagus: make 2 curls for garnish
2 whole endive leaves
Tuna Sauce Ingredients
1 can (7-8 oz) tuna fish in oil (not water, unless you insist)
1 fresh garlic clove
1 tablespoon anchovy paste
1 tablespoon capers
2 tablespoons fresh lemon, juice
1/4 cup extra-virgin olive oil
3 tablespoons Kraft mayonnaise
Pinch black pepper
Pinch chili flakes
This was a great corn year and it’s still in season. Don’t even need to cook it, it’s so sweet this year.
©Joyce Hays, Target Health Inc.
Using same cutting board for celery, egg white, radish, kale and or cilantro, etc.
Joyce Hays, Target Health Inc.
Make the Tuna Sauce (use the last 9 items on list above)
1. Put the tuna fish in a food processor.
2. Add the anchovy paste, capers, lemon juice, oil. Start the food processor and turn the ingredients into a very fine, smooth paste. If the sauce is too thick, very slowly, add tiny amounts of olive oil (or 1 teaspoon) of chicken broth until you get the right consistency.
3. Transfer the mix to a bowl and stir in the mayonnaise, and mix until obtaining a paste.
Keep this sauce in the fridge until you’re ready to serve it.
Making the tuna sauce is as easy as 1 – 2 – 3! All you really need is a food processor.
©Joyce Hays, Target Health Inc.
Into a bowl, add the first six items on the list of ingredients, above. Stir to combine all the ingredients. Set aside until ready to serve.
Put all your veggies into a medium size bowl. ©Joyce Hays, Target Health Inc.
Prepare the garnishes (black olive, parsley, 2 asparagus curls) and set aside. Make curls from the whole asparagus stalk, and use the 1 or 2 curls that have part of the asparagus tip.
Clean the endive leaves and set aside.
When ready to serve, get out small salad plates. Put 1 whole endive leaf on each plate. On each endive leaf, add 1 or two tablespoons from your salad bowl. Next, add 2 or more Tablespoons of tuna sauce, over the salad. Garnish with a few slices of black olive and a tiny sprinkling of well-chopped parsley and 1 asparagus curl on each plate. Serve.
Getting ready to prepare each individual salad plate, using the above ingredients.
©Joyce Hays, Target Health Inc.
On a small appetizer or salad plate, place one or two endive leaves. Fill them with the corn
veggie mixture. ©Joyce Hays, Target Health Inc.
Put a little or a lot of tuna sauce over and/or under the veggies.
©Joyce Hays, Target Health Inc.
Finally, on top of the tuna sauce, garnish with one thin peel of raw asparagus, and 1/2 of a thin slice of
black olive. ©Joyce Hays, Target Health Inc.
This past summer, mangoes were as good as it gets. We simply slurped them down.
Summer desserts consisted of bowls and bowls of this beyond yummy fruit. I can’t remember
a better summer for mangoes. ©Joyce Hays, Target Health Inc.
Save any unused veggies and the egg yolk, for something else, like another salad the next day, or soup, or whatever you think of. Michael Pollan and many others are in the news, more and more, telling of how Americans at home, on farms, in stores and in restaurants, discard tons of usable food. Not only do we have hungry homeless Americans, but all food represents many carbon footprints, which in turn, are strongly and directly related to climate change.
Well chilled, Santa Margherita Pinot Grigio is a tasty reliable wine, that goes well with the
salad recipe, above. Tonight, we’re raising our glasses Goodbye summer!
©Joyce Hays, Target Health Inc.
From Our Table to Yours !
First direct measurements of base-pair bonding strength
September 8, 2016
Technical University of Munich (TUM)
DNA, our genetic material, normally has the structure of a twisted rope ladder. Experts call this structure a double helix. Among other things, it is stabilized by stacking forces between base pairs. Scientists have now succeeded at measuring these forces for the very first time on the level of single base pairs. This new knowledge could help to construct precise molecular machines out of DNA.
DNA, our genetic material, normally has the structure of a twisted rope ladder. Experts call this structure a double helix. Among other things, it is stabilized by stacking forces between base pairs. Scientists at the Technical University of Munich (TUM) have succeeded at measuring these forces for the very first time on the level of single base pairs. This new knowledge could help to construct precise molecular machines out of DNA.
Over 60 years ago, the researchers Crick and Watson identified the structure of deoxyribonucleic acid, which is more commonly known as DNA. They compared the double helix to a rope ladder that had been twisted into a spiral. The rungs of this ladder consisted of guanine/cytosine and thymine/adenine base pairs. But what keeps the DNA strands in that spiral structure?
Special measuring system for molecular interactions
Prof. Hendrik Dietz from the Chair of Experimental Biophysics uses DNA as construction material to create molecular structures. Hence, he is greatly interested in gaining a better understanding of this material. “There are two types of interactions which stabilize double helices,” he explains. For one, DNA contains hydrogen bonds.
For another, there are what experts call base pair stacking forces, which act between the stacked base pairs along the spiral axis. The forces of the hydrogen bonds, on the other hand, act perpendicular to the axis. “So far, it is not quite clear to which extent these two forces each contribute to the overall stability of the DNA double helix,” explains Dietz.
Directly measuring the weak stacking forces between base pairs was a big technical challenge for the researchers, who worked on the problem for six years. In collaboration with the TUM Chair of Molecular Biophysics (Prof. Matthias Rief) and the TUM Chair of Theoretical Biophysics — Biomolecular Dynamics (Prof. Martin Zacharias), they succeeded in developing a special experimental setup that now makes it possible to measure extremely weak contact interactions between individual molecules.
A trillionth of a bar of chocolate
To put it simply, the measurement system is designed hierarchically and involves microscopic beams, at the tips of which one or more double helix structures running in parallel are located. These have been modified such that each end carries one base pair. Two of these microscopic beams are connected with a flexible polymer. On the other side, the beams are coupled to microscopic spheres which can be pulled apart using optical laser tweezers. In solution, the base pairs on the end of one of the beam can now interact with the base pairs on the end of the other beam. This also makes it possible to measure how long a stacking bond between them lasts before they fall apart again, as well as the force acting between the base pairs.
The forces measured by the researchers were in the range of piconewtons. “A newton is the weight of a bar of chocolate,” explains Dietz. “What we have here is a thousandth of a billionth of that, which is practically nothing.” Forces in the range of two piconewtons are sufficient to separate the bond created by stacking forces.
Furthermore, the scientists also observed that the bonds spontaneously broke up and formed again within just a few milliseconds. The strength and the lifetime of the interactions depends to a great extent on which base pairs are stacked on each other.
Creating DNA machines
The results of the measurements may help to better understand mechanical aspects of fundamental biological processes such as DNA replication, i.e. the reproduction of genetic material. For example, the short life of the stacking interactions could mean that an enzyme tasked with separating the base pairs during this process just needs to wait for the stacking bonds break up on their own — instead of having to apply force to separate them.
However, Dietz also intends to apply the data directly to his current research: He uses DNA as programmable building material to construct machines on the order of nanometers. When doing so, he draws inspiration from the complex structures which can e.g. be found in cells and, among other things, serve as molecular “factories” to synthesize important compounds such as ATP, which stores energy. “We now know what would be possible if we could just build structures that were sufficiently sophisticated,” says Dietz. “Naturally, when we have a better understanding of the properties of the molecular interactions, we are better able to work with these molecules.”
At the moment, the lab is building a molecular rotational motor out of DNA, the components of which interlock and are held together via stacking forces. The goal is to be able to control a directed rotation via chemical or thermal stimuli. To do so, the timing of the movement of the rotor in the stator is crucial, and this task has now been made significantly easier with the new findings on the stacking forces.
- F. Kilchherr, C. Wachauf, B. Pelz, M. Rief, M. Zacharias, H. Dietz. Single-molecule dissection of stacking forces in DNA. Science, 2016; 353 (6304): aaf5508 DOI:10.1126/science.aaf5508
Source: Technical University of Munich (TUM). “Measuring forces in the DNA molecule: First direct measurements of base-pair bonding strength.” ScienceDaily. ScienceDaily, 8 September 2016. <www.sciencedaily.com/releases/2016/09/160908150918.htm>.
September 6, 2016
Washington University School of Medicine
Zika virus is capable of infecting the eye, according to a new study. The study, in mice, helps explain why some people with Zika virus develop eye disease, and suggests that contact with infected eyes may play a role in spreading the disease.
Researchers have found that Zika virus can live in eyes and have identified genetic material from the virus in tears, according to a study from Washington University School of Medicine in St. Louis. The study, in mice, helps explain why some Zika patients develop eye disease including a condition known as uveitis which can lead to permanent vision loss.
The study, published Sept. 6 in Cell Reports, describes the effect of Zika virus infection in the eyes of mouse fetuses, newborns and adults. The researchers now are planning complementary studies in human patients infected with the virus.
“Our study suggests that the eye could be a reservoir for Zika virus,” said Michael S. Diamond, MD, PhD, the Herbert S. Gasser Professor of Medicine and one of the study’s senior authors. “We need to consider whether people with Zika have infectious virus in their eyes and how long it actually persists.”
Zika virus causes mild disease in most adults but can cause brain damage and death in fetuses. About a third of all babies infected in utero with Zika show eye disease such as inflammation of the optic nerve, retinal damage or blindness after birth. In adults, Zika can cause conjunctivitis — redness and itchiness of the eyes — and, in rare cases, uveitis.
To determine what effect Zika infection has on the eye, the researchers infected adult mice under the skin — similar to the way humans are infected by mosquitoes — and found live virus in the eyes seven days later. These observations confirm that Zika is able to travel to the eye. It is not yet known whether the virus typically makes that trip by crossing the blood-retina barrier that separates the eye from the bloodstream, traveling along the optic nerve that connects the brain and the eye, or some other route.
Eye infection raises the possibility that people could acquire Zika infection through contact with tears from infected people. The researchers found that the tears of infected mice contained Zika’s RNA — the genetic material from the virus — but not infectious virus when tested 28 days after infection.
“Even though we didn’t find live virus in mouse tears, that doesn’t mean that it couldn’t be infectious in humans,” said Jonathan J. Miner, MD, PhD, an instructor in medicine and the study’s lead author. “There could be a window of time when tears are highly infectious and people are coming in contact with it and able to spread it.”
The eye is an immune privileged site, meaning the immune system is less active there, to avoid accidentally damaging sensitive tissues responsible for vision in the process of fighting infection. Consequently, infections sometimes persist in the eye after they have been cleared from the rest of the body.
“We are planning studies in people to find out whether infectious virus persists in the cornea or other compartments of the eye, because that would have implications for corneal transplantation,” said Rajendra S. Apte, MD, PhD, the Paul A. Cibis Distinguished Professor of Ophthalmology and Visual Science, and the study’s other senior author. Other blood-borne viruses such as herpes simplex virus have been transmitted accidentally through corneal transplants.
Zika researchers are increasingly considering alternative routes of transmission because the virus is spreading more quickly than would be expected by mosquito-borne transmission alone. Epidemiologists can predict the spread of a disease based on known rates of transmission for related viruses and the viral level in the bloodstreams of infected people. By those calculations, Zika is moving unusually fast.
“The Zika epidemic has been very explosive, more explosive than we can account for by just mosquitoes and the level of Zika virus in human blood. Some other factor may be at play,” said Diamond, who is also a professor of molecular microbiology, and of pathology and immunology. “Sexual transmission is probably not playing a major role, but it could be some other bodily fluid — saliva, or urine or tears.”
Even if human tears do not turn out to be infectious, the researchers’ detection of live virus in the eye and viral RNA in tears still has practical benefits. Human tears potentially could be tested for viral RNA or antibodies, a less painful way to diagnose recent Zika infection than drawing blood. The mouse eye could be used to test anti-Zika drugs.
“The advantage to using the eye is that your dosing requirements are very small, and you don’t have to worry as much about effects of larger dosages of therapeutic agents on the rest of the body such as liver toxicity,” said Apte, who is also a professor of developmental biology and of medicine. “If you know you have virus replicating in the eye, you can just give the drug locally and measure any change in viral replication. If you use the eye as a model to study drug delivery or drug efficacy, you could then use the knowledge you gain to treat viral infection in other places.”
- Miner JJ, Sene A, Richner JM, Smith AM, Santeford A, Ban N, Weger-Lucarelli J, Manzella F, Rückert C, Govero J, Noguchi KK, Ebel GD, Diamond MS, Apte RS. . Zika virus infection in mice causes pan-uveitis with shedding of virus in tears. Cell Reports, Sept. 6, 2016. DOI:10.1016/j.celrep.2016.08.079
Source: Washington University School of Medicine. “Zika virus may persist in eyes: Disease may spread from infected eyes.” ScienceDaily. ScienceDaily, 6 September 2016. <www.sciencedaily.com/releases/2016/09/160906130949.htm>.
September 6, 2016
Moscow Institute of Physics and Technology
Scientists have discovered that the depths of Uranus, Neptune and their satellites may contain extraordinary compounds, such as Carbonic and Orthocarbonic acids (the latter also known as Hitler’s acid).It is no accident researchers have chosen these planets as a subject for their research. These gas giants consist mainly of hydrogen, carbon and oxygen, which are the three cornerstones of organic chemistry.
Using computer modeling, chemists from MIPT and Skoltech (the Skolkovo Institute of Science and Technology) have found out which molecules may be present in the interiors of Uranus, Neptune, and the icy satellites of the giant planets. The scientists discovered that at high pressures, which are typical for the interiors of such planets, exotic molecular and polymeric compounds are formed. These compounds include carbonic acid and orthocarbonic acid, the latter also known as ‘Hitler’s Acid’. The results of the study have been published in the journal Scientific Reports.
“The smaller gas giants — Uranus and Neptune — consist largely of carbon, hydrogen and oxygen. We have found that at a pressure of several million atmospheres unexpected compounds should form in their interiors. The cores of these planets may largely consist of these exotic materials,” says the study’s lead author Artem Oganov, professor of Skoltech and the head of MIPT’s Computational Materials Discovery Lab.
A team led by Professor Oganov developed the world’s most universal and powerful algorithm for crystal structure and compound prediction — USPEX (Universal Structure Predictor: Evolutionary Xtallography). In recent years, scientists have used this algorithm to discover several substances that are ‘forbidden’ in classical chemistry and that may be stable at high pressures. These include a number of previously unknown variants of salt — Na3Cl, NaCl3, NaCl7 and even Na3Cl2 andNa4Cl3, as well as exotic new oxides of magnesium, silicon and aluminium which may exist in the interiors of super-Earths.
Now Oganov and his co-author Gabriele Saleh from MIPT have decided to study the chemical behaviour of the carbon-hydrogen-oxygen system under high pressure. “This is an extremely important system because all organic chemistry ‘rests on’ these three elements, and until now it had not been entirely clear how they behave under extreme pressures and temperatures. In addition, they play an essential role in the chemistry of the giant planets,” says Oganov.
The scientists knew that under atmospheric pressure all compounds of carbon, hydrogen, and oxygen, except for methane, water, and carbon dioxide, are thermodynamically unstable. With an increase in pressure, water and carbon dioxide remain stable, but at pressures above 93 gigapascals (0.93 million atmospheres)methane begins to decompose forming heavy hydrocarbons — ethane, butane, and polyethylene. At a lower pressure — approximately 4 GPa — methane and molecular hydrogen interact, forming co-crystals (where two molecules together create one crystal structure), and at 6 GPa, hydrates — CO-crystals made of methane and water — are formed. To put this into A context, the pressure at the bottom of the Mariana Trench(the deepest part of the world’s oceans) is 108.6 megapascals, which is one thousand times lower.
Oganov and Saleh took on the task of finding all stable compounds in the range up to 400 GPa (around 4 million atmospheres) and discovered several new substances. These included a clathrate (inclusion compound, a type of co-crystal) of molecular hydrogen and methane 2CH4:3H2, which is stable in the pressure range 10-215 GPa.
The scientists also found that at a pressure above 0.95 GPa (approximately 10,000 atmospheres), carbonic acid (H2CO3) becomes thermodynamically stable. This is very unusual for a substance that is highly unstable under normal conditions — strong acids are needed for its synthesis and it can only exist in a vacuum at very low temperatures, the authors write.
“It is possible that the cores of Neptune and Uranus may contain significant amounts of a polymer of carbonic acid and orthocarbonic acid,” says Oganov.
- Gabriele Saleh, Artem R. Oganov. Novel Stable Compounds in the C-H-O Ternary System at High Pressure. Scientific Reports, 2016; 6: 32486 DOI:10.1038/srep32486
Source: Moscow Institute of Physics and Technology. “Scientists discover what extraordinary compounds may be hidden inside Uranus and Neptune.” ScienceDaily. ScienceDaily, 6 September 2016. <www.sciencedaily.com/releases/2016/09/160906103159.htm>.
September 5, 2016
University of California – San Diego
Biochemists have uncovered patterns in the outer protein coat of group A Streptococcus that could finally lead to a vaccine against this highly infectious bacteria — responsible for more than 500,000 deaths a year, including toxic shock syndrome and necrotizing fasciitis or ‘flesh-eating disease.’
Biochemists at the University of California San Diego have uncovered patterns in the outer protein coat of group A Streptococcus that could finally lead to a vaccine against this highly infectious bacteria — responsible for more than 500,000 deaths a year, including toxic shock syndrome and necrotizing fasciitis or “flesh-eating disease.”
In a paper published in this week’s issue of Nature Microbiology, the researchers report that they had uncovered “hidden sequence patterns in the major surface protein and virulence factor” of group A Strep, called the M protein, that limit the body’s immune response against these bacteria.
“At present, there is no vaccine against group A Strep, and our discovery of hidden sequence patterns has offered up a novel way to devise such a vaccine,” said Partho Ghosh, chair of UC San Diego’s Department of Chemistry and Biochemistry, who headed the team of researchers.
Ghosh said that one of the biggest obstacles to the development of a vaccine against these bacteria is the “hyper-variability” of the M protein. Group A Streptococcus bacteria have a multitude of different strains, each of which displays a different protein on its surface. Because our immune systems must recognize these different proteins before launching an immune response with antibodies specific to the outer protein coat, the hyper-variability of the M proteins make it difficult for our immune systems to attach antibodies specific to each these proteins from different strains.
“When we become infected with a particular strain of group A Strep, we generally mount an immune response against the particular M protein displayed by that strain,” explains Ghosh. “But this immunity works only against the infecting strain. We remain vulnerable to infection by other group A Strep strains that display other types of M proteins on their surfaces. This is because the antibody response against the M protein is almost always specific to the sequence of that M protein, and M proteins of different types appear to be unrelated in sequence to one another.”
The key to resolving the problem was the recognition that a human protein called C4BP had been discovered by another group of researchers to be recruited to the surface of Group A Strep by many different protein types.
“This was a puzzle, because the antibody response is specific and limited to a single M protein type, while C4BP binds a broad variety of M protein types, perhaps up to 90 percent of them,” said Ghosh. “Group A Strep brings C4BP to its surface to dampen the immune response. We wanted to combat this recruitment by blocking the interaction between M proteins and C4BP, but equally as importantly, we wanted to take advantage of the broad recruitment of C4BP by M proteins that would pave a path to the development of a vaccine.”
To determine if this was possible, a graduate student in Ghosh’s lab, Cosmo Buffalo, collaborated with another graduate student, Sophia Hirakis, in the laboratory of Rommie Amaro, a professor of chemistry and biochemistry who uses computers to study protein structures, to first study the complex interactions between M protein and C4BP.
“This allowed us to understand some detailed features of the interaction,” said Ghosh. The research team, which also included an undergraduate researcher, Adrian Bahn-Suh, collaborated extensively with Victor Nizet, an expert in infectious diseases who is a professor at UC San Diego’s School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences.
In their experimental and computational study, the biochemists painstakingly detailed four crystal structures of four different M protein types, each bound to human C4BP.
“These structures revealed that even though the different M protein types appeared to be unrelated in sequence, there were common sequence patterns hidden within the differences that linked all these M proteins together,” said Ghosh. “These common patterns are what is used to recruit C4BP to the surface of group A Strep by the different M protein types.”
“The idea now is to have antibodies do the same thing as C4BP — that is, recognize many different M protein types,” he added. “That way, the antibody response will not be limited to one M protein type and one strain of group A Strep, but will extend to most, if not all, M protein types and most, if not all strains, of group A Strep.”
The UC San Diego chemists, in collaboration with Nizet, are now working on developing a vaccine that, they hope, will be protective against most, if not all, strains of group A Strep.
- Cosmo Z. Buffalo, Adrian J. Bahn-Suh, Sophia P. Hirakis, Tapan Biswas, Rommie E. Amaro, Victor Nizet, Partho Ghosh. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nature Microbiology, 2016; 1: 16155 DOI: 10.1038/nmicrobiol.2016.155
Source: University of California – San Diego. “Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria.” ScienceDaily. ScienceDaily, 5 September 2016. <www.sciencedaily.com/releases/2016/09/160905114504.htm>.
September 1, 2016
University of Notre Dame
New research suggests that Africa has gradually become wetter over the past 1.3 million years — instead of drier as was thought previously.
From the depths of Lake Malawi, Melissa Berke has helped uncover evidence that offers new insights into a long-held theory about Africa’s climate history.
The research from Berke, assistant professor in the Department of Civil and Environmental Engineering and Earth Sciences at the University of Notre Dame and Environmental Change Initiative affiliate, suggests that Africa has gradually become wetter over the past 1.3 million years — instead of drier as was thought previously. The findings shine new light on the “savanna hypothesis,” which held that humans in Africa as a whole migrated to grasslands due to a changing climate.
The sediment samples that Berke studied came from Lake Malawi in southeast Africa, whereas data used for the savanna hypothesis came from the north. Her research suggests that climate conditions across Africa may have been more variable than once thought.
Importantly, Berke’s samples also reflect the longest continuous record of temperature data ever collected on the African continent. Apart from their age, the materials she analyzed were of exceptional quality.
“Lake Malawi is one of the deepest lakes in Africa, and the sediment samples taken from it are finely laminated. You can readily see how it changes across intervals of time,” said Berke.
Berke’s research specialty is to look for biochemical markers — “chemical fossils” that help scientists measure changes in vegetation and climate over time. One of the most enduring markers she examines is a commonplace substance known as leaf wax.
“All terrestrial leaves have wax,” she said. “It’s what makes water bead on grass or an oak leaf. Long after stems and roots have faded away, leaf wax residue can be preserved for hundreds of millions of years. Each leaf has its own chemistry, so when it washes into a lake or ocean we use it to tell us about its environment.”
Earlier this year, Berke boarded a research vessel in the Indian Ocean with 29 international scientists to retrieve sediment cores off the coast of southern Africa. Her findings will build on the Lake Malawi research and examine sediments that date seven million years, the oldest such samples taken in this location.
Berke’s work takes a decidedly long view. As a geologist, she can speak of events that happened “only 23,000 years ago.” Yet she’s also quick to point out why this look back at Africa’s geologic past should matter now.
“When we look at today’s climate, at flooding in Louisiana or West Virginia, or fires in California, we need historical context to understand what’s happening,” she said. “We can’t just rely on modern climate data to understand the past. Those records only go back 150 years. The more data we have about what’s happened across millions of years of climate, the better our predictions of the future will be.”
- T. C. Johnson, J. P. Werne, E. T. Brown, A. Abbott, M. Berke, B. A. Steinman, J. Halbur, S. Contreras, S. Grosshuesch, A. Deino, C. A. Scholz, R. P. Lyons, S. Schouten, J. S. Sinninghe Damst�. A progressively wetter climate in southern East Africa over the past 1.3 million years. Nature, 2016; DOI:10.1038/nature19065
Source: University of Notre Dame. “Clues in ancient mud hold answers to climate change.” ScienceDaily. ScienceDaily, 1 September 2016. <www.sciencedaily.com/releases/2016/09/160901152444.htm>.
August 31, 2016
Cell lines are cultured cells that are commonly used in medical research. New results show that such cells are not always what they are assumed to be. Using genetic analyses, the researchers showed that a commonly used cell line that was established almost 50 years ago does not originate from the patient it is claimed to stem from.
Cell lines are cultured cells that are commonly used in medical research. New results from Uppsala University show that such cells are not always what they are assumed to be. Using genetic analyses, the researchers showed that a commonly used cell line which was established in Uppsala, Sweden, almost fifty years ago does not originate from the patient it is claimed to stem from. The findings are published in the journalScience Translational Medicine.
A cell line consists of cultured cells that often originate from a tumor. In contrast to other cultured cells, such tumor cells can divide indefinitely and a cell line can therefore be cultured for many years. It is also easy to study, simple to handle and results can be obtained with high reproducibility. Cell lines are therefore indispensable in medical research and a large number of cell lines exist that originate from many different tumor types.
Researchers studying the brain tumor type glioma often use a cell line called U87MG that was established at Uppsala University almost fifty years ago. It is presently publicly available from the American Type Culture Collection (ATCC), where researchers can order it to use it in their studies. Bengt Westermark is senior professor at the Department of Immunology, Genetics and Pathology, which is the present name for the department where U87MG was established. His research group has often used the original U87MG line and their experience led them to question the authenticity of the ATCC cell line.
Marie Allen, an expert in DNA fingerprinting, works at the same department. DNA fingerprinting is an important tool for determining genetic identity, for instance in crime scene investigations.
‘Marie and her colleagues helped us genetically compare the cell lines with each other. We found that the U87MG cell line from ATCC had a different DNA profile than the original cell line in Uppsala’, says Bengt Westermark.
When the cell line was established in the 1960s, material from the original tumor was saved as thin sections on microscope slides. Using a very sensitive DNA analysis technique that can also be employed when only very small amounts of DNA from old tissue are available, the researchers could compare the two current cell lines with the tumor from which the cell line was established.
‘The comparison showed that the Uppsala cell line was genetically identical with the original tumor whereas the U87MG cell line from ATCC had a different, unknown origin. We don’t know at which point during the fifty years of culturing the mix-up occurred but we have been able to show that the ATCC U87MG line is most likely from a human glioma tumor’, says Bengt Westermark.
Many scientific journals require researchers who report results based on cell line experiments to use DNA profiling to establish the identity of the used cells. The new findings show that proper identification of a cell line also requires that the DNA profile matches the tissue of origin. This is essential if one wants to claim that the cells, and thereby the research results, are true representatives of the original tumor.
- Marie Allen et al. Origin of the U87MG glioma cell line: Good news and bad news. Science Translational Medicine, August 2016 DOI:10.1126/scitranslmed.aaf6853
Source: Uppsala University. “Forensic DNA analysis checks the origin of cultured cells.” ScienceDaily. ScienceDaily, 31 August 2016. <www.sciencedaily.com/releases/2016/08/160831142856.htm>.
Changes linked to unstable genomes, cancer and other defects
August 30, 2016
Although genetic variants are scattered throughout the human genome, scientists have largely ignored the stretches of repetitive genetic code known as ‘junk’ DNA in their search for differences that influence human health and disease. Now, researchers have discovered that variation in these overlooked regions can affect the stability of the genome and the proper function of the chromosomes that package our genetic material, leading to an increased risk of birth defects, infertility, and cancer.
All humans are 99.9 percent identical, genetically speaking. But that tiny 0.1 percent variation has big consequences, influencing the color of your eyes, the span of your hips, your risk of getting sick and in some ways even your earning potential.
Although variants are scattered throughout the genome, scientists have largely ignored the stretches of repetitive genetic code once dismissively known as “junk” DNA in their search for differences that influence human health and disease.
A new study shows that variation in these overlooked repetitive regions may also affect human health. These regions can affect the stability of the genome and the proper function of the chromosomes that package genetic material, leading to an increased risk of cancer, birth defects and infertility. The results appear online in the journal Genome Research.
“Variation is not only important for how genes and proteins function, but it can also occur in the noncoding, repetitive portions of the genome,” said Beth A. Sullivan, Ph.D., senior author of the study and associate professor of molecular biology and microbiology at Duke University School of Medicine.
“What we found in this study is probably the tip of the iceberg,” Sullivan said. “There could be all sorts of functional consequences to having variation within the complex, repetitive portion of the genome that we don’t know about yet.”
Even though the sequence of the human genome was declared complete more than a decade ago, it retains several glaring gaps, especially in the repetitive sequences around centromeres, the twisty ties that hold a pair of chromosomes together in a floppy X shape and coordinate their movement during cell division.
These centromere sequences — called satellite DNA — are made up of blocks of exactly 171 A’s, C’s, T’s and G’s, repeated over and over for millions of base-pairs. Researchers once believed that each chromosome contained a single stretch of this satellite DNA, which determined where its centromere would reside. But a few years ago, Sullivan’s lab discovered that many human chromosomes possessed more than one of these regions, and depending on the individual, the centromere could form at either site.
In this study, Sullivan wanted to see how the chromosome decides where to put its centromere, and whether one site builds a “better” centromere than the other. Of the 23 pairs of human chromosomes, she focused on chromosome 17, which is structurally rearranged or mutated in many different cancers and birth defects.
First, Sullivan and her team combined molecular and visual assays, stretching the chromosome out into long chromatin fibers that were painted with fluorescent probes to map the variation in genomic sequence at the two different regions of satellite DNA. Then they looked at each satellite region for the presence of proteins necessary to construct a fully functioning centromere.
The researchers found that genomic variation at one of these satellite DNA regions — either in the size or sequence of its repeated 171 base pair units — ultimately determines whether the centromere is built at the primary site or the alternate site.
When they interrogated samples from a human DNA bank, they found that about 70 percent of humans have little genomic variation at the primary site, while 30 percent have differing degrees of variation. Most of the time, the centromeres aren’t built at the primary site if it contains variation and instead are assembled at the “backup” site nearby. But when this happens, the result may be a dysfunctional centromere that is architecturally unsound and an unstable chromosome that may be present in too many or too few copies.
“It is immensely fascinating to think that there are so many people walking around who are essentially centromere mosaics,” said Sullivan. “One of their centromeres, on one of their chromosomes, has the potential to be dangerously unstable, and it could affect their ability to reproduce, or predispose them to cancer.”
In the future, Sullivan plans to investigate just how big of a risk the variant satellite regions pose for those who carry them, and possibly develop a way to use these sequences as biomarkers for the chromosomal defects that can lead to disease.
- Megan E Aldrup-MacDonald, Molly E Kuo, Lori L Sullivan, Kimberline Chew, Beth A Sullivan. Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. Genome Research, 2016; gr.206706.116 DOI: 10.1101/gr.206706.116
Source: Duke University. “Variation in ‘junk’ DNA leads to trouble: Changes linked to unstable genomes, cancer and other defects.” ScienceDaily. ScienceDaily, 30 August 2016. <www.sciencedaily.com/releases/2016/08/160830121720.htm>.
August 29, 2016
Queensland University of Technology
An unnatural balance of nutrients threatens biodiversity in a survival of the fittest scenario, according to new research. A global network of researchers who have tested the impact increased nutrient levels is having on grasslands across six continents.
An unnatural balance of nutrients threatens biodiversity in a survival of the fittest scenario, according to the results of a world-first global experiment published in the journal Nature. Professor Jennifer Firn, from QUT’s Science and Engineering Faculty, is part of a global network of researchers who have tested the impact increased nutrient levels is having on grasslands across six continents.
The article is titled “Addition of multiple limiting resources reduces grassland diversity” and was led by Professor Stan Harpole from UFZ and iDIV, Germany.
“As part of the Nutrient Network, researchers tested the Charles Darwin ‘entangled bank’ observation which is used to explain how species can coexist even if they require the same limiting resources.
“This theory explains the mechanism of how a number of species should be competing for resources when they are actually coexisting because of the subtle differences in their resource needs.
“But what we found was that if you change the limiting resources and add an abundance of resources such as nutrients like phosphorus, nitrogen and potassium, it will lead to a favouring of some species over others because competition is then shifted above ground for light.
“This will in turn evoke competition between species, leading to one species dominating the land area.”
The experiment was conducted across 45 grassland sites spanning the multi-continent Nutrient Network.
Professor Firn said the human influence on the nutrient cycle through greater globalisation, was having a damaging effect on ecosystem biodiversity.
“The loss of diversity was not driven by the addition of any single added resource for example nitrogen or potassium, we found greatest diversity loss occurred with the addition of a combination of two or more resources,” she said.
“Simply put, the more nutrients, the less biodiversity.”
She said many of the ecosystem functions that humans need to survive were provided by richly diverse ecosystems, such as oxygen production, water filtration, nutrient cycling, pollination, and carbon sequestration.
“The irreplaceable loss of native biodiversity is accelerating at an alarming rate globally,” she said.
“What this research does is provide tangible evidence that global change is driving environmental conditions beyond our planetary boundaries.”
The Nutrient Network is the only collaborations of its kinds in which individual researchers have set up the same experiments at sites around the world. It is coordinated through the US-based National Science Foundation’s funding to biologists Prof. Elizabeth Borer and Prof. Eric Seabloom of the University of Minnesota.
- W. Stanley Harpole, Lauren L. Sullivan, Eric M. Lind, Jennifer Firn, Peter B. Adler, Elizabeth T. Borer, Jonathan Chase, Philip A. Fay, Yann Hautier, Helmut Hillebrand, Andrew S. MacDougall, Eric W. Seabloom, Ryan Williams, Jonathan D. Bakker, Marc W. Cadotte, Enrique J. Chaneton, Chengjin Chu, Elsa E. Cleland, Carla D’Antonio, Kendi F. Davies, Daniel S. Gruner, Nicole Hagenah, Kevin Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Rebecca L. McCulley, Joslin L. Moore, John W. Morgan, Suzanne M. Prober, Anita C. Risch, Martin Schuetz, Carly J. Stevens, Peter D. Wragg. Addition of multiple limiting resources reduces grassland diversity. Nature, 2016; DOI: 10.1038/nature19324
Source: Queensland University of Technology. “An imbalance in nutrients threatens plant biodiversity.” ScienceDaily. ScienceDaily, 29 August 2016. <www.sciencedaily.com/releases/2016/08/160829105742.htm>.