Student psychologists help the depressed

Liisa Luuk and Lisa Backlund are in the last term of their Psychology programme. During the spring they will be doing a graduation project in which they will evaluate the effects of cognitive behavioural therapy on depression, where the treatment is a combination of online treatment and actual face-to-face meetings. Their study is a part of a larger European research project in which the results from eight European countries are brought together.

Liisa Luuk och Lisa Backlund There is good support in research for both traditional face-to-face CBT and for treatment delivered online, Ms Backlund explains. What is new, and has not been researched as much, is that in this study there are four face-to-face meetings with the therapist in addition to the online treatment. Many patients request meeting their therapist, and it can result in more people completing their therapy.

“We will be taking part in the entire project,” Ms Luuk says. “We have received general guidelines from the other EU countries taking part, but we have been able to design the online treatment and the form of the treatment meetings. And we are also part of the recruitment process, conducting interviews with the participants prior to treatment. Then we follow up the results afterward, and we will also take part as therapists.”

Meeting and treating patients is not new for them.

“We see patients for three terms during our course at the university clinic ,” Ms Backlund explains. “During that time we are given basic psychotherapy training. And last term we went out for twelve weeks on professional placement, working with patients.”

In Sweden the studies will be carried out in Linköping and Stockholm. There will be places for 150 people who feel depressed to receive treatment and take part in the study, which is free. The criteria for taking part include being over 18 and having access to a telephone and a smart-phone. The treatment itself will start in February and run over ten weeks. Those interested in taking part may indicate their interest now.

“It’s important for us to have a large number of participants to make the results as reliable as possible and so that they can be compared with the various other EU countries,” Ms Luuk says. “It’s great being part of a real research project that is so big, it’s wonderful. Gaining experience of seeing how the research is done when these big names in the field are the ones doing it.”

“If we were to work as psychologists in primary care in the future, it is very possible that we would be the ones actually putting this treatment into practice,” Ms Luuk says.

Ms Backlund agrees with her.

“Yes, there's a good chance that treatment will go in this direction – more online treatment – so it’s an excellent experience for us.”

The treatment includes four face-to-face meetings with the therapist; in between, the treatment is internet-based. The participants will read some texts that talk about depression and how it is dealt with in CBT. Some of it deals with changing what you do – how to do things differently in order to deal with your depression – and part of it deals with how to manage your thinking. These are two key parts of CBT. Then there are small tasks. They might be answering questions or doing some exercises. Then you apply what you’ve read to your daily life.

Later, the treatment will be evaluated.

“We will compare it with a control group,” Ms Backlund says. “We have various questionnaires that the participants will fill in before and after the study, where they will assess how they feel. We will compare the severity of the depression symptoms before and after the treatment. We will also have a control group, that does not take part, to compare with. They will receive online treatment after the study has been completed. So everyone who takes part in the study will receive treatment.”

Professor Gerhard Andersson of the Department of Behavioural Sciences and Learning at Linköping University is behind the project. Naira Topooco is a PhD student in Clinical Psychology, and a part of Professor Andersson’s research team. She is a project manager in the research study and Ms Luuk’s and Ms Backlund’s immediate supervisor. DAY treatment was developed by researchers and psychologists from Linköping University and is based on Cognitive Behavioural Therapy (CBT).

Source: The DAY-studie (article in Swedish)

SETTLING FOR ‘MR. RIGHT NOW’ BETTER THAN WAITING FOR ‘MR. RIGHT’

Evolutionary researchers have determined that settling for “Mr. Okay” is a better evolutionary strategy than waiting for “Mr. Perfect.” When studying the evolution of risk aversion researchers found that it is in our nature – traced back to the earliest humans – to take the safe bet when stakes are high, such as whether or not we will mate. Photo by D.L. Turner

Evolutionary researchers have determined that settling for “Mr. Okay” is a better evolutionary strategy than waiting for “Mr. Perfect.”

When studying the evolution of risk aversion, Michigan State University researchers found that it is in our nature – traced back to the earliest humans – to take the safe bet when stakes are high, such as whether or not we will mate.

“Primitive humans were likely forced to bet on whether or not they could find a better mate,” said Chris Adami, MSU professor of microbiology and molecular genetics and co-author of the paper.

“They could either choose to mate with the first, potentially inferior, companion and risk inferior offspring, or they could wait for Mr. or Ms. Perfect to come around,” he said. “If they chose to wait, they risk never mating.”

Adami and his co-author Arend Hintze, MSU research associate, used a computational model to trace risk-taking behaviors through thousands of generations of evolution with digital organisms. These organisms were programmed to make bets in high-payoff gambles, which reflect the life-altering decisions that natural organisms must make, as for example choosing a mate.

“An individual might hold out to find the perfect mate but run the risk of coming up empty and leaving no progeny,” Adami said. “Settling early for the sure bet gives you an evolutionary advantage, if living in a small group.”

Adami and his team tested many variables that influence risk-taking behavior and concluded that certain conditions influence our decision-making process. The decision must be a rare, once-in-a-lifetime event and also have a high payoff for the individual’s future – such as the odds of producing offspring.

How risk averse we are correlates to the size of the group in which we were raised. If reared in a small group – fewer than 150 people – we tend to be much more risk averse than those who were part of a larger community.

It turns out that primitive humans lived in smaller groups, about 150 individuals. Because resources tend to be more scarce in smaller communities, this environment helps promote risk aversion.

“We found that it is really the group size, not the total population size, which matters in the evolution of risk aversion,” Hintze said.

However, not everyone develops the same level of aversion to risk. The study also found that evolution doesn’t prefer one single, optimal way of dealing with risk, but instead allows for a range of less, and sometimes more-risky, behaviors to evolve.

“We do not all evolve to be the same,” Adami said. “Evolution creates a diversity in our acceptance of risk, so you see some people who are more likely to take bigger risks than others. We see the same phenomenon in our simulations.”

The research was part of an interdisciplinary collaboration with Ralph Hertwig of the Max Planck Institute for Human Development in Berlin.

Also contributing to the study was Randal Olson, graduate student, MSU Department of Computer Science and Engineering and BEACON Center for the Study of Evolution in Action.

Source: Michigan State University

Feelings of awe and joy can bolster your mental and physical health.

              POSITIVE EMOTIONS CAN STRENGTHEN YOUR IMMUNE SYSTEM
                                         Image Credit: Mens Health

The wonders of the world can be just as good for your health as they are for your enjoyment, suggests a UC Berkley study.

Researchers have linked positive emotions—awe, contentment, spirituality—with lower levels of pro-inflammatory cytokines, proteins that signal your immune system to work harder and bolster good health.

In two separate experiments, more than 200 young adults were asked to log the extent to which they experienced amusement, awe, compassion, joy, love, and pride on a given day. Samples of gum and cheek tissue taken that same day showed that those who experienced more of these positive emotions had the lowest levels of the cytokine Interleukin 6, a marker of inflammation that can cause autoimmune disease and depression.

“That awe, wonder and beauty promote healthier levels of cytokines suggests that the things we do to experience these emotions—a walk in nature, losing oneself in music, beholding art—has a direct influence upon health and life expectancy,” says UC Berkeley psychologist Dacher Keltner, a co-author of the study.

An added emphasis on spirituality and mindfulness may just be enough to get you through this winter happy and healthy. 

Source: Mensfitness

The mystery of the Alpine long-eared bat

                              An Alpine long-eared bat fully airborne , UPV/EHU

The alpine long-eared bat was discovered in the Austrian Alps in 2003; hence its name. Yet later on specimens were found in other milder environments as well, in Croatia, Greece and Crete, and what is more, often close to sea level. Members of the Behavioural Ecology and Evolution Group of the UPV/EHU’s Faculty of Science and Technology studied the distribution and way of life of this species, and found that it forages and reproduces in mostly alpine environments (above the treeline), a unique case among bats. As the biologist Antton Alberdi explained, “the common name of the species not only refers to the place where it came from but describes its nature, too.” Indeed, the researcher concluded that the resources used by the Alpine long-eared bat are the same as the ones used by alpine birds and rodents: in the Pyrenees, for example, it lives at an altitude of between 1,500 and 2,500 metres and hides under rocks, in crevices and on ledges.

Nevertheless, how is it possible that an animal that only lives above 1,500 metres in the Pyrenees can be found at sea level in Croatia? Alberdi was involved in seeking the answer to this question in his PhD thesis. Alberdi identified and quantified the environmental conditions that determine the distribution of the Alpine long-eared bat (Plecotus macrobullaris) to try to understand why this species is restricted to mountain environments and why it can appear at sea level at the same time. After that, in order to see whether the results obtained could be extrapolated to other species, he compared the distributions of 503 vertebrates with those of the bats, and found five vertebrates that have similar geographical distributions to that of the bat: the white-winged snowfinch, the Alpine chough or yellow-billed chough, the wallcreeper, the Alpine accentor and the European snow vole. The distribution of all of them is very broad, from Western Europe all the way to Asia, but they are restricted to the main mountainous areas. He studied their ecological features to see whether they were all following a common biogeographical pattern in order to work out whether they were following a common distribution model.

They need rugged places

The basic ecological features of these vertebrates and those of the Alpine long-eared bat are very similar: they all use rocks (crevices, ledges or crushed stones) as places to hide, and they need open spaces to forage. They have also seen that they can be found in cold mountain environments (in the Alps) as well as in hot ones (in the mountains of Iran and Syria, etc.) and that suggests that the reasons that restrict these species to mountainous areas are not climatic ones: they are linked to topography. In other words, they are not in mountainous areas because they cannot withstand a hot environment, but because high mountain habitats offer them the characteristics they need. In some cases, in Croatia, for example, these conditions can be found at lower altitudes, and that explains why the species can be found at sea level. Furthermore, as they have the capacity to withstand the cold, they can use the alpine habitats that other species cannot exploit and thus avoid competition. In any case, “it cannot be said that the climate does not exert any influence,” said the researcher. “In fact, the climate determines the altitude ranges that each species can live in.”

According to the researcher, to preserve the species it is essential to know everything about them: how they live, why they are present in the places where they are present, etc. In the case of these species, therefore, climate change will not exert such an effect in the future; “more attention will need to be devoted to other factors: human exploitation, pasture use, etc.,” he explained. The researcher believes that the rise in treelines taking place as a result of the decline in the pressure of livestock will affect these species most. Indeed, as the treelines recede, the surface area suited to the habitats of these species will be reduced, because other species will also recede and that way the pressure will increase. They are now working to quantify that effect.

Source: Elhuyar Fundazioa

Climate change accelerates maturing of grape in wine production

                             Johann Martínez-Lüscher , Nafarroako Unibertsitatea

The increase in temperatures and of CO2 levels – the consequences of climate change – accelerates the maturing of grapes in wine production, affecting colour and possibly aromas”. This was the conclusion of the PhD thesis defended by Johann Martínez-Lüscher, undertaken jointly by the University of Navarra and the University of Bordeaux.

The biologist explained that if the forecasts by the Intergovernmental Panel on Climate Change of a level of 700ppm of carbon dioxide and a temperature increase of 4ºC are proved correct, “the accumulation of sugars could be so rapid that the rest of these processes that depend on this will not be capable of keeping up. This will mean that, on comparing grapes with the same concentration of sugars or degree of alcohol, the crops under climate change conditions will have poorer colouration and this will be noticed in the wine”.

In fact, “it is increasingly more frequent to find wines with a higher alcoholic degree due to the over maturing of the grape”. Nonetheless, in the framework of climate change, the consequences can vary. “For example, the changes in levels of ultraviolet radiation or the decrease in rainfall may have antagonistic effects to those caused by an increase in temperature or CO2 levels. Thus, there are many unknowns about what the future holds”, he added.

Wine in a new scenario

In this way wine production will have to find solutions in order to confront environmental challenges. “The use of slower maturing ‘clones’ (sub-varieties) could be one of the possible strategies. It would also be very tempting to substitute the varieties planted in each location by others better adapted to warmer climates, but this would to a great extent mean giving up the typical characteristics of each variety of our wines – something unthinkable to date”.

Nevertheless, as this expert pointed out, climate change can provide new opportunities: for example, the production of a type of wine in cooler climes where it was not possible before. “This is the case of the incipient wine industry in the United Kingdom where I intend to continue working”, stated the researcher.

Mr. Martínez-Lüscher’s research has been financed by the University of Navarra, the Navarre-Aquitane Cross-Border Cooperation Programme, the Spanish Ministry of Science and Innovation, and the 7th European Union Framework Programme.

Source: Elhuyar Fundazioa

The Power of the Past

If you grow up in the working class, neither love nor money can trump your blue-collar roots, a Duke sociologist has found.

Her study of couples from different social classes suggests that those who “marry up” still make life decisions based on their upbringing.

                             Cover of Streib book by Eric Ferreri, Duke News & Communications
                          Sociologist Jessi Streib’s book “The Past” is about class structure in marriages.

“Your social class never goes away,” says Jessi Streib, an assistant professor of sociology whose findings are revealed in her new book: The Power of the Past: Understanding Cross-Class Marriages. “It stays with you in terms of how you live your life. The class you’re born into sticks with you and shapes you, even when you marry into more money and a far more financially secure life.”

Streib’s findings derive from interviews she conducted with white, heterosexual Midwestern couples. She interviewed 32 couples in which one spouse came from a working class background, the other from the middle class. For comparison, she also interviewed 10 couples in which both spouses grew up in the middle class.

Streib defines working class as people raised by parents with high school educations; the middle class subjects were raised by college-educated parents.

Her findings run contrary to the notion held by many scholars that strivers can outrun a difficult childhood by getting a college degree and good-paying middle-class job.

While the findings suggest that a middle class upbringing isn’t required to excel in the American workplace, those upwardly mobile people from working class roots may still miss out on opportunities if they can’t or don’t subscribe to the unspoken norms of middle class culture, Streib notes.

Streib found that couples from different classes held onto their own, firmly-rooted beliefs regarding money and parenting, often negotiating fervently with each other over the proper amount of career planning and nurturing of children. Should children be left to grow and discover on their own, or should goals and schedules be set for them?

“Those are the sorts of tiny battles cross-class couples have all the time,” Streib said. “These are not insurmountable obstacles, but they are certainly common and consistent.”

Source: Duke Univesity

UA to Serve Up Fresh Approach to Health

The commitment of the Department of Nutritional Sciences to promoting and adapting Mediterranean diet principles will continue through all three areas of the University’s land grant mission: academic programs, research and Cooperative Extension outreach programs. Credit: UA

The Mediterranean diet has seen growing global popularity as researchers find that the dietary pattern can help prevent or reduce obesity, heart disease, type 2 diabetes and certain types of cancer.

Responsive to that popularity, the University of Arizona Department of Nutritional Sciences is hosting a series of events meant to explore and share current research related to the dietary pattern, which focuses on fresh fruits and vegetables, whole grains, beans and nuts, along with lesser amounts of lean fish, meats, dairy, olive oil and red wine.

"We want to emphasize how this pattern of eating has been demonstrated to contribute to disease prevention," said Donato Romagnolo, a professor in the Arizona Cancer Center and the nutritional sciences department, which is housed in the UA College of Agriculture and Life Sciences. 

National Geographic Blue Zones speaker Rudy Maxa, a Washington Post reporter and columnist, and five Tucson-area celebrity chefs will kick off the Jan. 28 opening-night reception, "A Food, Wine and Healthy Living Event," at the Tucson Museum of Art.

The 6-8 p.m. event is open to the public and will feature food prepared by the chefs, award-winning wine provided by the Arizona Wine Growers Association and live flamenco and Spanish guitar.

Then the UA will will host the Jan. 29-30 "Health Benefits of the Mediterranean Diet – Bringing Science to the Plate (With an Arizona Twist!)" scientific conference at the Student Union Memorial Center.

Supported in part by a grant from the U.S. Department of Agriculture, the conference is geared toward public health and nutrition professionals, nurses, physicians, physical therapists and chiropractors, and it is offered for continuing professional credit. The event is also open to students and features a student showcase.

A full agenda and registration for the conference are available online.

Promoting the health benefits of the Mediterranean lifestyle is just one of numerous initiatives sponsored by the UA Department of Nutritional Sciences to advance optimal health and well-being for Arizonans and to focus on ways of preventing and treating chronic diseases. 

After the conference, a four-part, hands-on cooking series will be offered to the public during February and March at the UA Cooperative Extension's Garden Kitchen, "The Many Faces of the Mediterranean Diet: Four Evenings," featuring the cuisines of Spain, France, Morocco and Italy. Information is available online. 

Also, the Mediterranean Diet and Health course will be offered for academic credit during summer 2015 (one week in Tucson and three weeks in Verona, Italy) for students through the UA Global Initiatives Study Abroad Program.

Much of the interest in the Mediterranean diet stems from evidence that it can reduce the risk of death associated with heart disease and cancer. Other research indicates that the diet can reduce the incidence of Parkinson's and Alzheimer's diseases.

Romagnolo, also the program director of the Mediterranean Diet and Health Study Abroad Program, said the benefits are especially important given pervasive health concerns across the nation. He noted that about 60 percent of people in the U.S. are overweight and 30 percent are obese.

"The latter is a risk factor for diabetes, cancer and metabolic syndrome," Romagnolo said.
During the conference, more than 20 presenters from the UA College of Agriculture and Life Sciences, the UA College of Medicine, national and international universities, institutes and organizations will talk. 

Presenters will cover four general areas: the Mediterranean diet and regional trends; obesity, diabetes and healthy aging; cancer prevention and control; and methods for translating science to the plate.

Live demonstrations by Arizona growers, vendors and educators will provide attendees with tasting opportunities, meal preparation ideas and information on where to find local products that help make healthful eating easy in the Southwest.

Also, prominent diet researchers from Spain, France and Greece will present current research on the health benefits of the traditional Mediterranean diet and offer ways to adapt it using local agricultural ingredients and cooking techniques. Speakers include:

Lluis Serra-Majem of the University of Las Palmas de Gran Canaria, Spain, who will present the keynote address on "The Mediterranean Diet as an Intangible and Sustainable Food Culture."

Mariette Gerber of the INSERM-Institut du Cancer de Montpellier, France, who will discuss "Implementing the Mediterranean Diet: The French Perspective." 

Antonia Trichopoulou of the University of Athens, Greece, who will speak on "Mediterranean Diet and Longevity."

"The conference is an opportunity to present ideas and concepts that may be adopted by the food industry, nutritionists, researchers and policymakers to help reduce the burden of these chronic diseases," Romagnolo said. "We want to show people how they can do it on their own and apply the basic tenets of the diet here in Arizona."

Source: University of Arizona

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

Identifying gene-enhancers: New technique

Diane Dickel is the lead author of Nature Methods paper describing a new technique for identifying gene enhancers in the genomes of humans and other mammals. Credit: Roy Kaltschmidt

An international team led by researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) has developed a new technique for identifying gene enhancers -- sequences of DNA that act to amplify the expression of a specific gene -- in the genomes of humans and other mammals. Called SIF-seq, for site-specific integration fluorescence-activated cell sorting followed by sequencing, this new technique complements existing genomic tools, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing), and offers some additional benefits.

"While ChIP-seq is very powerful in that it can query an entire genome for characteristics associated with enhancer activity in a single experiment, it can fail to identify some enhancers and identify some sites as being enhancers when they really aren't," says Diane Dickel, a geneticist with Berkeley Lab's Genomics Division and member of the SIF-seq development team. "SIF-seq is currently capable of testing only hundreds to a few thousand sites for enhancer activity in a single experiment, but can determine enhancer activity more accurately than ChIP-seq and is therefore a very good validation assay for assessing ChIP-seq results."

Dickel is the lead author of a paper in Nature Methods describing this new technique. The paper is titled "Function-based identification of mammalian enhancers using site-specific integration." The corresponding authors are Axel Visel and Len Pennacchio, also geneticists with Berkeley Lab's Genomics Division.

With the increasing awareness of the important role that gene enhancers play in normal cell development as well as in disease, there is strong scientific interest in identifying and characterizing these enhancers. This is a challenging task because an enhancer does not have to be located directly adjacent to the gene whose expression it regulates, but can instead be located hundreds of thousands of DNA base pairs away. The challenge is made even more difficult because the activity of many enhancers is restricted to specific tissues or cell types.

"For example, brain enhancers will not typically work in heart cells, which means that you must test your enhancer sequence in the correct cell type," Dickel says.

Currently, enhancers can be identified through chroma­tin-based assays, such as ChIP-seq, which predict enhancer elements indirectly based on the enhancer's association with specific epigenomic marks, such as transcription factors or molecular tags on DNA-associated histone proteins. Visel, Pennacchio, Dickel and their colleagues developed SIF-seq in response to the need for a higher-throughput functional enhancer assay that can be used in a wide variety of cell types and devel­opmental contexts.

"We've shown that SIF-seq can be used to identify enhancers active in cardiomyocytes, neural progenitor cells, and embryonic stem cells, and we think that it has the potential to be expanded for use in a much wider variety of cell types," Dickel says. "This means that many more types of enhancers could potentially be tested in vitro in cell culture."

In SIF-seq, hundreds or thousands of DNA fragments to be tested for enhancer activity are coupled to a reporter gene and targeted into a single, reproducible site in embryonic cell genomes. Every embryonic cell will have exactly one potential enhancer-reporter. 

Fluorescence-activated sorting is then used to identify and retrieve from this mix only those cells that display strong reporter gene expression, which represent the cells with the most active enhancers.

"Unlike previous enhancer assays for mammals, SIF-seq includes the integration of putative enhancers into a single genomic locus," says Visel. "Therefore, the activity of enhancers is assessed in a reproducible chromosomal context rather than from a transiently expressed plasmid. Furthermore, by making use of embryonic stem cells and in vitro differentia­tion, SIF-seq can be used to assess enhancer activity in a wide variety of disease-relevant cell types."

Adds Pennacchio, "The range of biologically or disease-relevant enhancers that SIF-seq can be used to identify is limited only by currently available stem cell differentiation methods. Although we did not explicitly test the activity of species-specific enhancers, such as those derived from certain classes of repetitive elements, our results strongly suggest that SIF-seq can be used to identify enhancers from other mammalian genomes where desired cell types are difficult or impossible to obtain."

The ability of SIF-seq to use reporter assays in mouse embryonic stem cells to identify human embryonic stem cell enhancers that are not present in the mouse genome opens the door to intriguing research possibilities as Dickel explains.

"Human and chimpanzee genes differ very little, so one hypothesis in evolutionary genomics holds that humans and chimpanzees are so phenotypically different because of differences in the way they regulate gene expression. It is very difficult to carry out enhancer identification through ChIP-seq that would be useful in studying this hypothesis," she says. 

"However, because SIF-seq only requires DNA sequence from a mammal and can be used in a variety of cell types, it should be possible to compare the neuronal enhancers present in a large genomic region from human to the neuronal enhancers present in the orthologous chimpanzee region. This could potentially tell us interesting things about the genetic differences that differentiate human brain development from that of other primates."

Source DOE/Lawrence Berkeley National Laboratory

Gene silencing instructions acquired through 'molecular memory' tags on chromatin

Epigenetic inheritance is a two-step process, with a heritable molecular memory first forming to maintain a chromatin state required later for actual silencing of a genetic locus. Credit: Craig Pikaard and Todd Blevins

Scientists at Indiana University have unlocked one of the mysteries of modern genetics: how acquired traits can be passed between generations in a process called epigenetic inheritance. The new work finds that cells don't know to silence some genes based on information hardwired into their DNA sequences, but recognize heritable chemical marks that are added to the genes. These chemical tags serve as a form of molecular memory, allowing cells to recognize the genes and remember to silence them again in each new generation.

The discovery made by a 12-member all-Indiana University team of scientists led by IU biologist and biochemist Craig Pikaard provides important new insight into how plant cells know to silence a genetic locus -- that specific place on a chromosome where a gene is located -- in every successive generation.

Rather than rely on intrinsic, DNA sequence-based information, the cells instead must recall the need to silence specific loci by relying on chemical marks displayed on the complex of DNA and proteins called chromatin. Addition, or removal, of one-carbon (methyl) or two-carbon (acetyl) chemical tags are ways of modifying chromatin that can impart additional, epigenetic (literally, "above genetic") information to a locus beyond the genetic information encoded in the DNA.

The ability to perpetuate chromatin marks serves as a form of epigenetic memory that confers what Pikaard calls silent locus identity, a pre-established state that is needed for the cell to deliver to the loci the machinery that actually accomplishes silencing in a multi-step process known as RNA-directed DNA methylation (RdDM). RdDM involves short-interfering RNAs (siRNA), tiny RNA molecules that are 24 nucleotides long and that guide the addition of methyl groups to matching DNA strands, ultimately rendering the genes inactive.

"Importantly, this work shows that silent locus identity is required for, but separable from, actual gene silencing," Pikaard said. "We've found that epigenetic inheritance is a two-step process, with the heritable specification of silent locus identity occurring before actual silencing of the locus can occur."

Scientists are interested in epigenetic inheritance because it's a process by which heritable modifications occur in gene function without changes in the base sequence of an organism's DNA being required. Disease states such as cancer, which occur sporadically during an individual's lifetime, are increasingly recognized as having an epigenetic basis. Pikaard said the new work not only sheds important new light on the mechanisms responsible for epigenetic inheritance, a topic of broad interest in the fields of genetics and chromosome biology, but it also helps explain the basis for the recruitment of two plant-specific gene silencing enzymes -- the RNA polymerases Pol IV and Pol V -- first identified by Pikaard in 1999.

Specifically, the researchers tested and identified the relationship between histone deacetylase 6 (HDA6), an enzyme that removes acetyl groups from histones, and the CG DNA sequence maintenance methyltransferase, MET1, and discovered that their partnership in maintenance methylation can explain the perpetuation of epigenetic memory that accounts for silent locus identity.

"Collectively, our results show that silent locus identity is perpetuated from generation to generation through the actions of HDA6 and MET1," Pikaard said. "These activities are not sufficient to silence the loci but maintain a chromatin state that is required for Pol IV recruitment, siRNA biogenesis and RdDM, which is what ultimately silences the loci." When the team removed the RdDM pathway in Pol IV and Pol V mutant strains of the model plant Arabidopsis thaliana (rockcress), all gene silencing was lost, but silent locus identity remained. They then removed the HDA6 and MET1-dependent process that specifies silent locus identity and, importantly, the epigenetic memory required for silent locus identity was lost and unable to be regained.

Source:Indiana University

Mysteries of 'molecular machines' revealed: Phenix software uses X-ray diffraction spots to produce 3-D image

This is a membrane protein called cysZ, imaged in 3 dimensions with Phenix software using data that could not previously be analyzed. Credit: Los Alamos National Laboratory

Scientists are making it easier for pharmaceutical companies and researchers to see the detailed inner workings of molecular machines.

'Inside each cell in our bodies and inside every bacterium and virus are tiny but complex protein molecules that synthesize chemicals, replicate genetic material, turn each other on and off, and transport chemicals across cell membranes,' said Tom Terwilliger, a Los Alamos National Laboratory scientist.

'Understanding how all these machines work is the key to developing new therapeutics, for treating genetic disorders, and for developing new ways to make useful materials.'

To understand how a machine works you have to be able to see how it is put together and how all its parts fit together. This is where the Los Alamos scientists come in. These molecular machines are very small: a million of them placed side by side would take up less than an inch of space. Researchers can see them however, using x-rays, crystals and computers. Researchers produce billions of copies of a protein machine, dissolve them in water, and grow crystals of the protein, like growing sugar crystals except that the machines are larger than a sugar molecule.

Then they shine a beam of X-rays at a crystal and measure the brightness of each of the thousands of diffracted X-ray spots that are produced. Then researchers use the powerful Phenix software, developed by scientists at Los Alamos, Lawrence Berkeley National Laboratory, Duke and Cambridge universities, to analyze the diffraction spots and produce a three-dimensional picture of a single protein machine. This picture tells the researchers exactly how the protein machine is put together.

The 3-D Advance

Recently Los Alamos scientists worked with their colleagues at LBNL and Cambridge University to make it even easier to visualize a molecular machine. In a report in the journal Nature Methods this month, Los Alamos scientists and their team show that they can obtain three-dimensional pictures of molecular machines using X-ray diffraction spots that could not previously be analyzed.

Some molecular machines contain a few metal atoms or other atoms that diffract X-rays differently than the carbon, oxygen, nitrogen, and hydrogen atoms that make up most of the atoms in a protein. The Phenix software finds those metal atoms first, and then uses their locations to find all the other atoms. For most molecular machines, however, metal atoms have to be incorporated into the machine artificially to make this all work.

The major new development to which Los Alamos scientists have contributed was showing that powerful statistical methods could be applied to find metal atoms even if they do not scatter X-rays very differently than all the other atoms. Even metal atoms such as sulfur that are naturally part of almost all proteins can be found and used to generate a three-dimensional picture of a protein. Now that it will often be possible to see a three-dimensional picture of a protein without artificially incorporating metal atoms into them, many more molecular machines can be studied.

Cracking the Cascade

Molecular machines that have recently been seen in three-dimensional detail include a 'huge' molecular machine called Cascade that was reported in the journal Science this summer. The Cascade machine is present in bacteria and can recognize DNA that comes from viruses that infect the bacteria. The Cascade machine is made up of 11 proteins and an RNA molecule and looks like a seahorse, with the RNA molecule winding through the whole 'body' of the seahorse. If a foreign piece of DNA in the bacterial cell is complementary to part of the RNA molecule then another specialized machine can come by and chop up the foreign DNA, saving the bacterium from infection.

Los Alamos and Cambridge University scientists who were developing the Phenix software were part of the team that visualized this protein machine for the first time. The Phenix software has been used to determine the three-dimensional shapes of over 15,000 different protein machines and has been cited by over 5000 scientific publications.

Source: DOE/Los Alamos National Laboratory

Mechanics of cells' long-range communication modeled by researchers

As fibrosis progresses, "bridges" of extracellular matrix appear between cells. Credit: Image courtesy of University of Pennsylvania

Interdisciplinary research at the University of Pennsylvania is showing how cells interact over long distances within fibrous tissue, like that associated with many diseases of the liver, lungs and other organs.

By developing mathematical models of how the collagen matrix that connects cells in tissue stiffens, the researchers are providing insights into the pathology of fibrosis, cirrhosis of the liver and certain cancers.

Tissue stiffness has long been know to be clinically relevant in these diseases, but the underlying changes that alter the mechanics of tissues are poorly understood. Consisting of a complex network of fibers, tissues have proven difficult to simulate and model beyond local, neighbor-to-neighbor interactions.

Developing a better understanding of the large-scale mechanical changes that occur over longer distances, specifically the process by which the extracellular matrix is pulled into compact, highly-aligned "bridges," could eventually form the basis of treatments for related diseases.

Vivek Shenoy, professor in the Department of Materials Science and Engineering in Penn's School of Engineering and Applied Science, has led an interdisciplinary research team to tackle this problem, authoring a pair of papers that were published in Biophysical Journal.

One, "Remodeling of Fibrous Extracellular Matrices by Contractile Cells: Predictions from Discrete Fiber Network Simulations" involved developing simulations that extrapolated the overall remodeling of the extracellular matrix based on the behavior of neighboring pairs of cells. The other, "Long Range Force Transmission in Fibrous Matrices Enabled by Tension-Driven Alignment of Fibers," took a more mathematical approach, producing a coarse-grained model of this remodeling that could be more broadly applied to fibrotic tissue.

"We're trying to understand how force is transmitted in tissues," Shenoy said. "Cells are the ones that generate force, and it has to be transmitted through what surrounds the cell, the extracellular matrix, or ECM. But imagine trying to model the ECM by trying to keep track of each collagen fibril in your liver; there are tens of millions of those. So we're taking what we learn from simulating those networks to turn it into a model that captures the main features with only a few parameters.

"The key here is the mechanics," he said. "In particular, how does ECM, as a fibrous material, differ from solids, gels and other materials that are better studied."

Rebecca Wells, an associate professor in Penn's Perelman School of Medicine and a co-author on the latter paper, provided insight into the clinical relevance of the mechanics that characterize ECM-related disorders.

"Fibrosis occurs when you have an injury and the tissue responds by depositing ECM, forming scar tissue," Wells said. "In liver fibrosis, the liver can stiffen by up to an order of magnitude, so measuring stiffness is a common diagnostic test for the disease. Increased stiffness also occurs in cancer, where tumors are typically stiffer than the surrounding tissue."

Existing experimental evidence showed that mechanical forces were at play in the changes in both fibrosis and cancer and that these forces were important to their development and progression but could not explain the long-ranging changes cells were able to produce to change their environments. When put in tissue-simulating gels, cells can deform their immediate surroundings but are unable to pull on more distant cells. In real, ECM-linked tissue, however, cells' range of influence can be up to 20 times their own diameter.

"If you look at a normal tissue," Shenoy said, "you see the cells are more rounded, and the network of ECM fibers is more random. But as cancer progresses, you see more elliptical cells, more ECM, and you see that the ECM fibers are more aligned. The cells are the ones generating force, so they're contracting and pulling the fibers, stretching them out into bridges."

"That's also the pathology of cirrhosis," Wells said. "My group had been looking at the early mechanical changes associated with liver fibrosis, which progresses to cirrhosis, but then, by collaborating with Vivek, we started to wonder if these large scale changes in the architecture of the liver could have a mechanical basis and if something similar to what is seen in gels might be occurring in the liver. This is a new way of approaching the problem, which has largely been thought of as biochemical in origin. And there are other tissues where it is probably the same thing, the lung, for example."

The researchers found that the critical difference between the existing models and ECM's long-range behavior was rooted in its elastic properties. Materials with linear elasticity cannot transmit force over the distances observed, but the team's simulations showed that nonlinear elasticity could arise from the ECM's fibrous structure.

"In our model, every component is linearly elastic," Shenoy said, "but the collective behavior is nonlinear; it emerges because of the connectivity. When you deform the network, it's easy to bend the 'sticks' that represent collagen fibers but hard to stretch them. When you deform it to a small extent, it's all the bending of the fibers, but, as you deform further, it can't accommodate bending any more and moves over to stretching, forming the bridges we see in the tissue."

Such simulations can't predict which fibers will end up in which bridge, necessitating the coarser-grained model the researchers described in their second paper. By showing the point at which linear elasticity gives way to its nonlinear counterpart, the team produced a more complete picture of how the alignment of collagen bridges under tension transmit force between distant cells.

Further studies are needed to elucidate the feedback loops between ECM stiffening and cell contraction strength. The team is conducting physical experiments to confirm and refine their in silico findings.

"Right now," Wells said," we're hypothesizing that the mechanical interactions modeled by the Shenoy lab explain aspects of cancer and fibrosis, and we're developing the experimental systems to confirm it with real cells."

Source: University of Pennsylvania

The bloody truth: How blood donations can save animals' lives

Donated blood can be quickly regenerated by the animal’s organism. Credit: Felizitas Steindl / Vetmeduni Vienna

Blood transfusions are of importance not only in human medicine. Also animals do need blood donations. The University of Veterinary Medicine, Vienna operates a blood bank for dogs for more than a decade. But also cats can donate blood for acute emergencies. Horses need blood donations especially during operations that involve high blood loss. Sheep, goats and other ruminants require transfusions when plagued by serious infestations of parasites. Three vets from different areas of expertise explain how blood transfusions work with different animal species and how they can save lives.

Blood can hardly be created through artificial means, but it can be transferred within a species. Reasons for a blood transfusion among dogs and cats are usually serious accidents, large operations, certain types of cancer, cases of intoxication with rat poison, serious infectious diseases such as the tick-borne babesiosis, and blood illnesses including haemolytic or inherited bleeding disorders such as haemophilia.

At the University of Veterinary Medicine, Vienna dog owners can bring their animals to donate blood regularly or as needed. Blood donations two to four times a year per dog is the maximum. About 15 minutes are required for a donation. Dogs must have a minimum weight of 25 kilograms and usually donate about 450 millilitres of blood. For cats, depending on their size, the amount taken is about 50 millilitres. Cats are typically sedated for the procedure. For most dogs, on the other hand, donating blood does not involve any serious stress. Should a donation cause too much anxiety or stress, the animal will be excluded as a donor.

Not all blood is alike

As with people, animals also have different blood types. Animal blood, as well as human blood, is divided into various groups based on different surface proteins found on the red blood cells. More than twelve different blood type systems have been described for dogs, although in practice dogs are only tested for DEA 1.1 positive or DEA 1.1 negative. Cats exhibit three different types of blood, horses eight and bovines eleven. The transfusion of an unsuitable blood type can have fatal consequences for animals, especially when a cat with blood type B receives type A blood. For horses and ruminants, the first time transfusion of 'wrong' donor blood is generally safe. With each additional transfusion, however, blood types become crucial, as the animals have produced antibodies against the foreign blood that can cause serious immune reactions.

Blood donations come with a health check

Dogs and cats can be registered as blood donors at the Clinical Unit of Internal Medicine Small Animals of the Vetmeduni Vienna. The animals receive a donor card and undergo a thorough examination before each donation. This mandatory health check includes a complete blood count, a test for blood parasites, and a check-up for viral infections.

"Donating blood does not harm the animals. The donated amount can be quickly regenerated by the animal's organism," says specialist for small animal internal medicine and blood bank coordinator Nicole Luckschander-Zeller. "We pay special attention to making sure that donor animals feel good during donation. That's why, after every donation, we give the animals a little snack."

Dog and cat blood is not only used as a whole. Individual blood components, such as plasma or erythrocyte concentrates, are stored and used when needed.

Horses as blood donors and recipients

There are various reasons for blood donations in equine medicine. These include clotting disorders of the blood, anaemia, poisonings or serious infectious diseases as well as perioperative blood loss. For the latter, blood is stored and kept ready for use during surgery in areas with strong blood supply, such as the nose and jaw. A blood transfusion helps to sustain adequate circulation of the animal during the operation and speeds recovery.

"The owners of diseased horses occasionally bring the suitable donor animal with them," says René van den Hoven, director of the Clinical Unit for Equine Internal Medicine at the Vetmeduni Vienna. The hospital also maintains a number of its own donor horses. The number of donations and the volume of the blood collected are registered in the horse's file, making it possible to plan future dates for donations without compromising the animal's health.

A maximum of five to seven litres of blood can be collected from a horse per donation. The blood must then be transfused into a patient within just a few hours. Storing whole equine blood is not a suitable option. As only plasma is desired for some treatments, the plasma is separated from the whole blood. Plasma is used for specific applications, for example to improve the healing of complicated wounds or during eye operations. Patients with massive protein loss can also be successfully treated with plasma. Protein loss may occur as a consequence of serious burn trauma, severe diarrhoea, tumours or chronic inflammatory intestinal disease, pleurisy or peritonitis.

Ruminants with anaemia need donated blood

Sheep, goats, lamas and alpacas are especially at risk of being infested by blood-sucking parasites out on the pasture. Ingested through the mouth, the worms come to inhabit the intestinal tract. A high level of parasitic infestation leads to serious cases of anaemia that may be fatal for the animals. "These acute patients require a rapid blood transfusion. Ruminants also receive blood for wounds with heavy blood loss, though this luckily is not often the case," explains the specialist for ruminant medicine, Lorenz Khol

Source:University of Veterinary Medicine -- Vienna

PHS gene prevents wheat from sprouting: Fewer crop losses anticipated

Preharvest sprouting can cause significant losses in wheat crops, particularly in white wheat crops. Credit: Kansas State University Photo Services

A new study about the common problem of preharvest sprouting, or PHS, in wheat is nipping the crop-killing issue in the bud.

Researchers at Kansas State University and the U.S. Department of Agriculture-Agricultural Research Service, or USDA-ARS, found and cloned a gene in wheat named PHS that prevents the plant from preharvest sprouting. Preharvest sprouting happens when significant rain causes the wheat grain to germinate before harvest and results in significant crop losses.

"This is great news because preharvest sprouting is a very difficult trait for wheat breeders to handle through breeding alone," said Bikram Gill, university distinguished professor of plant pathology and director of the Wheat Genetics Resource Center. "With this study, they will have a gene marker to expedite the breeding of wheat that will not have this problem."

Gill conducted the study with Guihau Bai, a researcher with the Hard Winter Wheat Genetics Research Unit of the USDA-ARS, adjunct professor of agronomy at Kansas State University and the study's lead author. Also involved were Harold Trick, professor of plant pathology; Shubing Liu, research associate in agronomy; Sunish Sehgal, senior scientist in plant pathology; Jiarui Li, research assistant professor; and Meng Lin, doctoral student in agronomy, all from Kansas State University; and Jianming Yu, Iowa State University.

Their study, "Cloning and Characterization of a Critical Regulator for Pre-Harvest Sprouting in Wheat," appears in a recent issue of the scientific journal Genetics.

The finding will to be most beneficial to white wheat production, which loses $1 billion annually to preharvest sprouting, according to Gill.

He said consumers prefer white wheat to the predominant red wheat because white wheat lacks the more bitter flavor associated with red wheat. Millers also prefer white wheat to red because it produces more flour when ground. The problem is that white wheat is very susceptible to preharvest sprouting.

"There has been demand for white wheat in Kansas for more than 30 years," Gill said. "The very first year white wheat was grown in the state, though, there was rain in June and then there was preharvest sprouting and a significant loss. The white wheat industry has not recovered since and has been hesitant to try again. I think that this gene is a big step toward establishing a white wheat industry in Kansas."

Gill said identifying the PHS gene creates a greater assurance before planting a crop that it will be resistant to preharvest sprouting once it grows a year later. Wheat breeders can now bring a small tissue sample of a wheat plant into a lab and test whether it has the preharvest sprouting resistance gene rather than finding out once the crop grows.

Much of the work to isolate the PHS gene came from Gill and his colleagues' efforts to fully sequence the genome -- think genetic blueprint -- of common wheat. Wheat is the only major food plant not to have its genome sequenced. The genome of wheat is nearly three times the size of the human genome.

Researchers were able to study sequenced segments of the common wheat genome and look for a naturally occurring resistance gene. Gill said without the sequenced segments, finding the PHS gene would have been impossible.

Source: Kansas State University