HIV virus in disguise tricks immune system, Marie Larsson is Professor of Molecular Virology

Name: Marie LarssonTitle: Professor of Molecular Virology
Department: IKE

CONTACT

Phone: +46 (0)10-103 10 55
E-mail: marie.larsson@liu.se

Address:
Linköping University
Department of Clinical and Experimental Medicine
Virology
SE-581 85 Linköping
Sweden

Marie Larsson is Professor of Molecular Virology. Her research is in the area of immunovirology, specifically HIV research with focus on the immunomodulatory effect this virus has on dendritic cells and T cells. She has also ongoing projects exploring new adjuvants and vaccine constellations for cancer and virus. Furthermore, she is investigating the induction and sustainment of cancer associated inflammation and the deleterious effect this has on host immune defense.

Immunomodulatory effects of HIV-1’s interactions with DCs and T cells from

blood and mucosa
So far over 30 million people have died from HIV-1 infection (figure 1), the majority of them in the developing countries, and this epidemic is still cause for major concern. The existing antiretroviral therapy dampens the infection and the destruction of the immune system, i.e. AIDS, but does not cure the disease. Sadly, this therapy is not available to all HIV infected and is a very expensive lifelong commitment with severe side effects.

A vaccine blocking HIV infection is theDendritic cell sought-after solution but there is no hope that we will have such a vaccine in the near future. Instead we can hope for a therapy that induces a potent long lasting immune response consisting of CD4+ and CD8+ T cells, two types of control cells involved in the immune defense, that have proven to be important to control the infection. There exists a unique cell in all tissues in our bodies, the dendritic cell (DC) (Figure 2) with unique ability to activate T cells so they can perform their job in the body. DCs in the vaginal and rectal tissues are one of the first cells to encounter HIV during intercourse with an infected individual (Figure 3 and 4). Unfortunately, HIV hijacks the DCs, which makes this cell responsible for spreading the virus to interacting T cells in the body which provokes HIV-infection of T cells and cell death when it should be initiating immune responses to fight the infection.DC HIV

My research aspires to elucidate the mechanisms behind the immunomodulatory effects HIV exerts on DCs and on their ability to activate T cells. Focus will be on; Elucidation of the mechanisms involved in HIV’s binding to and uptake by DCs and the subsequent degradation that leads to DC antigen presentation of HIV peptides for activation of HIV specific T cells. Elucidation of the mechanisms responsible for the negative effects HIV exerts on DCs and if presence of HIV virions during DC T cell priming impairs the T cell function. Elucidate the effect opsonized HIV-1 exerts on immune cells such as DCs, NK cells and T cells. Identification of receptors and cells involved in the initial HIV infection of cervical mucosa and colorectal mucosa,  and potential microbiocides that can block the initial infection, and elucidation of why HIV affects the T cells in the gut to a higher extent than the T cells in blood.

HIV will continue to kill people and have a great impact on mankind until we have a drug that can stop this infection. My ambition is that the planed research will answer some basic questions regarding the role of DCs in HIV pathogenesis and induction of potent immune response against this virus. This knowledge will guide how a vaccine/therapy needs to be constructed in order to have high efficacy.

                                                             Mucosal transmission

                                                                Cervix

Cancer research

Elucidation the role of IL-1α and the microenvironment in development of pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is a common gastrointestinal malignancy with an exceptional poor prognosis and a mortality rate that nearly matches the rate of incidence. The cross-talk between PDAC and stroma cells, e.g. cancer associated fibroblasts (CAF), and immune cells, may create an environment with chronic inflammation augmenting tumor transformation and maintenance.

In PDAC, more than 70% of the total tumor mass can consist of fibrotic stroma, which makes CAFs the major component in this cancer. PDAC inflammatory environment consists of many mediators, e.g. IL-1, COX-2, IL-6, and CXCL8, and some of these factors correlate to tumor development and poor prognosis. Of note, elevated expression of IL-1 in tumors has been associated with more aggressive disease. Several studies, including ours have reported that dendritic cells (DCs), one of the immune cells found in the tumor microenvironment, show phenotypic and functional abnormalities when isolated from tumor bearing animals and individuals with PDAC. Recent findings provided some evidence that the COX-2 metabolite PGE2 is involved in the upregulation of immunomodulatory factors in DCs impairing their T cell stimulatory ability. The aims are to examine the receptor-ligands and signaling pathways involved in the cross talk between stroma cells, i.e. CAFs, and PDAC cells giving rise to the inflammatory environment and creating an environment sustaining the PDAC. To examine the role IL-1 cytokine family and effects these cytokines cell signaling have on creating the inflammatory environment and in tumor development and survival. To examine whether neutralization of IL1 signaling pathway enhances the survival and quality of life for individuals with pancreatic cancer.

The information gained from the proposed research will help us understand the mechanisms underlying the development of PDAC and the effect this solid tumor exert on the body and may help designing therapies for PDAC.

Source: Linköping University

Scheduling tool a big help in healthcare

The HIV virus avoids the body’s immune cells by disguising itself using proteins that normally take part in the defence against infections. These are the findings of research conducted at the Division of Molecular Virology.

Professor Marie LarssonThese “complement proteins” are soluble molecules that attach themselves to foreign particles and those of the body in different patterns. These patterns help the immune system to identify and attack dangerous intruders such as viruses and bacteria.

Phd student Rada EllegårdInstead, HIV exploits the complement proteins present in all body fluids in order to make its way into the body tissues without being attacked. It was known previously that infections are much more effective if the virus is surrounded by the bodily fluids normally present in blood or sexual contagion than if it is isolated in a laboratory environment. In an article in the Journal of Immunology Marie Larsson, professor of molecular virology (left) and PhD student Rada Ellegård (right) provide an explanation of this phenomenon.

“The ability to use our complement proteins in this way is probably key to the success of HIV in being transmitted. We are currently carrying out further work to investigate these mechanisms in the male genital mucous membrane – the tissue where the virus infection takes place in sexual transmission,” says Ms Larsson.

The first thing HIV particles come into contact with is dendritic cells, immune cells that function as sentry posts. Their job is to identify viruses as dangerous and hostile to the body, and to respond by producing the substances that combat infections and moving to a lymph node to set a specific immune defence in motion.

In the case of HIV, this process does not seem to work very well. The disguise stops the dendritic cells recognising the virus, which instead establishes an infection in the mucous membrane and uses the movement to the lymph nodes as a way to spread around the whole body.

As more and more cells are infected and killed, the virus slowly breaks down our immune system. Without treatment this sequence of events leads to AIDS, a condition where the victim becomes extremely vulnerable to infection and where normally harmless viruses and bacteria become life-threatening.

Related content

Marie Larsson - research presentation >>

                                       HIV-illustration

When a virus is captured by a dendritic cell, it is recognised by a virus sensor that normally sets in motion infection reduction factors which inhibit the production of new virus particles (picture, left). HIV has the ability to clothe itself in complements, a type of protein present in our bodily fluids. In this way it can dampen the signals from the virus sensors and produce many new particles (picture, right).


Source: Linköping University

New Molecular Target Identified for Treating Cerebral Malaria

                                                             Mosquito Anopheles

A drug already approved for treating other diseases may be useful as a treatment for cerebral malaria, according to researchers at Harvard T. H. Chan School of Public Health. They discovered a novel link between food intake during the early stages of infection and the outcome of the disease, identifying two molecular pathways that could serve as new targets for treatment.

“We have known for a long time that nutrition can affect the course of infectious disease, but we were surprised at how rapidly a mild reduction in food intake could improve outcome in a mouse malaria model,” said senior author James Mitchell, associate professor of genetics and complex diseases. “However, the real importance of this work is the identification of unexpected molecular pathways underlying cerebral malaria that we can now target with existing drugs.”

The study appears online January 30, 2015 in Nature Communications.

Cerebral malaria — a severe form of the disease — is the most serious consequence of infection by the parasite Plasmodium falciparum, resulting in seizures, coma, and death. Currently there is a lack of safe treatment options for cerebral malaria, particularly for use in children, who represent the majority of cases. Even patients who receive early treatment with standard antimalarial chemotherapeutic agents run a high risk of dying, despite clearance of the parasite. Moreover, around 25% of survivors develop neurological complications and cognitive impairment.

Lead authors Pedro Mejia and J. Humberto Treviño-Villarreal, both researchers at Harvard T.H. Chan School of Public Health, found that leptin—a hormone secreted from fat tissue with roles in suppressing appetite, but also in activating adaptive immune and inflammatory responses—is increased upon infection in a mouse model of cerebral malaria, and turns out to be a major bad actor in promoting neurological symptoms and death. Remarkably, Mejia, Treviño-Villarreal and colleagues showed that reducing leptin using a variety of means, either genetically, pharmacologically, or nutritionally by reducing food intake during the first two days of infection, protected against cerebral malaria.

The researchers also found that leptin acted primarily on cytotoxic T cells by turning on the well-studied mTOR protein, for which pharmacologic inhibitors are readily available. In their animal model, treating mice with the mTOR inhibitor rapamycin protected them against the neurological complications of cerebral malaria. Protection was due in part to a preservation of the blood brain barrier, which prevented the entry of blood cells carrying the parasites into the brain. As rapamycin is already FDA-approved for use in humans, trials in humans for cerebral malaria treatment with this drug may be possible, according to the researchers.

This study was the result of an ongoing collaboration between the Mitchell lab in the Department of Genetics and Complex Diseases and the labs of Manoj Duraisingh and Dyann Wirth in the Department of Immunology and Infectious Diseases. Other Harvard T.H. Chan School of Public Health authors included  Christopher Hine, Eylul Harputlugil, Samantha Lang, Ediz Calay and Rick Rogers.

This study was supported in part by grants from NIH (DK090629 and AG036712) and the Glenn Foundation for Medical Research to J.R.M.; a Harvard T.H. Chan School of Public Health Yerby postdoctoral fellowship to Mejia, and financial support from the Universidad Auto´noma de Nuevo Leo´n to Treviño-Villarreal.

Source: Harvard

An Advanced Method of DNA Nanostructure Formation Developed

Figure 1: Uni-molecular magnetic tweezers orchestrating the DNA nanostructure formation

Professor Tae-Young Yoon’s research team from the Department of Physics at KAIST has developed a new method to form DNA nanostructures by using magnetic tweezers to observe and to induce the formation of the structure in real time.

Unlike traditional designs of "DNA origami" which relies on thermal or chemical annealing methods, the new technology utilizes a completely different dynamic in DNA folding. This allows the folding to be done within only ten minutes.

Developed in 2006, the "DNA origami" allows a long skeleton of DNA to be folded into an arbitrary structure by using small stapler DNA pieces. This has been a prominent method in DNA nanotechnology.
 

Figure 2: The evolution of DNA nanostructure formation using magnetic tweezers. The DNA nanostructure with a 21-nanometer size was formed in about eight minutes.

However, the traditional technology which adopts thermal processes could not control the DNA formation during the folding because every interaction among DNAs occurs simultaneously. Thus, the thermal processes, which take dozens of hours to complete, had to be repeated multiple times in order to find the optimal condition.

The research team designed a DNA folding using uni-molecular magnetic tweezers that applied force to a single DNA molecule while measuring the state of the DNA. Through this technology, they were able to induce the formation of DNA nanostructure and observe it at the same time.

During high temperature heat treatment, the first stage of conventional thermal processes, the internal structure of the long skeleton DNA untangles. To induce such state, after attaching one side of the skeleton DNA to the surface of glass and the other side to a magnetic material, the team unfolded the internal structure of the DNA by pulling the two sides apart with magnetic force.

Unlike the conventional thermal processes, this method lets the stapler DNA swiftly adhere to the skeleton DNA within a minute because the sites are revealed at room temperature.

After the stapler pieces connected to the skeleton, the team removed the magnetic force. Next, the structure folded through self-assembly as the stapler DNAs stuck to different sites on the skeleton DNA.

Professor Yoon said, “With the existing thermal methods, we could not differentiate the reactions of the DNA because the response of each DNA pieces mutually interacted with each other.” He added that “Using the magnetic tweezers, we were able to sort the process of DNA nanostructure formation into a series of reactions of DNA molecules that are well known, and shorten the time taken for formation in only ten minutes.”

He commented, “This nanostructure formation method will enable us to create more intricate and desirable DNA nanostructures by programming the folding of DNA origami structures.”

Conducted by Dr. Woori Bae under the guidance of Professor Yoon, the research findings were published online in the December 4th issue of Nature Communications.


Source: KAIST

Understanding, improving body's fight against pathogens

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

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

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

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

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

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

Findings hold potential for improved treatment

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

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

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

Multiple allergic reactions traced to single protein

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

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

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

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

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

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

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

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

Source: Johns Hopkins Medicine

Together, humans and computers can figure out plant world

A Web-based system was built for palynologists to interact with stored data and search for pollen images. This screen shows search capabilities by morphology semantics. From Han et al., part of the special issue 'Bioinformatic and Biometric Methods in Plant Morphology' in Applications in Plant Sciences. Credit: Image credit Han et al. Han, J. G., H. Cao, A. Barb, S. W. Punyasena, C. Jaramillo, and C.-R. Shyu. 2014. A neotropical Miocene pollen database employing image-based search and semantic modeling. Applications in Plant Sciences 2(8): 1400030. doi:10.3732/apps.1400030.

As technology advances, science has become increasingly about data -- how to gather it, organize it, and analyze it. The creation of key databases to analyze and share data lies at the heart of bioinformatics, or the collection, classification, storage, and analysis of biochemical and biological information using computers and software. The tools and methods used in bioinformatics have been instrumental in the development of fields such as molecular genetics and genomics. But, in the plant sciences, bioinformatics and biometrics are employed in all fields -- not just genomics -- to enable researchers to grapple with the rich and varied data sources at their disposal.

In July 2013, Surangi Punyasena of the University of Illinois at Urbana-Champaign and Selena Smith of the University of Michigan organized a special session at Botany 2013, the annual meeting of the Botanical Society of America in New Orleans, Louisiana. They invited plant morphologists, systematists, and paleobotanists, as well as computer scientists, applied mathematicians, and informaticians -- all of whom were united in their interest in developing or applying novel biometric or bioinformatic methods to the form and function of plants. The goal: to provide a forum for a cross-disciplinary exchange of ideas and methods on the theme of the quantitative analysis of plant morphology.

As Punyasena explains, "The quantitative analysis of morphology is the next frontier of bioinformatics. Humans are very good at learning to recognize shape and texture, but there are many problems where accuracy and consistency are difficult to achieve with only expert-derived, qualitative data, and in many fields there are often a limited number of experts trained in these visual assessments."

The results of that session, along with invited papers, are published in the August issue of Applications in Plant Sciences as a special issue on Bioinformatic and Biometric Methods in Plant Morphology. Morphology is, of course, the study of form, and form as represented in this collection of articles has a broad scope -- from microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems. The methods presented in the issue, both recent and emerging, are varied as well, including automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment.

Three articles in the issue look at the application of biometric and bioinformatic methods in palynology: Han et al. (2014) introduce an online Miocene pollen database with semantic image search capabilities; Holt and Bebbington (2014) test the applications of an automated pollen classifier; and Mander et al. (2014) analyze differences in human and automated classification of grass pollen based on surface textures. Other papers highlight how biometric and bioinformatic methods apply to plants more broadly, including using skeleton networks to examine plant morphology such as roots (Bucksch, 2014), improving the quantification of geometric leaf shape metrics with a new protocol to measure leaf circularity (Krieger, 2014), comparing human and automated methods of quantifying aspects of leaf venation (Green et al., 2014), and applying morphometrics to charcoalified plant remains (Crawford and Belcher, 2014).

Taken as a whole, the issue presents a compelling argument for the importance of both computational and morphometric approaches.

"I think that there's been a renaissance in morphometric approaches," notes Punyasena. 

"New techniques are using easy access to high-quality digital imaging, powerful computers, and advances in computational analyses like machine learning to rethink the way we gather and analyze morphological data."

As advances in technology allow researchers to gather more and more morphological and image-based data, it has become increasingly important to be able to analyze and interpret those data quickly, accurately, consistently, and objectively. Biometric and bioinformatic methods make this possible, and reveal the potential of data collected from the shape and form of plants to be as rich of a data source as genetic data.

Access to specific articles can be found online at: http://www.bioone.org/toc/apps/2/8

Source: American Journal of Botany

The biology of fun and playfulness

Dog and child (stock image). Credit: © Irina84 / Fotolia

Current Biology celebrates its 25th birthday with a special issue on January 5, 2015 on the biology of fun (and the fun of biology). In a collection of essays and review articles, the journal presents what we know about playfulness in dogs, dolphins, frogs, and octopuses. It provides insights on whether birds can have fun and how experiences in infancy affect a person's unique sense of humor.

"Fun is obviously--almost by definition--pleasurable, rewarding, but in a way that is distinct from the pleasures of satisfying basic needs, such as the drives to reduce thirst or hunger or to reproduce," says Current Biology Editor Geoffrey North. "The articles in this special issue consider examples of what appear to be fun and play in a broad range of animal species and the insights that can be gained into how the behaviors might contribute to evolutionary fitness."

How do we get our sense of humor?

Psychologists Vasu Reddy and Gina Mireault, of the University of Portsmouth and Johnson State College respectively, offer a comprehensive overview of how, in infancy, reactions to absurd behavior like pulling hair or blowing raspberries, as well as teasing others, offer a window into how aware young children are of others' intentions. "As [infants] discover others' reactions and, indeed, others' minds, they also discover the meaning of 'funny', a construct that varies across and within cultures, regions, families, and even dyads," write the authors. "Infants become attuned to the nuances in humour through their social relationships, which create the practice of contexts of humorous exchange." The scientists note that children with atypical patterns of development may exhibit different senses of humor compared to their peers.

Why do adult apes play?

Based on her observations of a wild bonobo community, primatologist Isabel Behncke of the University of Oxford makes the case that play in bonobo adults could be a key adaptation that underlies social bonding and intelligence. She describes how bonobos in the Wamba community of Central Africa naturally engage in chasing, hanging, and water games despite differences in age and sex. "Play makes individuals more adaptable because it makes them more social; and more successful in their sociality as a result of being more adaptable," Dr. Behncke writes. "Life-long play is a bridge between sociality and adaptability."

Does playfulness spur creativity?

Ethologist Sir Patrick Bateson of the University of Cambridge wants to know why playfulness is so connected to creativity in the realms of science, music, and business. Working with behavioral biologist Daniel Nettle, he asked over 1,500 people to rank their creativity and then provide up to ten potential uses for a jam jar or paperclip. Those who considered themselves the most playful were most likely to provide many uses for the items. 

"Play is an effective mechanism for encouraging creativity since creativity also involves breaking away from established patterns of thought and behavior," Dr. Bateson writes.

Source: Cell Press

Lost memories might be able to be restored, suggests research into marine snail

New UCLA research indicates that lost memories can be restored. The findings offer some hope for patients in the early stages of Alzheimer's disease.

New UCLA research indicates that lost memories can be restored. The findings offer some hope for patients in the early stages of Alzheimer's disease.

For decades, most neuroscientists have believed that memories are stored at the synapses -- the connections between brain cells, or neurons -- which are destroyed by Alzheimer's disease. The new study provides evidence contradicting the idea that long-term memory is stored at synapses.

"Long-term memory is not stored at the synapse," said David Glanzman, a senior author of the study, and a UCLA professor of integrative biology and physiology and of neurobiology. 

"That's a radical idea, but that's where the evidence leads. The nervous system appears to be able to regenerate lost synaptic connections. If you can restore the synaptic connections, the memory will come back. It won't be easy, but I believe it's possible."

The findings were published recently in eLife.

Glanzman's research team studies a type of marine snail called Aplysia to understand the animal's learning and memory. The Aplysia displays a defensive response to protect its gill from potential harm, and the researchers are especially interested in its withdrawal reflex and the sensory and motor neurons that produce it.

They enhanced the snail's withdrawal reflex by giving it several mild electrical shocks on its tail. The enhancement lasts for days after a series of electrical shocks, which indicates the snail's long-term memory. Glanzman explained that the shock causes the hormone serotonin to be released in the snail's central nervous system.

Long-term memory is a function of the growth of new synaptic connections caused by the serotonin, said Glanzman, a member of UCLA's Brain Research Institute. As long-term memories are formed, the brain creates new proteins that are involved in making new synapses. If that process is disrupted -- for example by a concussion or other injury -- the proteins may not be synthesized and long-term memories cannot form. (This is why people cannot remember what happened moments before a concussion.)

"If you train an animal on a task, inhibit its ability to produce proteins immediately after training, and then test it 24 hours later, the animal doesn't remember the training," 

Glanzman said. "However, if you train an animal, wait 24 hours, and then inject a protein synthesis inhibitor in its brain, the animal shows perfectly good memory 24 hours later. In other words, once memories are formed, if you temporarily disrupt protein synthesis, it doesn't affect long-term memory. That's true in the Aplysia and in human's brains." (This explains why people's older memories typically survive following a concussion.)

Glanzman's team found the same mechanism held true when studying the snail's neurons in a Petri dish. The researchers placed the sensory and motor neurons that mediate the snail's withdrawal reflex in a Petri dish, where the neurons re-formed the synaptic connections that existed when the neurons were inside the snail's body. When serotonin was added to the dish, new synaptic connections formed between the sensory and motor neurons. But if the addition of serotonin was immediately followed by the addition of a substance that inhibits protein synthesis, the new synaptic growth was blocked; long-term memory could not be formed.

The researchers also wanted to understand whether synapses disappeared when memories did. To find out, they counted the number of synapses in the dish and then, 24 hours later, added a protein synthesis inhibitor. One day later, they re-counted the synapses.

What they found was that new synapses had grown and the synaptic connections between the neurons had been strengthened; late treatment with the protein synthesis inhibitor did not disrupt the long-term memory. The phenomenon is extremely similar to what happens in the snail's nervous system during this type of simple learning, Glanzman said.

Next, the scientists added serotonin to a Petri dish containing a sensory neuron and motor neuron, waited 24 hours, and then added another brief pulse of serotonin -- which served to remind the neurons of the original training -- and immediately afterward add the protein synthesis inhibitor. This time, they found that synaptic growth and memory were erased. When they re-counted the synapses, they found that the number had reset to the number before the training, Glanzman said. This suggests that the "reminder" pulse of serotonin triggered a new round of memory consolidation, and that inhibiting protein synthesis during this "reconsolidation" erased the memory in the neurons.

If the prevailing wisdom were true -- that memories are stored in the synapses -- the researchers should have found that the lost synapses were the same ones that had grown in response to the serotonin. But that's not what happened: Instead, they found that some of the new synapses were still present and some were gone, and that some of the original ones were gone, too.

Glanzman said there was no obvious pattern to which synapses stayed and which disappeared, which implied that memory is not stored in synapses.

When the scientists repeated the experiment in the snail, and then gave the animal a modest number of tail shocks -- which do not produce long-term memory in a naive snail -- the memory they thought had been completely erased returned. This implies that synaptic connections that were lost were apparently restored.

"That suggests that the memory is not in the synapses but somewhere else," Glanzman said. 

"We think it's in the nucleus of the neurons. We haven't proved that, though."

Glanzman said the research could have significant implications for people with Alzheimer's disease. Specifically, just because the disease is known to destroy synapses in the brain doesn't mean that memories are destroyed.

"As long as the neurons are still alive, the memory will still be there, which means you may be able to recover some of the lost memories in the early stages of Alzheimer's," he said.

Glanzman added that in the later stages of the disease, neurons die, which likely means that the memories cannot be recovered.

The cellular and molecular processes seem to be very similar between the marine snail and humans, even though the snail has approximately 20,000 neurons and humans have about 1 trillion. Neurons each have several thousand synapses.

Glanzman used to believe that traumatic memories could be erased but he has changed his mind. He now believes that, because memories are stored in the nucleus, it may be much more difficult to modify them. He will continue to study how the marine snail's memories are restored and how synapses re-grow.

Co-authors of the study include Shanping Chen, Diancai Cai and Kaycey Pearce, research associates in Glanzman's laboratory.

The research was funded by the National Institutes of Health's National Institute of Neurological Disorders and Stroke, the National Institute of Mental Health and the National Science Foundation.

Almost all the processes that are involved in memory in the snail also have been shown to be involved in memory in the brains of mammals, Glanzman said.

In a 1997 study published in the journal Science, Glanzman and colleagues identified a cellular mechanism in the Aplysia that plays an important role in learning and memory. A protein called N-methyl D-aspartate, or NMDA, receptor enhances the strength of synaptic connections in the nervous system and plays a vital role in memory and in certain kinds of learning in the mammalian brain as well. Glanzman's demonstration that the NMDA receptor plays a critical role in learning in a simple animal like the marine snail was entirely unexpected at the time.

Source: University of California, Los Angeles

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

In search of the origin of our brain

Nervous system in Nematostella vectensis embryos with different nerve cell populations, where the different neurons (here in green, blue and magenta) evidence asymmetry. Credit: Hiroshi Watanabe, Thomas Holstein / Nature Communication 5:5536, Macmillan Publishers Limited

While searching for the origin of our brain, biologists at Heidelberg University have gained new insights into the evolution of the central nervous system (CNS) and its highly developed biological structures. The researchers analysed neurogenesis at the molecular level in the model organism Nematostella vectensis. Using certain genes and signal factors, the team led by Prof. Dr. Thomas Holstein of the Centre for Organismal Studies demonstrated how the origin of nerve cell centralization can be traced back to the diffuse nerve net of simple and original lower animals like the sea anemone. The results of their research will be published in the journal "Nature Communications."

Like corals and jellyfish, the sea anemone -- Nematostella vectensis -- is a member of the Cnidaria family, which is over 700 million years old. It has a simple sack-like body, with no skeleton and just one body orifice. The nervous system of this original multicellular animal is organised in an elementary nerve net that is already capable of simple behaviour patterns. Researchers previously assumed that this net did not evidence centralization, that is, no local concentration of nerve cells. In the course of their research, however, the scientists discovered that the nerve net of the embryonic sea anemone is formed by a set of neuronal genes and signal factors that are also found in vertebrates.

According to Prof. Holstein, the origin of the first nerve cells depends on the Wnt signal pathway, named for its signal protein, Wnt. It plays a pivotal role in the orderly evolution of different types of animal cells. The Heidelberg researchers also uncovered an initial indication that another signal path is active in the neurogenesis of sea anemones -- the BMP pathway, which is instrumental for the centralization of nerve cells in vertebrates.

Named after the BMP signal protein, this pathway controls the evolution of various cell types depending on the protein concentration, similar to the Wnt pathway, but in a different direction. The BMP pathway runs at a right angle to the Wnt pathway, thereby creating an asymmetrical pattern of neuronal cell types in the widely diffuse neuronal net of the sea anemone. "This can be considered as the birth of centralization of the neuronal network on the path to the complex brains of vertebrates," underscores Prof. Holstein.

While the Wnt signal path triggers the formation of the primary body axis of all animals, from sponges to vertebrates, the BMP signal pathway is also involved in the formation of the secondary body axis (back and abdomen) in advanced vertebrates. "Our research results indicate that the origin of a central nervous system is closely linked to the evolution of the body axes," explains Prof. Holstein.

Source: Heidelberg, Universität

Revolutionizing genome engineering

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

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

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

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

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

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

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

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

Source: Helmholtz Centre for Infection Research

How spiders spin silk: Mechanism elegantly explains how spider silk can form so quickly and smoothly

Spider silk is an impressive material; lightweight and stretchy yet stronger than steel. But the challenge that spiders face to produce this substance is even more formidable. Credit: © Tamas Zsebok / Fotolia

Spider silk is an impressive material; lightweight and stretchy yet stronger than steel. But the challenge that spiders face to produce this substance is even more formidable. Silk proteins, called spidroins, must convert from a soluble form to solid fibers at ambient temperatures, with water as a solvent, and at high speed. How do spiders achieve this astounding feat? In new research publishing in the open access journal PLOS Biology on August 5, Anna Rising and Jan Johansson show how the silk formation process is regulated. The work was done at the Swedish University of Agricultural Sciences (SLU) and Karolinska Institutet in collaboration with colleagues in Latvia, China and USA.

Spidroins are big proteins of up to 3,500 amino acids that contain mostly repetitive sequences, but the most important bits for the conversion of spidroins into silk are the ends. 

These terminal regions of the proteins are unique to spider silk and are very similar between different spiders. Spidroins have a helical and unordered structure when stored as soluble proteins in silk glands, but when converted to silk their structure changes completely to one that confers a high degree of mechanical stability. These changes are triggered by an acidity (pH) gradient present between one end of the spider silk gland and the other. The gland proceeds from a narrow tail to a sac to a slender duct, and it is known that silk forms at a precise site within the duct. However, further details of spider silk production have been elusive.

By using highly selective microelectrodes to measure the pH within the glands, the authors showed the pH falls from a neutral pH of 7.6 to an acidic pH of 5.7 between the beginning of the tail and half-way down the duct, and that the pH gradient was much steeper than previously thought. The microelectrodes also showed that the concentration of bicarbonate ions and pressure of carbon dioxide simultaneously rise along the gland. Taken together, these patterns suggested that the pH gradient might form through the action of an enzyme called carbonic anhydrase, which converts carbon dioxide and water to bicarbonate and hydrogen ions (and thereby creating an acidic environment). Using a method developed by the authors, they were able to identify active carbonic anhydrase in the narrower part of the gland and confirm that carbonic anhydrase is indeed responsible for generating the pH gradient.

The authors also found that pH had opposite effects on the stability of the two regions at each end of the spidroin proteins, which was surprising given that these regions had been suggested to have similar roles in silk formation. While one of the ends (the "N-terminal domain") tended to pair up with other molecules at the beginning of the duct and became increasingly stable as the acidity increased along the duct, the other end (the "C-terminal domain") destabilized as the acidity increased, and gradually unfolded until it formed the structure characteristic of silk at the acidic pH of 5.5. These findings show that both ends of the protein undergo dramatic structural changes at the pH found at the beginning of the duct, which is also the point where carbonic anhydrase activity is concentrated.

These insights led the authors to propose a new "lock and trigger" model for spider silk formation, in which gradual pairing up of the N-terminal domains locks spidroins into a network of many protein molecules, while the changes of structure in the C-terminal domains could trigger the rapid polymerization of spidroins into fibers. Interestingly, the structure of the C-terminal domain is similar to those in the "amyloid" fibrils found in the brains of individuals with diseases such as Alzheimer's disease. This mechanism elegantly explains how spider silk can form so quickly and smoothly within the spinning duct of these amazing animals. Besides helping humans to understand how they might mimic the spiders to produce biomimetic spidroin fibers for our own purposes, knowing how spiders spin silk could give insights into natural ways of hindering the amyloid fibrils associated with diseases like dementia.

Source: PLOS

A taxonomic toolkit ends a century of neglect for a genus of parasitic wasps

This is Ophion keala, one of the newly described species of Ophion." Credit: Dr. Marla Schwarzfeld; CC-BY 4.0

In 1912, three species in the parasitic wasp genus Ophion were described by two different entomologists, increasing the number of known species in North America to eleven. It has long been known that the actual diversity is much higher; however, it took 102 years for any additional species to be described.

"The main reason for this is that everyone has assumed that Ophion are just too difficult to tell apart. Museum collections are full of unidentified Ophion, but nobody has wanted to face the challenge of sorting them out" said Marla Schwarzfeld, an entomologist who recently completed her Ph.D. at the University of Alberta, Canada.

In fact, the author of one of the species described in 1912, Claude Morley, stated: "Without abundant material it were ridiculous to attempt a wide revision of these insects; and ... a mass of this material causes one's courage to sink at the sight of so uniform and apparently characterless a group."

However, with the advent of new taxonomic tools, it is no longer necessary to rely solely on the challenging morphology of the group. Schwarzfeld and her Ph.D. supervisor, Felix Sperling, used a combination of molecular and morphometric analyses to define a new species group within Ophion, and to delimit and describe six new species within this group. The molecular work involved the analysis of three different genetic markers, while the morphometric analyses included both an analysis of wing venation and a more traditional approach of measuring various body parts. The study, including the new descriptions, has recently been published in the open-access journal, ZooKeys.

"The exciting part about this work is that these techniques all gave remarkably congruent results, which gives us a lot of confidence in these new species. This takes a lot of the guesswork out of describing species, and will be a really valuable toolkit for studying additional species of Ophion, as well as species in other morphogically-challenging groups" declared Schwarzfeld.

Source:  Pensoft Publishers