Tuesday, June 29, 2010

Pirate Bay Founders Disband

Site of the day: no site

The Bureau of Piracy is no more

The controvertial group that founded the filesharing website Pirate Bay has disbanded.

Based in Sweden, Piratbyran (or ‘piracy bureau’ in English) was opposed to copyright and promoted file sharing, much to the chagrin of the entertainment industry. The site provided an index of films, games, music and TV programmes, directing users to BitTorrent files where they could be illegaly downloaded.

Since the site went live in 2003, its founders have been raided by the police and charged with copyright infringement, with a variety of lawsuits being brought against them.

One of these founders, Marcin de Kaminski, told BBC News that the group no longer feels “needed”. He went on to comment on the sudden death of one of the other core members, Ibi Kopimi Botani:

“The discussions about abolishing Piratbyrån have been going on for years already, but this weekend a beloved friend and member died, and we decided it was time to move on for real, since the group could not be the same without him anyhow. It felt like a good time for passing this part of life”.

The move to dissolve Piratbyran was announced on a blog post, where Marcin de Kaminski encouraged file sharers to continue The Pirate Bay’s work:

“If you want to honour Ibi or The Bureau of Piracy, please make something cool out of it. We all need that”.

(http://www.geeks.co.uk/24299-pirate-bay-founders-disband)

http://www.inquisitr.com/77365/original-pirate-bay-founders-disband/

http://torrentfreak.com/pirate-bays-founding-group-piratbyran-disbands-100623/
http://dekaminski.se/2010/06/nu-finns-inte-piratbyran-mer/

Just no words.

LHC News

Site of the day: no site

http://news.bbc.co.uk/2/hi/science_and_environment/10430234.stm

Ohhh, what a messy month...

Sunday, June 20, 2010

In Pursuit of the Energy of Life: Researchers Decipher Makeup of Generators in Cellular Power Plants

Site of the day: http://uberaffiliate.com/

ScienceDaily (June 21, 2010) — Scientists from the Institute of Biochemistry and Molecular Biology and Collaborative Research Center 746 of the University of Freiburg have discovered a new mechanism which plays an essential role in the assembly and growth of mitochondria, the "power plants" of the cell.

These organelles make energy stored in food ready for use by the cell. The generators in the cellular power plants are biological membranes located inside the mitochondria. Even minute errors in the composition of the inner mitochondrial membrane can lead to severe metabolic derangements, which can have an especially negative impact on the energy-hungry muscle and nerve cells.

In order to function, the cellular generators depend on the support of numerous highly specialized membrane proteins in the inner mitochondrial membrane. For the most part, these proteins are synthesized outside of the organelles and then imported with the help of protein translocases. Fundamental processes like this follow the same principles in all organisms, from unicellular life forms to human beings. The scientists were thus able to use mitochondria from baker's yeast as a model system for their study, which has now been published in the journal Current Biology.

In investigating the insertion of a family of membrane proteins which is of great pharmacological interest, the so-called ABC transporters, the research team made the surprising discovery that some segments of the transporters are evidently initially skipped by the insertion machinery and transported completely over the membrane. "These errors in membrane insertion are then repaired by another translocase which is very old from an evolutionary perspective," says Maria Bohnert, doctoral student and Boehringer-Ingelheim Scholarship recipient. Thus, the scientists were able to demonstrate for the first time that at least two different protein translocases cooperate closely to insert proteins with complex structures into the inner mitochondrial membrane.

In clarifying this coupled mechanism of membrane insertion, project head Dr. Martin van der Laan and his team have solved a hotly debated scientific problem and made a major contribution to our understanding of the composition and functioning of cellular power plants. The findings may help scientists to throw light on the mechanisms of diseases caused by defects in the biogenesis of mitochondria.

Journal Reference:
Maria Bohnert, Peter Rehling, Bernard Guiard, Johannes M. Herrmann, Nikolaus Pfanner, and Martin van der Laan. Cooperation of Stop-Transfer and Conservative Sorting Mechanisms in Mitochondrial Protein Transport. Current Biology, 2010; DOI: 10.1016/j.cub.2010.05.058


(http://www.sciencedaily.com/releases/2010/06/100618082215.htm)

Fuzzy Logic Predicts Cell Aging

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ScienceDaily (June 18, 2010) — The process of aging disturbs a broad range of cellular mechanisms in a complex fashion and is not well understood. Computer models using fuzzy logic might help to unravel these complexities and predict how aging progresses in cells and organisms, according to a study from Drexel University in Philadelphia and Children's Hospital Boston.

"One important goal of computational approaches in aging is to develop integrated models of a unifying aging theory in order to better understand the progression of aging phenotypes grounded on molecular mechanisms," said Andres Kriete, Associate Professor at Drexel's School of Biomedical Engineering, Science and Health Systems and lead author of the study.

The study, which will appear in the June issue of PLoS Computational Biology, relates progressive damage and dysfunction in aging, dubbed a vicious cycle, to inflammatory and metabolic stress response pathways. Interestingly, the activation of these pathways remodels the inner functioning of the cell in a protective and adaptive manner and thus extends lifespan.

This is the first time that scientists have applied fuzzy logic modeling to the field of aging. "Since cellular biodynamics in aging may be considered a complex control system, a fuzzy logic approach seems to be particularly suitable," said Dr. William Bosl, co-author of this study. Dr. Bosl, a staff scientist in the Informatics Program at Children's Hospital Boston, developed a fuzzy logic modeling platform called Bionet together with a cell biologist, Dr. Rong Li of the Stowers Institute for Medical Research in Kansas City, to study the complex interactions that occur in a cell's machinery using the kind of qualitative information gained from laboratory experiments.

Fuzzy logic can handle imprecise input, but makes precise decisions and has wide industrial applications from air conditioning to anti-lock break systems in cars, using predefined rules. In a similar fashion, the aging model relies on sets of rules drawn from experimental data to describe molecular interactions. "Integration of such data is the declared goal of systems biology, which enables simulation of the response of cells to signaling cues, cell cycling and cell death," said Glenn Booker, who is Faculty at the College of Information Science and Technology at Drexel and co-author on the study.

Applications in aging are currently geared towards deciphering the underlying connections and networks. "We have to realize that the real strength of computational systems biology in aging is to be able to predict and develop strategies to control cellular networks better as they may be related to age related diseases," said Dr. Kriete, "and our approach is just a first step in this direction."


Journal Reference:
Kriete A, Bosl WJ, Booker G. Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses. PLoS Computational Biology, 2010; 6 (6): e1000820 DOI: 10.1371/journal.pcbi.1000820


(http://www.sciencedaily.com/releases/2010/06/100617185127.htm)

Protein's Role in Cell Division Uncovered

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ScienceDaily (June 16, 2010) — A Florida State University researcher has identified the important role that a key protein plays in cell division, and that discovery could lead to a greater understanding of stem cells.

Timothy L. Megraw, an associate professor in the College of Medicine, has outlined his findings in the cover story of the June 15 issue of Developmental Cell. The article was co-authored by researchers from the University of Texas Southwestern Medical Center at Dallas and the University of North Texas.

In August, Megraw received a four-year, $1.2 million grant from the National Institutes of Health to explore the role of centrosomes and cilia in cell division and their connections to human disease.

One long-term goal of Megraw's research has been to discover which parts of the cell play which roles in cell division. The centrosome is an important player. When a cell is ready to divide, it typically has two centrosomes, each containing a "mother and daughter" pair of centrioles tightly connected to each other, or "engaged."

"Two is important," Megraw said, "because you divide your genetic material into two equal sets. Each of these centriole pairs organizes the cytoskeletal machinery that pulls the chromosomes apart. So you don't want there to be more than two, because then you run the risk of unequal separation of the chromosomes."

The centrioles are supposed to replicate only once during the cell cycle. What keeps them from replicating more often was discovered a few years ago, Megraw said, when researchers identified mother-daughter engagement as the key. Once those two become disengaged, it acts as the "licensing" step, in effect giving the centrioles permission to replicate.

Unknown until now, Megraw said, was what regulated those centrioles to remain engaged until the proper time, to prevent excess replication. He suspected that the protein CDK5RAP2 was at least partly responsible. His team tested the protein's role using a mutant mouse in which the protein was "knocked out" and not functioning. These researchers looked for any effects on engagement and "cohesion," in which centriole pairs are tethered by fibers.

They noted in the mutant mouse that engagement and cohesion did not occur in their typical orderly fashion and that centrioles were more numerous and often single rather than paired. The amplified centrioles assembled multipolar spindles, a potential hazard for chromosomal stability. The researchers concluded that CDK5RAP2 is required to maintain centriole engagement and cohesion, thereby restricting centriole replication.

They are looking at how this discovery might apply to the human brain.

"The two mouse mutants we made mimic the two known mutations in humans in CDK5RAP2 -- which has another name, MCPH3, in humans," Megraw said. "The disease associated with that is a small brain.

"Our next step is to look at the brains of the mice and try to determine what's wrong. We think it's the stem cells -- that the progenitors that give rise to all the neurons in the brain are dying early or changing from a progenitor into a neuron too early."

Another gene called myomegalin might be functionally redundant to CDK5RAP2, Megraw said, adding, "Our goal is to knock that out, too."

The research his lab has done might also be applicable to cancer drugs for humans, he said. Centrosomes organize microtubules, which are structures in the cell that many important anti-cancer drugs target.

"The amplified centrioles and multipolar spindles suggest that the mutant mice may be more susceptible to developing cancers," Megraw said. "We are in a position to test this with our new mouse models."


Journal Reference:
Jose A. Barrera, Ling-Rong Kao, Robert E. Hammer, Joachim Seemann, Jannon L. Fuchs, Timothy L. Megraw. CDK5RAP2 Regulates Centriole Engagement and Cohesion in Mice. Developmental Cell, 2010; 18 (6): 913 DOI: 10.1016/j.devcel.2010.05.017

(http://www.sciencedaily.com/releases/2010/06/100615163156.htm)

Biomolecular Modeling: Scientists Discover 'Breakwater' to Help Control Electron Transfer

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ScienceDaily (June 16, 2010) — Researchers at the University of Calgary found that amino acid residues form a type of barrier to help in the process of electron transfer between proteins.

"This raises the bar for biomolecular modeling," says Dennis Salahub, U of C co-author of a paper published in the journal Proceedings of the National Academy of Sciences (PNAS). "At a fundamental level, it is by far the most detailed insight that has been obtained for the dynamic role of water in this kind of electron transfer, or for that matter any biochemical reaction."

Electron transfer between proteins is the cornerstone of biological energy transfer. Every life-form uses this process to convert food or sunlight into chemical energy.

The interdisciplinary team of researchers found that the electron travels over a bridge made of a water molecule, while residues on one of the proteins form a sort of 'molecular breakwater' to keep other water molecules away while the electron travels across the bridge.

"You don't want too many (water molecules around the bridge) because it gets too crowded and they're all bumping into each other and you can't get one to fit at just the right position and the right angle (for the bridge) for any length of time," says PhD student and co-author Nathan Babcock. "It's like being on a crowded subway where you can't get comfortable."

In artificial mutations with a faulty breakwater, the water bridge is disrupted and the rate of electron transfer is markedly reduced, he says.

Using the CHARMM molecular simulation computer program, the research team examined a 40 nanosecond period of electronic coupling of the proteins methylamine dehydrogenase and amicyanin from the bacterium Paracoccus denitrificans.

"This is fundamental research but you can imagine how studies like this can be applied to various genetically modified organisms, and if you can gain control over some, you can use it to either speed up or slow down a particular reaction," says Salahub.

He says the work was made possible with the collaboration of two of the U of C's interdisciplinary research institutes; the Institute for Biocomplexity and Informatics (IBI) and the Institute for Quantum Information Science (IQIS).

Babcock, whose background is in quantum information theory, was pleased to do research at the union of these two disciplines.

"When you think of quantum mechanics, usually you're thinking solid state semi conductors, atoms trapped with lasers, etc. It's usually cold laboratory stuff, not warm globby biological stuff," says the PhD student. "I think the union of biology and quantum mechanics is very, very exciting."

The study was published on June 14 in the journal Proceedings of the National Academy of Sciences by Nathan Babcock and Aurelien de la Lande, now at the CNRS in France, Jan Rezac, now at the Czech Academy of Science, Barry Sanders, iCORE Chair of Quantum Information Science at U of C and Dennis Salahub, Director of the Institute for Biocomplexity and Informatics and Professor in the Department of Chemistry.

Journal Reference:
Aurélien De La Lande, Nathan S. Babcock, Jan Řezáč, Barry C. Sanders, Dennis R. Salahub. Surface residues dynamically organize water bridges to enhance electron transfer between proteins. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.0914457107


(http://www.sciencedaily.com/releases/2010/06/100614160203.htm)

Alternative Pathway to Malaria Infection Identified

Site of the day: http://uberaffiliate.com/

ScienceDaily (June 17, 2010) — Discovery of a key red cell molecule used by the malaria parasite gives renewed hope for an effective vaccine in the future, according to an international team of researchers.

Plasmodium falciparum, a blood parasite that causes malaria by invading and multiplying in the red blood cells, kills 1 to 2 million people annually.

"How the parasite invades red blood cells is not completely understood," said Jose A. Stoute, M.D., senior investigator and team leader, Department of Medicine, Division of Infectious Diseases and Epidemiology, Penn State College of Medicine. "For many years it has been known that proteins called glycophorins are used by the parasite to gain entry into the red cell."

Because infection can take place without glycophorins, researchers suspected that another protein is also involved. The identity of this protein remained a mystery for 20 years and it was named the "X" receptor. A team of researchers now reports in PLoS Pathogens, the identity of this protein as the complement receptor 1 (CR1), also known to help protect red cells from attack by the immune system. CR1 has been suspected of having other roles in the development of malaria complications. The team was able to demonstrate that this protein is important in the invasion of red cells by using several laboratory strains of malaria as well as strains obtained from Kenya.

"Our findings suggest that for many malaria strains, CR1 is an alternative receptor to glycophorins on intact red cells," Stoute said.

According to the researchers, the reasons malaria may use the CR1 protein instead of glycophorins are if the parasite encounters a variant that lacks the glycophorin receptor; if the immune system mounts a response against parasite proteins involved in the dominant pathway due to a previous infection; or if the host were to be vaccinated with a vaccine that blocks the glycophorin pathway.

"This work has important implications for the future development of a vaccine against malaria," Stoute said. "Therefore, it is imperative that all the major invasion pathways be represented in a future malaria blood stage vaccine."

Vaccines that target parasite proteins involved in the dominant glycophorin pathway, but do not block the CR1 pathway, may cause proliferation of parasites that rely on the CR1 pathway for infection.

"The demonstration that CR1 is a receptor of P. falciparum will facilitate the identification of additional parasite proteins that allow it to bind to the blood cell, and the future development of a vaccine that effectively blocks red cell invasion," said Carmenza Spadafora, lead author and scientist at the Institute for Advanced Science and High Technology Studies, Republic of Panama.

Working with Stoute and Spadafora were scientists from the Walter Reed Army Institute of Research's malaria research program, including Gordon A. Awandare and parastiologists Karen M. Kopydlowski and J. Kathleen Moch. The collaboration also included Jozsef Czege, Biomedical Instrumentation Center, Uniformed Services University of the Health Sciences; Robert W. Finberg, University of Massachusetts Medical School; and George C. Tsokos, Beth Israel Deaconess Medical Center, Harvard Medical School.

The National Institutes of Health, the Fogarty International Center, and the Department of Defense supported this work. In addition, Carmenza Spadafora received support from the National Secretariat of Science and Technology, Republic of Panama.


Journal Reference:
Carmenza Spadafora, Gordon A Awandare, Karen M Kopydlowski, Jozsef Czege, J Kathleen Moch, Robert W Finberg, George C Tsokos, José A Stoute José A Stoute. Complement Receptor 1 Is a Sialic Acid-Independent Erythrocyte Receptor of Plasmodium falciparum. PLoS Pathogens, 2010; 6 (6): e1000968 DOI: 10.1371/journal.ppat.1000968


(http://www.sciencedaily.com/releases/2010/06/100617185123.htm)

Fundamental Process in Lysosomal Function and Protein Degradation: Disorder Leads to Serious Diseases

Site of the day: http://uberaffiliate.com/

ScienceDaily (June 15, 2010) — The degradation of proteins and other macromolecules in cells is vital to survival. Disruption of this process can result in serious disease. The research group of Professor Thomas Jentsch (Leibniz Institute for Molecular Pharmacology, FMP/ Max Delbrück Center for Molecular Medicine, MDC, Berlin-Buch) has now succeeded in identifying an essential cellular process necessary for the transport and degradation of macromolecules in endosomes and lysosomes, respectively.

In two studies published in the same issue of the journal Science, they showed that -- contrary to scientific consensus -the function of these tiny cell organelles not only depends on the pH, but also on chloride ion accumulation in their interior.

Proteins are the building blocks and machines of life. Tens of thousands of them are present in each cell, where they perform essential tasks for the organism. Once they have fulfilled their function, they must be degraded to avoid causing damage. One way in which proteins can be degraded is via the digestion processes inside tiny cellular organelles, the lysosomes. The transport of the proteins destined for degradation to these cellular "trash bins" is partly carried out by endosomes, which deliver proteins from the cell surface to the cell interior.

The functionality of both endosomes and lysosomes depends on the ion concentration within their membrane-enclosed interior. In particular, an important role is ascribed to a high concentration of hydrogen ions, i.e. an acidic pH, inside those organelles.

The two studies by Dr. Stefanie Weinert, Dr. Gaia Novarino and Professor Thomas Jentsch focus on two ion transport proteins, the chloride transporters ClC-5 and ClC-7. These are located in the membrane of endosomes and/or lysosomes and exchange negatively charged chloride ions for positively charged hydrogen ions (protons).

ClC-5 is located in the membrane of endosomes in renal cells. If ClC-5 is defective or lacking altogether, proteins can hardly be absorbed from the urine any longer. In a cascade of indirect mechanisms, this leads to the development of kidney stones in Dent's disease.

ClC-7 is located in the membrane of lysosomes in all cells of the body. The research group by Thomas Jentsch showed already a few years ago that mutations of ClC-7 in mice and humans lead to severe disease symptoms. Impaired lysosomal function in the brain results in severe degenerative changes that leads to massive neuronal death. A dysfunction of bone-degrading osteoclasts causes an excessive calcification of bones (osteopetrosis).

The chloride-proton exchangers ClC-5 and ClC-7 function parallel to proton pumps, which ensures an acidic environment within endosomes and lysosomes. ClC-5 and ClC-7 transport chloride ions into these organelles, thereby electrically balancing the inward transport of positively charged protons through the "pump." Hitherto researchers had assumed that maintaining the charge balance was the sole task of ClC-5 and ClC-7, without which both the transport of endosomes and lysosomal protein degradation are impaired.

However, Professor Jentsch and his team showed several years ago that the pH in lysosomes devoid of ClC-7 is normal and that nevertheless lysosomal storage disease and osteopetrosis ensue. This means that charge balancing in lysosomes may involve a different, previously unknown mechanism, and that the main task of ClC-7 may rather be the regulation of lysosomal chloride concentration. The Berlin research group proposed that the exchange of chloride for protons, which are more highly concentrated in the acidic environment of lysosomes than in the rest of the cell, accumulates chloride ions in lysosomes. A high lysosomal chloride concentration may be functionally important.

"In an elegant experimental approach" as Professor Jentsch explains the test of this hypothesis, "Dr. Novarino and Dr. Weinert converted the ClC-5 and ClC-7 chloride-proton exchangers in the mouse into pure chloride conductors (channels). They exchanged a single amino acid out of a total of around 800 present in the ion transporters." These mutated transport proteins are optimally suited to compensate the charge transfer by the proton pump and therefore should, according to the hypothesis of the research group, support the acidification of the organelles very well.

On the other hand, the uncoupling of chloride transport from proton transport should significantly lower the accumulation of chloride into these organelles. Indeed, this prediction was confirmed experimentally in their mouse model. "Surprisingly," Professor Jentsch said, "the corresponding mice showed almost the same disease symptoms as with a total lack of the respective proteins."

With this experiment, the MDC and FMP researchers were able to show for the first time that not only the lack of endosomal/lysosomal acidification, but also a reduced accumulation of chloride ions in these organelles plays a crucial role in generating the severe symptoms of these hereditary diseases, that is a form of kidney stone disease as well as neurodegeneration. A dysregulation of organellar chloride concentration may also play a role in other human diseases.

Journal References:
1. G. Novarino, S. Weinert, G. Rickheit, T. J. Jentsch. Endosomal Chloride-Proton Exchange Rather Than Chloride Conductance Is Crucial for Renal Endocytosis. Science, 2010; 328 (5984): 1398 DOI: 10.1126/science.1188070
2. S. Weinert, S. Jabs, C. Supanchart, M. Schweizer, N. Gimber, M. Richter, J. Rademann, T. Stauber, U. Kornak, T. J. Jentsch. Lysosomal Pathology and Osteopetrosis upon Loss of H -Driven Lysosomal Cl- Accumulation. Science, 2010; 328 (5984): 1401 DOI: 10.1126/science.1188072

(http://www.sciencedaily.com/releases/2010/06/100615141755.htm)

Liposome-Hydrogel Hybrids: No Toil, No Trouble for Stronger Bubbles

Site of the day: http://uberaffiliate.com/

ScienceDaily (June 14, 2010) — People have been combining materials to bring forth the best properties of both ever since copper and tin were merged to start the Bronze Age. In the latest successful merger, researchers at the National Institute of Standards and Technology (NIST), the University of Maryland (UM) and the U.S. Food and Drug Administration (FDA) have developed a method to combine two substances that individually have generated interest for their potential biomedical applications: a phospholipid membrane "bubble" called a liposome and particles of hydrogel, a water-filled network of polymer chains.

The combination forms a hybrid nanoscale (billionth of a meter) particle that may one day travel directly to specific cells such as tumors, pass easily though the target's cell membrane, and then slowly release a drug payload.

In a recent paper in the journal Langmuir, the research team reviewed how liposomes and hydrogel nanoparticles have individual advantages and disadvantages for drug delivery. While liposomes have useful surface properties that allow them to target specific cells and pass through membranes, they can rupture if the surrounding environment changes. Hydrogel nanoparticles are more stable and possess controlled release capabilities to tune the dosage of a drug over time, but are prone to degradation and clumping. The researchers' goal was to engineer nanoparticles incorporating both components to utilize the strengths of each material while compensating for their weaknesses.

To manufacture their liposome-hydrogel hybrid vesicles, the researchers adapted a NIST-UM technique known as COMMAND for COntrolled Microfluidic Mixing And Nanoparticle Determination that uses a microscopic fluidic (microfluidic) device (see "NIST, Maryland Researchers COMMAND a Better Class of Liposomes" in NIST Tech Beat, April 27, 2010). In the new work, phospholipid molecules are dissolved in isopropyl alcohol and fed via a tiny (21 micrometers in diameter, or three times the size of a yeast cell) inlet channel into a "mixer" channel, then "focused" into a fluid jet by a water-based solution added through two side channels. Hydrogel precursor molecules are mixed in with the focusing fluid.

As the components blend together at the interfaces of the fluid streams, the phospholipid molecules self-assemble into nanoscale vesicles of controlled size and trap the monomers in solution inside. The newly formed vesicles then are irradiated with ultraviolet light to polymerize the hydrogel precursors they carry into a solid gel made up of cross-linked chains. These chains give strength to the vesicles while permitting them to retain the spherical shape of the liposome envelope (which, in turn, would facilitate passage through a cell membrane).

To turn the liposome-hydrogel hybrid vesicles into cellular delivery vehicles, a drug or other cargo would be added to the focusing fluid during production.


Journal Reference:
Jennifer S. Hong, Samuel M. Stavis, Silvia H. DePaoli Lacerda, Laurie E. Locascio, Srinivasa R. Raghavan, Michael Gaitan. Microfluidic Directed Self-Assembly of Liposome%u2212Hydrogel Hybrid Nanoparticles. Langmuir, 2010: 100429105250028 DOI: 10.1021/la100879p


(http://www.sciencedaily.com/releases/2010/06/100609171847.htm)

How the Wrong Genes Are Repressed

Site of the day: http://uberaffiliate.com/

ScienceDaily (June 13, 2010) — The mechanism by which 'polycomb' proteins critical for embyronic stem cell function and fate are targeted to DNA has been identified by UCL scientists.

The discovery, which has implications for the fields of stem cell and tissue engineering, is detailed in research published in the journal Molecular Cell.

A key feature of stem cells is the suppression of genes that when later switched on lead to the differentiation of the cells into specific mature cell types, such as neurons or immune cells. Polycomb proteins, first discovered in fruit flies, are known to play a critical role in the suppression of these developmental genes. PRC2 (polycomb repressive complex-2) is present in all multicellular organisms and has been shown to be important in stem cell differentiation and early embryonic development.

The study authors found that PRC2 is brought to its target genes though binding to a new class of short RNAs transcribed by RNA polymerase II. PRC2 can then methylate chromatin, preventing the activation of developmental regulator genes that would otherwise act to alter the identity of the cell.

Senior author Dr Richard Jenner, UCL Infection & Immunity, said: "We knew that different sets of genes are turned on in different cells and that polycomb proteins prevent the wrong genes from being turned on, for example polycomb prevents the activation of neuronal genes in immune cells. However, although polycomb proteins repress genes, they are actually in a poised state -- some sort of gene activity seemed to be occurring.

"We wanted to find out what this activity was and our identification of these short RNAs explains this unusual gene state. Discovering that polycomb also binds to these RNAs shows how polycomb might be recruited to genes, which are then repressed to maintain the identities of different cell types. This has been a key question in the field for some time and has important implications for how we might be able to control cell fate in tissue engineering."

Journal Reference:
Aditi Kanhere, Keijo Viiri, Carla C. Araújo, Jane Rasaiyaah, Russell D. Bouwman, Warren A. Whyte, C. Filipe Pereira, Emily Brookes, Kimberly Walker, George W. Bell, Ana Pombo, Amanda G. Fisher, Richard A. Young, Richard G. Jenner. Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2. Molecular Cell, 2010; 38 (5): 675 DOI: 10.1016/j.molcel.2010.03.019


(http://www.sciencedaily.com/releases/2010/06/100611123839.htm)

Nuclear Pores Call on Different Assembly Mechanisms at Different Cell Cycle Stages

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ScienceDaily (June 12, 2010) — Nuclear pores are the primary gatekeepers mediating communication between a cell's nucleus and its cytoplasm. Recently these large multiprotein transport channels have also been shown to play an essential role in developmental gene regulation. Despite the critical role in nuclear function, however, nuclear pore complexes remain somewhat shadowy figures, with many details about their formation shrouded in mystery.

Now a team of investigators from the Salk Institute for Biological Studies has illuminated key differences in the mechanisms behind nuclear pores formed at two distinct stages in the cell cycle. Their findings, to be published in the June 12 issue of Cell, may provide insights into conditions such as cancer, developmental defects, and sudden cardiac arrest.

Nuclear pores, which are built from 30 different proteins, assemble during interphase, the period when the nucleus expands and replicates its DNA, and following mitosis, when the nuclear membrane reforms around the segregated chromosomes to create two identical nuclei.

But, explains Martin Hetzer, Ph.D., Hearst Endowment associate professor in Salk's Molecular and Cell Biology Laboratory, who led the study, there has been a longstanding question about whether assembly pathways at the distinct cell cycle stages use different or similar mechanisms. "Interphase assembly is different from post-mitotic assembly in that the nuclear membrane is fully formed around chromatin," he says, "whereas post-mitotic assembly occurs into the reforming nuclear membrane. So the topology of the nuclear membrane is very different during these two cell cycle stages."

While some aspects of post-mitotic assembly were known, almost nothing was understood about how assembly of the pores occurs during interphase, when the cell doubles the number of nuclear pores to provide sufficient levels of NPC components for the two daughter cells. A parallel process takes place during differentiation of an oocyte, when millions of nuclear pore components are integrated into the nuclear membrane of the egg cell, so any findings about interphase assembly could also be relevant to embryonic development.

"We were able to show for the first time that there are two distinct mechanisms behind how these large protein complexes assemble to accommodate cell cycle-dependent differences in nuclear membrane topology," says Hetzer.

The team identified a key difference in how the Nup107/160 complex, which is essential for NPC formation, is targeted to new assembly sites in the NE. Surprisingly, one of the complex members, Nup133, is directed to the pore assembly site via a completely novel mechanism that involves sensing of the nuclear membrane's curvature. "The sensor was identified in a bioinformatics screen, and it was not known whether it was really functional in vivo," says co-first author Christine Doucet, Ph.D., a postdoctoral fellow in Hetzer's lab. "But we thought it would fit in with the topology of the nuclear membrane and the sites of the new nuclear pore complexes because they are highly curved. So if the sensor was playing a role in assembly, it was a really neat way to coordinate the assembly of all the components at the right position and the right time."

The second difference the group discovered is that in post-mitotic assembly, but not during interphase, a protein called ELYS played a key role in directing the NUP107/160 complex, which is critical to the formation of pores, to the assembly sites. In contrast, the transmembrane Nup POM121, is specifically required for interphase assembly.POM121 is the earliest known protein at pore assembly sites yet how it is directed there is still under investigation.

"We knew both proteins were essential for pore assembly in different ways, but we didn't know how," says co-first author Jessica Talamas, also a postdoctoral fellow in Hetzer's lab. "There was a discrepancy in the literature about POM121, so we were trying to figure out what was going on. It was one of those lightbulb moments, we were looking at the data and realized that POM121 was only required for interphase assembly, and then everything just made sense."

Because these processes are at work in every cell that divides, the study is especially germane to one of the big questions in the field: how the number of nuclear pores is regulated. It's a question with multiple ramifications. Nuclear pore numbers are misregulated in cancer cells, for example, so the findings have applications in cancer research. In addition, because neurons require a large number of nuclear pores, evidence is mounting that defects in nuclear pore assembly are linked to developmental defects in the central nervous system. Assembly defects during development have also been implicated in conditions such as sudden cardiac arrest.

"In establishing differences between the two assembly pathways, the findings have provided the first glimpse of a mechanistic understanding," Hetzer says.

This study was supported by a grant from the National Institutes of Health.


Journal Reference:
Christine M. Doucet, Jessica A. Talamas, Martin W. Hetzer. Cell Cycle-Dependent Differences in Nuclear Pore Complex Assembly in Metazoa. Cell, Volume 141, Issue 6, 1030-1041 DOI: 10.1016/j.cell.2010.04.036


(http://www.sciencedaily.com/releases/2010/06/100610125625.htm)

New Type of Human Stem Cell May Be Easier to Manipulate

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ScienceDaily (June 11, 2010) — Researchers from the Massachusetts General Hospital Center for Regenerative Medicine (MGH-CRM) and the Harvard Stem Cell Institute have a developed a new type of human pluripotent stem cell that can be manipulated more readily than currently available stem cells. As described in the June 4 Cell Stem Cell, these new cells could be used to create better cellular models of disease processes and eventually may permit repair of disease-associated gene mutations.

"It has been fairly easy to manipulate stem cells from mice, but this has not been the case for traditional human stem cells," explains Niels Geijsen, PhD, of the MGH-CRM, who led the study. "We had previously found that the growth factors in which mouse stem cells are derived define what those cells can do, and now we've applied those findings to human stem cells."

The first mammalian embryonic stem cells (ESCs) were derived from mice and have proven very useful for studying gene function and the impact of changes to individual genes. But techniques used in these studies to introduce a different version of a single gene or inactivate a particular gene were ineffective in human ESCs. In addition, human ESCs proliferate much more slowly than do cells derived from mice and grow in flat, two-dimensional colonies, while mouse ESCs form tight, three-dimensional colonies. It is been extremely difficult to propagate human ESCs from a single cell, which prevents the creation of genetically manipulated human embryonic stem cell lines.

In previous work, Geijsen and his colleagues demonstrated that the growth factor conditions under which stem cells are maintained in culture play an important role in defining the cells' functional properties. Since the growth factors appeared to make such a difference, the researchers tried to make a more useful human pluripotent cell using a new approach. They derived human induced pluripotent stem cells (iPSCs) -- which are created by reprogramming adult cells and have many of the characteristics of human ECSs, including resistance to manipulation -- in cultures containing the growth factor LIF, which is used in the creation of mouse ESCs.

The resulting cells visibly resembled mouse ESCs and proved amenable to a standard gene manipulation technique that exchanges matching sequences of DNA, allowing the targeted deactivation or correction of a specific gene. The ability to manipulate these new cells depended on both the continued presence of LIF and expression of the five genes that are used in reprogramming adult cells into iPSCs. If any of those factors was removed, these hLR5- (for human LIF and five reprogramming factors) iPSCs reverted to standard iPSCs.

"Genetic changes introduced into hLR5-iPSCs would be retained when they are coverted back to iPSCs, which we then can use to generate cell lines for future research, drug development and someday stem-cell based gene-correction therapies," says Geijsen. He is an assistant professor of Medicine at Harvard Medical School and a principal faculty member of the Harvard Stem Cell Institute.

Co-authors of the Cell Stem Cell paper are lead author Christa Buecker, MGH-CRM and Harvard Stem Cell Institute (HSCI); Hsu-Hsin Chen, PhD, Laurence Dahern, and Konrad Hochedlinger, PhD, MGH-CRM and HSCI; Patricia Okwieka, MGH-CRM; Jose Polo, PhD, MGH Cancer Center; Lei Bu, PhD, MGH Cardiovascular Research Center; Tahsin Stefan Barakat and Joost Gribnau, PhD, University Medical Center, Rotterdam, The Netherlands; and Andrew Porter, PhD, Imperial College London, U.K. The study was supported by grants from the National Institutes of Health, the Dutch Science Organization, the Gottlieb Daimler and Karl Benz Foundation and the National Science Council of Taiwan.


Journal Reference:
Christa Buecker, Hsu-Hsin Chen, Jose Maria Polo, Laurence Daheron, Lei Bu, Tahsin Stefan Barakat, Patricia Okwieka, Andrew Porter, Joost Gribnau, Konrad Hochedlinger. A Murine ESC-like State Facilitates Transgenesis and Homologous Recombination in Human Pluripotent Stem Cells. Cell Stem Cell, 2010; 6 (6): 535 DOI: 10.1016/j.stem.2010.05.003


(http://www.sciencedaily.com/releases/2010/06/100608182649.htm)

Discovery of Mixer Cells: Mixer Cells Relax Tissue Tension During Embryogenesis

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ScienceDaily (June 9, 2010) — Researchers from CNRS and Université de Nice have recently identified cells that surprisingly change identity during embryogenesis in the Drosophila. By studying these "mixer cells" in a healing model, the scientists demonstrated that they helped to relax tissue tension, allowing perfect intercalation of the epidermis. Published on 8 June in PloS Biology, these findings reveal how tissues adapt at the intercalation stage during embryonic development. They may also open a new path for research in regenerative medicine.

Multi-cellular organisms are made up of different cell types (skin, liver or neuronal cells, etc.). Deriving from non-specialized precursor cells, they become specialized as a result of a differentiation mechanism. In addition, during embryonic development, the cells are organized into separate, independent compartments that are essential to the correct assembly of organs (1). Within these compartments, the cells comply with two rules: once differentiated they retain their specific identity, and cells in a given compartment remain together, never mixing with those from another compartment.

The scientists carried out their study on Drosophila embryos (2) during "dorsal closure." During this key stage of morphogenesis (3) in the Drosophila, two epidermises meet and close together. This tissue intercalation is similar to the healing of a wound after a cut, and thus constitutes a good model for healing. By observing living embryos during the period of dorsal closure, the researchers observed one cell type that broke the two rules mentioned above. Indeed, these "mixer cells" were able to change both identity and then compartment, under the normal conditions of embryonic development (e.g. without any lesion). This shift of identity, or cell plasticity, was already known in a pathological setting (regeneration following a wound or disease, etc.) when, in most cases, the re-differentiation of a cell requires one or more cellular divisions. In this case, cell plasticity occurred without such an event. The researchers demonstrated that it was controlled by specific genes that also intervene in tissue regeneration in the adult Drosophila: these genes constitute the JNK signaling pathway that also exists in vertebrates. This genetically-controlled cell plasticity mechanism is an unique type of cellular behavior that had never previously been observed during embryonic development.

Once differentiated, the mixer cells moved from one compartment to another, even though their boundaries were reputed to be impenetrable. Furthermore, tissue tension diminished as the number of cells that migrated to the destination compartment increased. The scientists discovered that by means of an as yet unknown process, the cell plasticity mechanism of mixer cells induced intercalation movements of nearby cells, thus endowing the tissues with an ability to adapt to the variations in tension that occur during embryonic morphogenesis. To achieve this, a zone called "relaxation compartment" was created: this allowed tissues (in this case, the epidermis) to relax their tension during tissue intercalation. In this way, the intercalation of tissues during dorsal closure in the Drosophila embryo (a phenomenon similar to that of epidermal healing) could occur perfectly, i.e. without any visible scar.

This work has demonstrated a novel cell plasticity mechanism during morphogenesis. In view of the similarities observed between the phenomenon of tissue intercalation studied here and skin healing, these results may provide a new path for the study of the cell mechanisms involved in the healing process.

(1) These compartments are called segments in insects or rhombomeres in vertebrates' forebrain.

(2) this organism is very often used as model

(3) Morphogenesis is a stage of embryogenesis during which the forms and organs of an organism develop.


Journal Reference:
Melanie Gettings, Fanny Serman, Raphaël Rousset, Patrizia Bagnerini, Luis Almeida, Stéphane Noselli. JNK Signalling Controls Remodelling of the Segment Boundary through Cell Reprogramming during Drosophila MorphogenesisNK Signalling Controls Remodelling of the Segment Boundary through Cell Reprogramming during Drosophila Morphogenesis. PloS Biology, June 8, 2010 DOI: 10.1371/journal.pbio.1000390


(http://www.sciencedaily.com/releases/2010/06/100609094138.htm)

New Shortcut to Cell Growth

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ScienceDaily (June 8, 2010) — People have them, cats have them and whales have some, too. Neurons, those interlinked nerve cells that carry sensations including pain, stretch from our spinal cords to the tips of our toes, paws or fins. According to a new study published in the journal Cell, scientists from the Harvard Medical School, the University of Montreal and the Dana-Farber Cancer Institute have found a new way by which nerve cells relay information that tell them to grow from millimeters to meters in length.

In other words, the researchers found a new signaling pathway that charters the course for cell progression to allow their growth. The team made an intriguing connection between nerve cells and a receptor called DCC (Deleted in Colorectal Carcinoma). The discovery means cells perform functions in unimagined ways -- challenging previous views on how cells respond to their environment -- that could prove beneficial in cell growth following nerve damage or detrimental in diseases such as cancer.

"We found an alternate way that helps nerve cells respond quickly and locally," says co-author Philippe P. Roux, a professor of pathology and cell biology and a researcher at the University of Montreal Institute for Research in Immunology and Cancer (IRIC). "This is just the beginning, since our findings suggest that more cellular receptors may function in the same way."

Dr. Roux, who is also Canada Research Chair in Signal Transduction and Proteomics, says the study could potentially open new treatment avenues: "We can envisage manipulating this alternate mechanism to make cells respond locally to their environment. Our findings mean that scientists must consider a new way that cells organize themselves to perform essential functions."

This study was supported by the National Institutes of Health, Canadian Cancer Society Research Institute, Howard Hughes Medical Institute, Canadian Institutes of Health Research and Human Frontier Science Program Organization.

Journal Reference:
Tcherkezian et al. Transmembrane Receptor DCC Associates with Protein Synthesis Machinery and Regulates Translation. Cell, 2010; 141 (4): 632 DOI: 10.1016/j.cell.2010.04.008


(http://www.sciencedaily.com/releases/2010/06/100608135034.htm)

Biosensors Reveal How Single Bacterium Gets the Message to Split Into a Swimming and a Stay-Put Cell

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ScienceDaily (June 4, 2010) — Some species of bacteria perform an amazing reproductive feat. When the single-celled organism splits in two, the daughter cell -- the swarmer -- inherits a propeller to swim freely. The mother cell builds a stalk to cling to surfaces.

University of Washington (UW) researchers and their colleague at Stanford University designed biosensors to observe how a bacterium gets the message to divide into these two functionally and structurally different cells. The biosensors can measure biochemical fluctuations inside a single bacteria cell, which is smaller than an animal or plant cell.

During cell division, a signaling chemical, found only in bacteria, helps determine the fate of the resulting two cells. The signal is a tiny circular molecule called cyclic diguanosine monophosphate or c-di-GMP.

By acting as an inside messenger responding to information about the environment outside the bacteria cell, c-di-GMP is implicated in several bacterial survival strategies. In harmless bacteria, some of these tactics keep them alive through harsh conditions. In disease-causing bacteria, c-di-GMP is thought to regulate antibiotic resistance, adhesiveness, biofilm formation, and cell motility.

In their study, the UW-led team of scientists looked at cell division in a species of disease bacteria that fends off treatment and establishes a stronghold by using these defenses, Pseudomonas aeruginosa. This is the rod-shaped pathogen that causes life-shortening, chronic lung infections in people with cystic fibrosis, burns, and suppressed immune systems associated with cancer. The researchers also examined cell-division in a harmless lake and stream dwelling bacteria, Caulobacter crescentus.

The researchers' findings will be published in the June 4 Science. The senior author is Dr. Samuel Miller, UW professor of medicine, microbiology, immunology, and genome science. Miller directs the Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research. The lead author is Dr. Matthias Christen, a UW postdoctoral fellow in immunology who has moved on to become a faculty member in the Biozentrum at the University of Basel, Switzerland.

To monitor the concentration of c-di-GMP within single living bacteria cells, the scientists developed a biosensor based on genetically encoded fluorescence resonance energy transfer.

C-di-GMP exerts control over several biological functions inside the cell by linking up with a diverse array of receptors. These include proteins required to build and drive waving, hair-like structures for moving cell. These also include riboswitches -- RNA molecules, transcription factors and proteins --that can alter gene activity.

Because C-di-GMP controls many different cell functions, the researchers believed it was highly likely that it manages its regulatory workload by appearing in the right amount, in the right place, at the right time in the cell cycle.

The researchers observed the living bacteria under a microscope that measures changes in fluorescent emissions from the biosensor. Emissions drop when the biosensor binds to c-di-GMP. Lower emissions reflected higher levels of c-di-GMP in the cell, and vice versa. In this way the researchers could record fluctuations in c-di-GMP levels during cell division

The researchers found that, immediately after a thin partition formed creating two distinct cells, the levels of c-di-GMP were low in the cell propelled by the whipping flagella and five times higher in the non-motile stalk cell. This asymmetrical distribution of the regulatory messenger occurred in both species of bacteria and was not an isolated event.

"In both organisms," the researchers noted, "c-di-GMP levels were always significantly lower in the flagellated cell than in the non-flagellated cell."

Some of the enzymes that sense the c-di-GMP messages are place-bound in distinct locations of the cell. The researchers reasoned that the unequal distribution of the messenger c-di-GMP might be caused by the spatially restricted production or activation (or inactivation) of these enzymes. The researchers found that strains of bacteria that produce more of these enzymes in the swarmer cell also had higher concentrations of c-di-GMP in the swarmer cell, suggesting that a localized drop in the enzyme activity would likely result in a localized drop in c-di-GMP.

Impairing the cellular distribution of c-di-GMP, the researchers noted, has major consequences for the development and function Caulobacter cells. Mixing the balance of the sensing enzymes would lead to a swarmer cell that couldn't swim or to a hypermotile swarmer cell, depending on how the balance of enzymes is tipped. The normal drop of c-di-GMP might also spur rapid take off of the swarmer as it swims away from its mother cell. Less than an hour later, the swarmer can no longer swim, and reverts to a stalk cell.

The researchers have also used the biosensor they developed to study the multi-flagellated Salmonella enterica, which causes food poisoning, as well as the non-flagellated Klebsiella pneumoniae, an air-borne lung pathogen. Both of these bacteria also have uneven distribution of a key internal messenger during cell division.

"This suggests that this phenomenon is not unique to Pseudomonas and Caulobacter," the researchers surmised, "and that cell properties other than motility are likely to be regulated by asymmetrical second-messenger distribution during cell division."

The asymmetrical distribution of c-di-GMP observed during cell division, the researcher added, may be an important regulatory step in making and powering nano-scale tools on the outside surface of the cell to carry out essential activities.

In addition to Miller, Hoffman, and Matthias Christen, the other scientists on this project were Hemantha Kulasekara of the UW Department of Immunology; Beat Christen of the Department of Developmental Biology at Stanford University; Bridget Kulasekara of the UW Molecular Cell Biology Program, and Luke Hoffman of the UW Department of Pediatrics. Hoffman is also a pediatrician specializing in lung disease at Seattle Children's.

The research was supported by grants from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, the Swiss National Foundation, the Novartis Foundation, the Cystic Fibrosis Foundation, and a graduate research fellowship from the National Science Foundation.

Journal Reference:
Matthias Christen, Hemantha D. Kulasekara, Beat Christen, Bridget R. Kulasekara, Lucas R. Hoffman, Samuel I. Miller. Asymmetrical Distribution of the Second Messenger c-di-GMP upon Bacterial Cell Division. Science, 4 June 2010: Vol. 328. no. 5983, pp. 1295 - 1297 DOI: 10.1126/science.1188658


(http://www.sciencedaily.com/releases/2010/06/100603140957.htm)

Study of microRNA Helps Scientists Unlock Secrets of Immune Cells

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ScienceDaily (June 7, 2010) — With the rapid and continuous advances in biotechnology, scientists are better able to see inside the nucleus of a cell to unlock the secrets of its genetic material. However, what happens outside of the nucleus has, in many ways, remained a mystery. Now, researchers with the National Institutes of Health are closer to understanding how activity outside of the nucleus determines a cell's behavior. They looked at mouse immune cells and examined the types, amount, and activity of microRNAs, genetic components that help regulate the production of proteins.

Their study provides a map to the variety of microRNAs contained within mouse immune cells and reveals the complexity of cellular protein regulation. The study appears online in the journal Immunity.

An organism is made up of cells containing genetic material in the form of deoxyribonucleic acid (DNA) residing within the nucleus. An organism's entire collection of DNA is called its genome and consists of genes, short segments of DNA that code for proteins, and many long segments of DNA that do not contain genes. While each cell contains the entire genome, not all of a cell's genes are making proteins all of the time. Which genes are turned on and which are turned off, and when, determine the behavior of a cell, such as the type of cell it becomes, where it goes, and what it does.

"A plethora of cellular functions, ranging from development, differentiation, metabolism, and host defense, are impacted by protein levels," said Rafael Casellas, Ph.D., the study's principal investigator from the Genomics and Immunity Group of the NIH's National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS). " We were interested in discovering how microRNAs contribute to the regulation of these functions."

A cell makes proteins through a process called transcription, in which genes are copied from DNA into messenger ribonucleic acid (RNA), which travels from the nucleus into the body of the cell. Not all RNA transcribed from DNA are messenger RNA, however. There are many other forms of RNA that do not code for proteins. MicroRNAs (miRNAs), for example, are small strands of RNA that modulate the production of proteins from messenger RNA, thereby helping to regulate protein levels in the cell. Previous studies have shown that cells are very sensitive to fluctuations in miRNA levels, which require tight control in order to regulate protein activity effectively.

In the current study, the NIH scientists used a new microsequencing technology to comprehensively identify all of the different miRNAs existing in mouse immune cells. In addition to increasing the number of known miRNAs, the scientists also discovered several cellular mechanisms that regulate miRNA abundance. The study found that some miRNA constructs exist in a dormant state within the nucleus until they receive signals from the epigenome to become active. The epigenome regulates transcription and comprises all of the non-genetic material in the nucleus. Other miRNAs, the researchers determined, are not hampered by these epigenetic mechanisms and are controlled simply through transcription. However, for some of these miRNAs, abundance depends upon the amount of target messenger RNA available in the cell.

According to NIAMS Director Stephen I. Katz, M.D., Ph.D., "The data generated from this study represent a useful tool for immunologists and cell biologists to use for future studies on functional aspects of the immune system and basic miRNA biology."


Journal Reference:
Kuchen et al. Regulation of MicroRNA Expression and Abundance during Lymphopoiesis. Immunity, 2010; DOI: 10.1016/j.immuni.2010.05.009



(http://www.sciencedaily.com/releases/2010/06/100605131811.htm)

A Turn-Off for Cancer

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ScienceDaily (June 7, 2010) — TAU discovers an ancient "switch" in plants that could halt cancer metastasis

Although plants and animals are very different organisms, they share a surprising number of biological mechanisms. A plant biologist at Tel Aviv University says that one of these mechanisms may be the answer for turning off cancer growth in humans.

Prof. Shaul Yalovsky, of the Molecular Biology and Ecology of Plants Department at Tel Aviv University, has identified a "switch" that can turn on cell growth in plants. Now, in a laboratory setting, he can apply the mechanism to reshape cells, grow new tissues, and respond to bacterial or viral invaders.

The switch is actually a fat molecule that modulates a group of proteins called ROPs. Reported in the scientific journal Current Biology, Prof. Yalovsky's research group, in collaboration with Prof. Yoav Henis and Dr. Joel Hirsch of TAU's Departments of Neurobiology and Biochemistry, has determined that this fat molecule is required for ROP activity. Proteins very similar to ROPs exist in humans and provide chemical signals that tell cancer when to metastasize. Now that they know how to regulate ROPs in plants, the researchers believe they are one step away from turning this ROP-like switch off in humans -- a process which could prevent tumor growth.

An ancient secret revealed

"We've stumbled upon an ancient mechanism that regulates the function of these proteins, proteins which are found in both plants and humans," says Prof. Yalovsky, explaining that this mechanism already regulates the immune response to pathogen invaders in the human body. ROP-like proteins are also involved in wound healing and development of nerve cells in the brain.

"When these proteins are turned 'on,' they can initiate processes like cell division and growth," says Prof. Yalovsky. "Through our genetic engineering, these proteins could be manipulated in humans to speed up tissue healing, or turned off to slow or stop the growth of tumors."

ROPs bind to a small molecule called GTP, which then breaks up into another molecule called GDP. When bound to GDP, ROPs become inactive, a known concept in the plant sciences community. Going one step further, Prof. Yalovsky has created a second type of mutant molecule that prevents ROP proteins from binding to the GTP molecule, creating an inhibitory effect.

A new line of defense

The team's research could also be applied in agriculture to reduce the need for chemical pesticides, they say. The mutant molecule they've devised induces plants to respond as though they are being attacked by pathogens. They then create a biological defense that protects them from infection.

In the research paper, the Tel Aviv University scientists describe how these mutations and mechanisms work, providing a new mechanism to control metastasis in cancer, or stop the deterioration of certain nerve cells in the brain. And in a broader sense, the researchers have created a long-desired platform to test the function of proteins.

"It is common for plant and animal geneticists to identify proteins, but remain unaware of their functions. We now have a mechanism to test our hypotheses," adds Prof. Yalovsky.

(http://www.sciencedaily.com/releases/2010/06/100607142219.htm)

Using Nature's Design Principles to Create Specialized Nanofabrics

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ScienceDaily (June 3, 2010) — In nature, cells and tissues assemble and organize themselves within a matrix of protein fibers that ultimately determines their structure and function, such as the elasticity of skin and the contractility of heart tissue. These natural design principles have now been successfully replicated in the lab by bioengineers at the Wyss Institute for Biologically Inspired Engineering and the School of Engineering and Applied Sciences (SEAS) at Harvard University.

The bioengineers have developed a new technology that can be used to regenerate heart and other tissues and to make nanometer-thick fabrics that are both strong and extremely elastic. The key breakthrough came in the development of a matrix that can assemble itself through interaction with a thermosensitive surface. The protein composition of that matrix can be customized to generate specific properties, and the nanofabric can then be lifted off as a sheet by altering temperature.

"To date it has been very difficult to replicate this extracellular matrix using manmade materials," said Adam W. Feinberg, a Postdoctoral Fellow at Harvard University who will be an Assistant Professor at Carnegie Mellon University in the fall. "But we thought if cells can build this matrix at the surface of their membranes, maybe we can build it ourselves on a surface too. We were thrilled to see that we could."

Feinberg is the lead author of the study, which appears in the current issue of Nano Letters, a publication of the American Chemical Society. Coauthor Kit Parker is a core faculty member of the Wyss Institute, the Thomas D. Cabot Associate Professor of Applied Science and Associate Professor of Bioengineering at SEAS, and a member of the Harvard Stem Cell Institute.

In the area of tissue regeneration, their technology, which is termed protein nanofabrics, represents a significant step forward. Current methods for regenerating tissue typically involve using synthetic polymers to create a scaffolding. But this approach can cause negative side effects as the polymers degrade. By contrast, nanofabrics are made from the same proteins as normal tissue, and thus the body can degrade them with no ill effects once they are no longer needed. Initial results have produced strands of heart muscle similar to the papillary muscle, which may lead to new strategies for repair and regeneration throughout the heart.

"With nanofabrics, we can control thread count, orientation, and composition, and that capability allows us to create novel tissue engineering scaffolds that direct regeneration," said Parker. "It also enables us to exploit the nanoscale properties of these proteins in new ways beyond medical applications. There are a broad range of applications for this technology using natural, or designer, synthetic proteins."

High-performance textiles are the second main application for this technology. By altering the type of protein used in the matrix, researchers can manipulate thread count, fiber orientation, and other properties to create fabrics with extraordinary properties. Today, an average rubber band can be stretched 500 to 600 percent, but future textiles may be stretchable by as much as 1,500 percent. Future applications for such textiles are as diverse as form-fitting clothing, bandages that accelerate healing, and industrial manufacturing.

The research is part of a larger program in Nanotextiles at the Wyss Institute and SEAS. In the same issue of Nano Letters, Parker's team also reported on the development of a new technology that fabricates nanofibers using a high-speed, rotating jet and nozzle. This invention has potential applications ranging from artificial organs and tissue regeneration to clothing and air filters.

"The Wyss Institute is very proud to be associated with two such significant discoveries," said Donald E. Ingber, M.D., Ph.D., Founding Director of the Wyss Institute. "These are great examples of realizing our mission of using Nature's design principles to develop technologies that will have a huge impact on the way we live."

The Wyss Institute works as an alliance among Harvard's schools of Medicine, Engineering, and Arts & Sciences in partnership with Beth Israel Deaconess Medical Center, Children's Hospital, Dana Farber Cancer Institute, the University of Massachusetts Medical School, and Boston University.

By emulating Nature's principles for self-organizing and self-regulating, Wyss researchers are developing innovative new solutions for healthcare, energy, architecture, robotics, and manufacturing. These technologies are translated into commercial products and therapies through collaborations with clinical investigators and corporate alliances.

The researchers acknowledge the support of the Nanoscale Science and Engineering Center at Harvard, the Materials Research Science and Engineering Center at Harvard, Harvard Center for Nanoscale Systems, the Defense Advanced Research Projects Agency, and the Wyss Institute for Biologically Inspired Engineering at Harvard.


Journal Reference:
Adam W. Feinberg, Kevin Kit Parker. Surface-Initiated Assembly of Protein Nanofabrics. Nano Letters, 2010; 100520125126081 DOI: 10.1021/nl100998p


(http://www.sciencedaily.com/releases/2010/06/100602152411.htm)

Ancient Viral Invasion Shaped Human Genome

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ScienceDaily (June 6, 2010) — Scientists at the Genome Institute of Singapore (GIS), a biomedical research institute of the Agency for Science, Technology and Research (A*STAR), and their colleagues from the National University of Singapore, Nanyang Technological University, Duke-NUS Graduate Medical School and Princeton University have recently discovered that viruses that ‘invaded’ the human genome millions of years ago have changed the way genes get turned on and off in human embryonic stem (ES) cells.

The study provides definitive proof of a theory that was first proposed in the 1950s by Nobel Laureate in physiology and medicine, Barbara McClintock, who hypothesized that transposable elements, mobile pieces of the genetic material (DNA), such as viral sequences, could be “control elements” that affect gene regulation once inserted in the genome.

This finding is an important contribution to the advancement of stem cell research and to its potential for regenerative medicine. Led by GIS Senior Group Leader Dr Guillaume Bourque, the study was published in Nature Genetics on June 6, 2010.

Through the use of new sequencing technologies, the scientists studied the genomic locations of three regulatory proteins (OCT4, NANOG and CTCF) in human and mouse embryonic stem (ES) cells. Interestingly, while the scientists found a lot of similarities, they also found many differences in the methods and the types of genes that are being regulated in humans. In particular, it was discovered that specific types of viruses that inserted themselves in the human genomes millions of years ago have dramatically changed the gene regulatory network in human stem cells.

"This study is a computational and experimental tour de force. It provides undeniable evidence that some transposable elements, which are too often dismissed as merely junk DNA, are key components of a regulatory code underlying human development," said Dr Cedric Feschotte, Associate Professor of the University of Texas Arlington.

The comparisons between the human and mouse model system in the study of gene regulatory networks help to advance the understanding of how stem cells differentiate into various cell types of the body. “This understanding is crucial in the improved development of regenerative medicine for diseases such as Parkinson’s disease and leukaemia,” said Dr Bourque. “Despite the advantages of using mouse ES cells in the study of gene regulatory networks, further research must focus more directly on human stem cells. This is due to the inherent challenges of converting the results of studies done from one species to that of the next. More research will need to be done in both human and non-human primate stem cells for findings on stem cells to be used in clinical application.”

Prof Raymond L. White, PhD, Rudi Schmid Distinguished Professor of Neurology, University of California said, “The paper reports very exciting new findings that establish a new and fundamentally distinct mechanism for the regulation of gene expression. By comparing the genomes of mouse with human, the scientists were able to show that the binding sites for gene regulatory factors are very often not in the same place between the two species. This by itself would be very surprising, but the investigators go further and demonstrate that many of the sites are imbedded within a class of DNA sequences called “transposable” elements because of their ability to move to new places in the genome. There are a number of such elements believed to be the evolutionary remnants of viral genomes, but it was very surprising to learn that they were carrying binding sites for regulatory elements to new locations. These changes in regulation would be expected to create major changes in the organisms which carry them. Indeed, many think that regulatory changes are at the heart of speciation and may have played a large role in the evolution of humans from their predecessors. This is likely to be a landmark paper in the field.”

Dr Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute and Director of the Genomics Division at Lawrence Berkeley National Laboratory in Berkeley added, "This study using a comparative genomics strategy discovered important human specific properties of the regulatory network in human ES cells. This information is significant and should contribute to helping move the regenerative medicine field forward.”


Journal Reference:
Kunarso et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nature Genetics, 2010; DOI: 10.1038/ng.600


(http://www.sciencedaily.com/releases/2010/06/100607101652.htm)

Scientists Capture Very Moment Blood Flow Begins

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ScienceDaily (June 5, 2010) — By capturing movies of both the blood and vasculature of zebrafish embryos, each less than two millimeters long, researchers have been able for the first time to see the very moment that blood begins to flow.

The observations, reported online on June 3rd in Current Biology, show that the earliest blood flow, involving what appear to be hundreds of cells, begins all at once.

Remarkably, that onset of life-giving circulation takes more than a beating heart. In fact, red blood cells remain stuck to the blood vessel wall initially, even after the heart starts to beat, says Atsuko Sehara-Fujisawa of Kyoto University.

"When most of the red blood cells finish their invasion into the vasculature, they are released into the circulation almost simultaneously," she says. "We could show that those blood cells release themselves into the flow, using 'molecular scissors' to disrupt their adhesion to blood vessels and enter the circulation dependent on plasma flow. Without those scissors, blood cells stagnate on the blood vessel wall."

Those molecular scissors come in the form of a protease enzyme known as ADAM8, the researchers report.

These findings raise an obvious question: Why would the onset of primitive blood circulation require such an active protease instead of just going with the flow, with blood cells entering the circulation one by one? First, the researchers say, proteolysis would allow for control over which blood cells enter the circulation and which get held back. It might also help to stop blood cells from entering the circulation too early, preventing leaks that might occur if blood vessels aren't fully formed, or avoiding stagnation before an adequate flow of plasma is established with the heartbeat, the researchers add. It may be that blood cells need plasma to flow before they can reach maturity.

The findings likely have application to other types of blood cells in zebrafish and to blood flow in other animals, even humans, the researchers say, noting that ADAM8 is found at high levels in the blood of humans and mice into adulthood.

The researchers include Atsuo Iida, Kyoto University, Kyoto, Japan; Kazuya Sakaguchi, Kyoto University, Kyoto, Japan; Kiyoaki Sato, Kyoto University, Kyoto, Japan; Hidetoshi Sakurai, Kyoto University, Kyoto, Japan; Daigo Nishimura, Kyoto University, Kyoto, Japan; Aya Iwaki, Kyoto University, Kyoto, Japan; Miki Takeuchi, University of Tsukuba, Tsukuba, Japan; Makoto Kobayashi, University of Tsukuba, Tsukuba, Japan; Kazuyo Misaki, RIKEN Center for Developmental Biology, Kobe, Japan; Shigenobu Yonemura, RIKEN Center for Developmental Biology, Kobe, Japan; Atsuo Kawahara, Kyoto University, Kyoto, Japan; and Atsuko Sehara-Fujisawa, Kyoto University, Kyoto, Japan.

Journal Reference:
Atsuo Iida, Kazuya Sakaguchi, Kiyoaki Sato, Hidetoshi Sakurai, Daigo Nishimura, Aya Iwaki, Miki Takeuchi, Makoto Kobayashi, Kazuyo Misaki, Shigenobu Yonemura, Atsuo Kawahara, and Atsuko Sehara-Fujisawa. Metalloprotease-Dependent Onset of Blood Circulation in Zebrafish. Current Biology, DOI: 10.1016/j.cub.2010.04.052

(http://www.sciencedaily.com/releases/2010/06/100603123711.htm)

Gene Related to Aging Plays Role in Stem Cell Differentiation

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ScienceDaily (June 5, 2010) — A gene shown to play a role in the aging process appears to play a role in the regulation of the differentiation of embryonic stem cells, according to researchers from the Center for Stem Cell Biology and Regenerative Medicine and the Department of Medicine at Thomas Jefferson University.

In the study, published online in the journal Aging Cell, the researchers identified a protein interaction that controls the silencing of Oct4, a key transcription factor that is critical to ensuring that embryonic stem cells remain pluripotent. The protein, WRNp, is the product of a gene associated with Werner syndrome, an autosomal recessive disorder hallmarked by premature aging. The gene expression in Werner syndrome closely resembles that of normal aging, and as a result, Werner syndrome is an accepted model of aging.

They first found that WRNp accumulates at the Oct4 promoter in differentiating stem cells. They then found that WRNp interacts with another protein called Dnmt3b to control DNA methylation at the Oct4 promoter, according to researchers led by René Daniel, M.D., Ph.D., associate professor of Medicine.

Previously, Dnmt3b was identified to be a key player in the DNA methylation of the Oct4 promoter. DNA methylation of the Oct4 promoter inactivates the Oct4 gene. The inactivation, or silencing, of this gene is necessary for stem cell differentiation.

"We showed that the depletion of WRNp blocked the recruitment of Dnmt3b to the Oct4 promoter, and resulted in reduced methylation," Dr. Daniel said. "The reduced DNA methylation was associated with continued Oct4 expression, which resulted in attenuated differentiation."

Until now, the focus of studies on the role of WRNp in aging has been on telomeres. These studies have shown that telomeres undergo accelerated shortening and loss in Werner syndrome cells. But it remains to be shown if this is the major role that WRNp plays in the aging process.

"These results reveal a novel function of WRNp, and demonstrate that WRNp controls a key step in pluripotent stem cell differentiation," Dr. Daniel said. "Our data support the emerging hypothesis that attenuated stem cell differentiation is involved in aging. This lack of differentiated cells may contribute to failure to maintain organ or tissue function in the later stages of life."


Journal Reference:
Johanna A. Smith, Abibatou M. N. Ndoye, Kyla Geary, Michael P. Lisanti, Olga Igoucheva, René Daniel. A role for the Werner syndrome protein in epigenetic inactivation of the pluripotency factor Oct4. Aging Cell, 2010; : no DOI: 10.1111/j.1474-9726.2010.00585.x


(http://www.sciencedaily.com/releases/2010/06/100604132038.htm)

Biosensors Reveal How Single Bacterium Gets the Message to Split Into a Swimming and a Stay-Put Cell

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ScienceDaily (June 4, 2010) — Some species of bacteria perform an amazing reproductive feat. When the single-celled organism splits in two, the daughter cell -- the swarmer -- inherits a propeller to swim freely. The mother cell builds a stalk to cling to surfaces.

University of Washington (UW) researchers and their colleague at Stanford University designed biosensors to observe how a bacterium gets the message to divide into these two functionally and structurally different cells. The biosensors can measure biochemical fluctuations inside a single bacteria cell, which is smaller than an animal or plant cell.

During cell division, a signaling chemical, found only in bacteria, helps determine the fate of the resulting two cells. The signal is a tiny circular molecule called cyclic diguanosine monophosphate or c-di-GMP.

By acting as an inside messenger responding to information about the environment outside the bacteria cell, c-di-GMP is implicated in several bacterial survival strategies. In harmless bacteria, some of these tactics keep them alive through harsh conditions. In disease-causing bacteria, c-di-GMP is thought to regulate antibiotic resistance, adhesiveness, biofilm formation, and cell motility.

In their study, the UW-led team of scientists looked at cell division in a species of disease bacteria that fends off treatment and establishes a stronghold by using these defenses, Pseudomonas aeruginosa. This is the rod-shaped pathogen that causes life-shortening, chronic lung infections in people with cystic fibrosis, burns, and suppressed immune systems associated with cancer. The researchers also examined cell-division in a harmless lake and stream dwelling bacteria, Caulobacter crescentus.

The researchers' findings will be published in the June 4 Science. The senior author is Dr. Samuel Miller, UW professor of medicine, microbiology, immunology, and genome science. Miller directs the Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research. The lead author is Dr. Matthias Christen, a UW postdoctoral fellow in immunology who has moved on to become a faculty member in the Biozentrum at the University of Basel, Switzerland.

To monitor the concentration of c-di-GMP within single living bacteria cells, the scientists developed a biosensor based on genetically encoded fluorescence resonance energy transfer.

C-di-GMP exerts control over several biological functions inside the cell by linking up with a diverse array of receptors. These include proteins required to build and drive waving, hair-like structures for moving cell. These also include riboswitches -- RNA molecules, transcription factors and proteins --that can alter gene activity.

Because C-di-GMP controls many different cell functions, the researchers believed it was highly likely that it manages its regulatory workload by appearing in the right amount, in the right place, at the right time in the cell cycle.

The researchers observed the living bacteria under a microscope that measures changes in fluorescent emissions from the biosensor. Emissions drop when the biosensor binds to c-di-GMP. Lower emissions reflected higher levels of c-di-GMP in the cell, and vice versa. In this way the researchers could record fluctuations in c-di-GMP levels during cell division

The researchers found that, immediately after a thin partition formed creating two distinct cells, the levels of c-di-GMP were low in the cell propelled by the whipping flagella and five times higher in the non-motile stalk cell. This asymmetrical distribution of the regulatory messenger occurred in both species of bacteria and was not an isolated event.

"In both organisms," the researchers noted, "c-di-GMP levels were always significantly lower in the flagellated cell than in the non-flagellated cell."

Some of the enzymes that sense the c-di-GMP messages are place-bound in distinct locations of the cell. The researchers reasoned that the unequal distribution of the messenger c-di-GMP might be caused by the spatially restricted production or activation (or inactivation) of these enzymes. The researchers found that strains of bacteria that produce more of these enzymes in the swarmer cell also had higher concentrations of c-di-GMP in the swarmer cell, suggesting that a localized drop in the enzyme activity would likely result in a localized drop in c-di-GMP.

Impairing the cellular distribution of c-di-GMP, the researchers noted, has major consequences for the development and function Caulobacter cells. Mixing the balance of the sensing enzymes would lead to a swarmer cell that couldn't swim or to a hypermotile swarmer cell, depending on how the balance of enzymes is tipped. The normal drop of c-di-GMP might also spur rapid take off of the swarmer as it swims away from its mother cell. Less than an hour later, the swarmer can no longer swim, and reverts to a stalk cell.

The researchers have also used the biosensor they developed to study the multi-flagellated Salmonella enterica, which causes food poisoning, as well as the non-flagellated Klebsiella pneumoniae, an air-borne lung pathogen. Both of these bacteria also have uneven distribution of a key internal messenger during cell division.

"This suggests that this phenomenon is not unique to Pseudomonas and Caulobacter," the researchers surmised, "and that cell properties other than motility are likely to be regulated by asymmetrical second-messenger distribution during cell division."

The asymmetrical distribution of c-di-GMP observed during cell division, the researcher added, may be an important regulatory step in making and powering nano-scale tools on the outside surface of the cell to carry out essential activities.

In addition to Miller, Hoffman, and Matthias Christen, the other scientists on this project were Hemantha Kulasekara of the UW Department of Immunology; Beat Christen of the Department of Developmental Biology at Stanford University; Bridget Kulasekara of the UW Molecular Cell Biology Program, and Luke Hoffman of the UW Department of Pediatrics. Hoffman is also a pediatrician specializing in lung disease at Seattle Children's.

The research was supported by grants from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, the Swiss National Foundation, the Novartis Foundation, the Cystic Fibrosis Foundation, and a graduate research fellowship from the National Science Foundation.


Journal Reference:
Matthias Christen, Hemantha D. Kulasekara, Beat Christen, Bridget R. Kulasekara, Lucas R. Hoffman, Samuel I. Miller. Asymmetrical Distribution of the Second Messenger c-di-GMP upon Bacterial Cell Division. Science, 4 June 2010: Vol. 328. no. 5983, pp. 1295 - 1297 DOI: 10.1126/science.1188658


(http://www.sciencedaily.com/releases/2010/06/100603140957.htm)

Gates Open on Understanding Potassium Channel Controls

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ScienceDaily (June 4, 2010) — Walter and Eliza Hall Institute scientists have made a significant advance in understanding how potassium channels, which permit the flow of electric currents central to many of the body's biological processes, control the flow of these currents.

Dr Jacqui Gulbis from the institute's Structural Biology division, who led the research, said previous studies that had identified what potassium channels look like had provided valuable insights into how they work. However, the way the channels open and close in response to regulatory signals has not been well understood.

"Potassium currents are central to many cellular processes, and particularly communication between cells," Dr Gulbis said.

"In the central nervous system, for example, electrical signaling underlies perception and movement; whilst in the heart, cardiac contraction relies upon the rhythmic ebb-and-flow of potassium. The electricity comes from the tiny charge associated with each potassium ion.

"Just as one would use a light switch to turn electrical current on and off, potassium channels use molecular gates to switch conduction on and off in response to physiological signals," Dr Gulbis said. "However, the nature of the gates and the gating process has remained unclear."

Potassium channels are specialised pores in cell membranes. They have a signature region termed the ion selectivity filter, which is responsible for ensuring that only potassium, and not sodium, permeates the membrane.

Dr Gulbis, with Mr Oliver Clarke, Dr Brian Smith and Mr Alex Caputo from the institute's Structural Biology division, in collaboration with Dr Jamie Vandenberg and Dr Adam Hill from the Victor Chang Cardiac Research Institute, has illuminated key aspects of the gating process.

Although previous studies have implicated a constriction in the ion conduction pathway in gating, this study describes a gate that is located in the ion selectivity filter.

Using the Australian Synchrotron, Dr Gulbis's team determined that once the conformation of a regulatory domain -- which is the part of the channel that sits inside the cell -- changes, it allows the selectivity filter to act as an on/off switch.

The findings have been published June 3 in the journal Cell.

The research was supported by the National Health and Medical Research Council and the Victorian Government.


Journal Reference:
Oliver B. Clarke, Alessandro T. Caputo, Adam P. Hill, Jamie I. Vandenberg, Brian J. Smith, Jacqueline M. Gulbissend. Domain Reorientation and Rotation of an Intracellular Assembly Regulate Conduction in Kir Potassium Channels. Cell, June 3, 2010 DOI: 10.1016/j.cell.2010.05.003


(http://www.sciencedaily.com/releases/2010/06/100603123717.htm)

Stem Cell Researchers Uncover Previously Unknown Patterns in DNA Methylation

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ScienceDaily (June 2, 2010) — A previously unknown pattern in DNA methylation -- an event that affects cell function by altering gene expression -- has been uncovered for the first time by stem cell researchers at UCLA, a finding that could have implications in preventing some cancers and correcting defects in human stem cell lines.

The team of scientists discovered a relationship between DNA methylation and the positioning of nucleosomes, which compact and regulate access to DNA in the nucleus of a cell. The discovery was made using high-throughput DNA sequencing to study the sites on DNA where high levels of methylation were occurring, said Matteo Pellegrini and Steve Jacobsen, researchers with the Broad Stem Cell Research Center at UCLA and senior co-authors of the study.

The study appeared Sun., May 30, 2010 in the early online edition of the peer-reviewed journal Nature.

The processes required for the survival of a cell depend on the cell's ability to store and read the genetic information encoded in its DNA. Packaging the long DNA into a tiny nucleus is complicated because the DNA still needs to be accessible to the cell's molecular machinery. The molecules that compact DNA are called the nucleosome core particles. Each one has about 147 base pairs of DNA wrapped around it. This interaction forms a sort of scaffolding for compaction of the long DNA polymer, while allowing it to be accessible for events such as methylation.

DNA methylation is important in regulating genes that play a role in the differentiation of embryonic stem cells and in the development of some cancers, Jacobsen said.

"Changes in DNA methylation are behind a lot of what makes a stem cell a stem cell. As the cell differentiates, the DNA methylation tends to change. One aspect of understanding methylation is understanding its pattern and how it's laid out within the cell," said Jacobsen, a professor of molecular, cell and developmental biology and a Howard Hughes Medical Institute investigator.

In this study, the UCLA team found that the DNA wrapped around nucleosomes is more highly methylated than flanking DNA, which links adjacent DNA/nucleosome complexes.

"These results indicate that nucleosome positioning influences DNA methylation patterning throughout the genome and that DNA methyltransfereases (the enzymes that methylates DNA) preferentially target nucloesome-bound DNA," said Pellegrini, an associate professor of molecular, cell and developmental biology and an informatics expert.

The work was initially done in Arabidopsis, a mustard weed commonly used in plant research. Once the DNA methylation and nucleosome positioning patterns emerged, they repeated the work in human stem cells. Pellegrini and Jacobsen found similar patterns in the human stem cells.

One of the most important, unknown aspects of DNA methylation, Jacobsen said, is how the cell determines where the event occurs, and the pattern of nucleosome positions has emerged as an important determinant of methylation.

The findings could have implications in fighting cancer because DNA methylation patterns go awry in cancer, often causing tumor suppressor genes to switch off. The more scientists know about the cellular mechanisms that lay down the correct DNA methylation patterns, the more that process can be manipulated. In the future, this type of research may lead to techniques that result in the ability to control the patterns that go awry and lead to cancer, thus preventing a malignancy.

And because DNA methylation is important in stem cell differentiation, this knowledge could lead to ways to correct defects in stem cells lines in the future.

Funding for the two-year study came from the National Science Foundation, the Howard Hughes Medical Institute and the Broad Stem Cell Research Center at UCLA.


Journal Reference:
Ramakrishna K. Chodavarapu, Suhua Feng, Yana V. Bernatavichute, Pao-Yang Chen, Hume Stroud, Yanchun Yu, Jonathan A. Hetzel, Frank Kuo, Jin Kim, Shawn J. Cokus, David Casero, Maria Bernal, Peter Huijser, Amander T. Clark, Ute Krämer, Sabeeha S. Merchant, Xiaoyu Zhang, Steven E. Jacobsen, Matteo Pellegrini. Relationship between nucleosome positioning and DNA methylation. Nature, 2010; DOI: 10.1038/nature09147


(http://www.sciencedaily.com/releases/2010/06/100602090327.htm)

Jumping Genes Provide Extensive 'Raw Material' for Evolution, Study Finds

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ScienceDaily (June 2, 2010) — Using high-throughput sequencing to map the locations of a common type of jumping gene within a person's entire genome, researchers at the University of Pennsylvania School of Medicine found extensive variation in these locations among the individuals they studied, further underscoring the role of these errant genes in maintaining genetic diversity.

The investigators determined that any two peoples' genomes differ at roughly 285 sites out of the 1139 sites studied. These results were found by scanning the genomes of 25 individuals, 15 of which were unrelated. They report their findings online in Genome Research.

Jumping genes -- also called transposons -- are sequences of DNA that move to different areas of the genome within the same cell.

"The significance of this work is that there is much more diversity in our genome due to insertions by this family of transposons than previously thought," said co-author Haig Kazazian, MD, Seymour Gray Professor of Molecular Medicine, in the Penn Department of Genetics. "This movement of genetic material provides the raw material of genetic evolution, and it doesn't take into account the insertions that we believe occur outside of the sperm and egg cells studied in this project."

Transposons are a source of diversity within a species' gene pool, with implications on many levels. For example, slight changes in genes help organisms adapt and survive in new environments, and populations with genetic diversity are less vulnerable to disease and problems with reproduction.

Insertions into certain spots in the genome can also cause cell function to go awry, so understanding their placement and variation in the human genome is important for a fundamental understanding of disease. Insertions can cause many genetic diseases, such as hemophilia and Duchenne muscular dystrophy, and may play a role in the development of cancer.

Retrotransposons are the major class of jumping genes, with the L1 family the most abundant type of retrotransposon in the human genome. L1s comprise about 17 percent of the human genome and were the subject of the Genome Research paper.

Eventually, continuous jumping by retrotransposons expands the size of the human genome and may cause shuffling of genetic content. For example, when retrotransposons jump, they may take portions of nearby gene sequences with them, inserting these where they land, and thereby allowing for the creation of new genes. Even otherwise unremarkable insertions of L1s may cause significant effects on nearby genes, such as lowering their expression.

Retrotransposons move by having their DNA sequence transcribed or copied to RNA, and then instead of the genetic code being translated directly into a protein sequence, the RNA is copied back to DNA by the retrotransposon's own enzyme called reverse transcriptase. This new DNA is then inserted back into the genome. The process of copying is similar to that of retroviruses, such as HIV, leading scientists to speculate that retroviruses were derived from retrotransposons.

The team also found that on average 1 in 140 individuals have obtained a new L1 insertion from their parents. When all retrotransposon insertions, including L1 and others, are considered about 1 in 40 individuals have received a new insertion from their parents.

The current study counted insertions in the heritable germ cell line, that is in egg and sperm cells. "The real elephant in the room is the question of the incidence of somatic insertions, insertions in cells that aren't eggs or sperm" says Kazazian. "We don't yet know the incidence of those somatic insertions."

Because the insertions detected in this study and others like it are present in some individuals and not others, there is the possibility of association with genetic disease. Future studies in the Kazazian lab funded by an ARRA stimulus grant through the National Institutes of Health will develop techniques to uncover such associations using these retrotransposon insertions as genetic markers.

Adam Ewing, a PhD candidate in the Kazazian lab is the paper's other co-author.

The work was funded by the National Institutes for General Medical Sciences.


Journal Reference:
A. D. Ewing, H. H. Kazazian. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Research, 2010; DOI: 10.1101/gr.106419.110



(http://www.sciencedaily.com/releases/2010/06/100601171838.htm)