What Holds Chromosomes Together - Max Planck Researchers Elucidate the Structure of DNA-Packaging Proteins

SMC-Kleisin-Complex. (Credit: Image courtesy of Max Planck Institute of Biochemistry)

In each cell about two meters of DNA must fit into a cell nucleus that has a diameter of only a few thousandths of a millimeter. There the DNA is organized in individual chromosomes in the form of very long filaments. If they are not equally and accurately distributed to the daughter cells during cell division, this can result in cancer or genetic defects such as trisomy 21. Therefore, to ensure safe transport of DNA during cell division the long and coiled DNA fibers must be tightly packed.

Scientists have only a sketchy understanding of this step. The SMC-kleisin protein complexes play a key role in this process. They consist of two arms (SMC) and a bridge (kleisin). The arms wrap around the DNA like a ring and thus can connect duplicated chromosomes or two distant parts of the same chromosome with each other.

Learning from bacteria
Simple organisms like bacteria also use this method of DNA packaging. The scientists, in collaboration with colleagues from South Korea, have now elucidated the structure of a precursor of human SMC-kleisin complexes of the bacterium Bacillus subtilis. The researchers showed that the bacterial SMC-kleisin complex has two arms made of identical SMC proteins that form a ring. The arms differ in their function only through the different ends of the kleisin protein with which they are connected.

In humans the DNA packaging machinery is similarly organized. “We suspect that this asymmetric structure plays an important role in the opening and closing of the ring around the DNA,” explains Frank Bürmann, PhD student in the research group ‘Chromosome Organization and Dynamics’ of Stephan Gruber. In addition, the scientists discovered how the ends of the kleisin can distinguish between correct and wrong binding sites on one pair of arms.

The cohesion of chromosomes is of critical importance for reproduction as well. In human eggs this cohesion must be maintained for decades to ensure error-free meiosis of the egg cell. Failure of cohesion is a likely cause for decreased fertility due to age or the occurrence of genetic defects such as trisomy 21. “The elucidation of the structure of SMC-kleisin protein complexes is an important milestone in understanding the intricate organization of chromosomes,” says group leader Stephan Gruber
source : http://www.biochem.mpg.de/en/news/pressroom/083_Gruber_Kleisin.html 

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New Look at Cell Membrane Reveals Surprising Organization

Researchers found that a class of molecules called sphingolipds congregate in large patches in the cell membrane. Red and yellow colors indicate local elevations in the sphingolipid abundance.

Using a completely new approach to imaging cell membranes, a study by researchers from the University of Illinois, Lawrence Livermore National Laboratory and the National Institutes of Health revealed some surprising relationships among molecules within cell membranes.
Led by Mary Kraft, a U. of I. professor of chemical and biomolecular engineering, the team published its findings in the Proceedings of the National Academy of Sciences.
Cells are enveloped in semi-permeable membranes that act as a barrier between the inside and outside of the cell. The membrane is mainly composed of a class of molecules called lipids, studded with proteins that help regulate how the cell responds to its environment.
"Lipids have multiple functions serving as both membrane structure and signaling molecules, so they regulate other functions inside the cell," Kraft said. "Therefore, understanding how they're organized is important. You need to know where they are to figure out how they're doing these regulatory functions."
One widely held belief among cell biologists is that lipids in the membrane assemble into patches, called domains, that differ in composition. However, research into how lipids are organized in the membrane, and how that organization affects cell function, has been hampered by the lack of direct observation. Although the cell membrane is heavily studied, the imaging techniques used infer the locations of certain molecules based on assumed associations with other molecules.
In the new study, Kraft's team used an advanced, molecule-specific imaging method that allowed the researchers to look at the membrane itself and map a particular type of lipid on mouse cell membranes. The researchers fed lipids labeled with rare stable isotopes to the cells and then imaged the distribution of the isotopes with high-resolution imaging mass spectrometry.
Called sphingolipids (SFING-go-lih-pids), these molecules are thought to associate with cholesterol to form small domains about 200 nanometers across. The direct imaging method revealed that sphingolipids do indeed form domains, but not in the way the researchers expected.
The domains were much bigger than suggested by prior experiments. The 200-nanometer domains clustered together to form much larger, micrometer-sized patches of sphingolipids in the membrane.
"We were amazed when we saw the first images of the patches of sphingolipids across the cell surface," said Peter Weber, who directed the team at Lawrence Livermore National Laboratory. "We weren't sure if our imaging mass spectrometry method would be sensitive enough to detect the labeled lipids, let alone what we would see."
Furthermore, when the researchers looked at cells that were low on cholesterol -- thought to play a key role in lipid aggregation -- they were surprised to find that the lipids still formed domains. On the other hand, disruption to the cell's structural scaffold seemed to dissolve the lipid clusters.
"We found that the presence of domains was somewhat affected by cholesterol but was more affected by the cytoskeleton -- the protein network underneath the membrane," Kraft said. "The central issue is that the data are suggesting that the mechanism that's responsible for these domains is much more complicated than initially expected."
In addition, the new study found that sphingolipids domains were incompletely associated with a marker protein that researchers have long assumed dwelled where sphingolipids congregated. This means that data collected with imaging techniques that target this protein are not as accurate in representing sphingolipid distribution as previously thought.
"Our data are showing that if you want to know where sphingolipids are, look at the lipid, don't infer where it is based on other molecules, and now there's a way to directly image them," said Kraft, who also is affiliated with the department of chemistry at the U. of I.
Next, the researchers plan to use the direct-imaging method in conjunction with other more conventional methods, such as fluorescence, to further determine the organization of different kinds of molecules in the membrane, their interactions and how they affect the cell's function. They plan to begin by targeting cholesterol.
"Cholesterol abundance is important," Kraft said. "You change that, you tremendously change cell function. How is it organized? Is it also in domains? That's related to the question, what's the mechanism responsible for these structures and what are they doing?"
source: http://news.illinois.edu/news/13/0128cell_membrane_MaryKraft.html

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The cell that isn’t:New technique captures division of membrane-less cells

This may look like yet another video of a dividing cell, but there’s a catch. You are looking at chromosomes (red) being pulled apart by the mitotic spindle (green), but it’s not a cell, because there’s no cell membrane. Like a child sucking an egg out of its shell, Ivo Telley from the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, removed these cellular ‘innards’ from a fruit fly embryo, at a stage when it is essentially a sac full of membrane-less ‘cells’ that divide and divide without building physical barriers to separate themselves from each other.
“It’s the first time we can study ongoing cell division without the cell membrane, and that means we can physically manipulate things,” says Telley, “so we can uncover the physical forces involved, and see what are the constraints.”
The new technique is described in detail today in Nature Protocols, and has already led Telley and colleagues to a surprising discovery. They found that, although successive divisions fill the embryo with more and more material, leaving less and less space for each spindle, and spindles become smaller as the embryo develops, simply squeezing the ‘cell’ into tighter quarters doesn’t make it produce a smaller spindle.
Combined with the genetic manipulation approaches commonly used in fruit fly studies, the scientists believe their new technique will help to unravel this and other mysteries of how a cell becomes two.

In a nutshell:

• New technique allows scientists to study cell division without cell membrane
  
• Advantages: can physically constrain and manipulate; can access nuclei normally buried deep in opaque embryo; combinable with wide-ranging fruit fly genetics techniques
  
• Revealed that, surprisingly, confined space not enough to restrict spindle size
   
  
  

 source:http://www.embl.de/aboutus/communication_outreach/media_relations/2013/130117_Heidelberg/index.html

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Protein Folding via Charge Zippers

Membrane proteins are the “molecular machines” in biological cell envelopes. They control diverse processes, such as the transport of molecules across the lipid membrane, signal transduction, and photosynthesis. Their shape, i.e. folding of the molecules, plays a decisive role in the formation of, e.g., pores in the cell membrane. In the Cell magazine, researchers of Karlsruhe Institute of Technology and the University of Cagliari are now reporting a novel charge zipper principle used by proteins to form functional units (DOI: 10.1016/j.cell.2012.12.017)

Like the teeth of a zipper, the charged amino acids (red, blue) form connections between protein segments. In this way, they can form pores in the cell membrane. (Figure: KIT)

“It is fascinating to see the elegant basic principles that are used by nature to construct molecular assemblies,” explains Anne Ulrich, Director of the KIT Institute for Biological Interfaces. “A charge zipper between the charged side chains is an entirely unexpected mechanism used by membrane proteins to neutralize their charges such that they can be immersed into hydrophobic cell membranes.”
In the study published now, Ulrich and her team investigate the so-called Twin-arginine translocase (Tat) that is used in the cell membrane of bacteria as an export machinery for folded proteins. Several TatA subunits assemble as a pore that can adapt its diameter to the size of the cargo to be transported. “But how can such a pore be built up from TatA proteins? How can they reversibly form a huge hole in the membrane for a variety of molecules to pass through, but without causing leakage of the cell?”, Ulrich formulates the questions studied.
To answer these questions, the researchers studied the molecular structure of TatA protein from the bacterium B. subtilis, which consists of a chain of 70 amino acids. The analysis showed that it folds into a rather rigid, rod-shaped helix that is followed by a flexible, extended stretch. Many amino acids in the helix and the adjacent stretch carry positive or negative charges. Surprisingly, the sequence of charges on the helix is complementary to those in the adjacent stretch of the protein. When the protein is folded up at the connection point like a pocket knife, positive and negative charges will always meet and attract each other. Hence, the protein links up both of its segments, similar to the interlocking teeth of a zipper.
“The clou is that this binding principle also works with the neighboring proteins,” Ulrich says. Instead of folding up alone, every TatA protein also forms charge zippers with both of its neighbors. Computer simulations showed that this leads to stable and, at the same time, flexible connections between the adjacent molecules. In this way, any number of proteins can be linked together to form an uncharged ring, which thus lines the TatA pore in the hydrophobic membrane. This novel charge zipper principle does not only seem to play a role in protein transport, but also in the attack of certain antimicrobial peptides on bacteria, or in their formation of biofilms as a response to stress.

source :http://www.kit.edu/visit/pi_2013_12526.php

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IMP Scientists shed light on the “dark matter” of DNA

In each cell, thousands of regulatory regions control which genes are active at any time. Scientists at the Research Institute of Molecular Pathology (IMP) in Vienna have developed a method that reliably detects these regions and measures their activity. The new technology is published online by Science this week.

Fluorescence image of ovarian tissue of the fruit fly.
 DNA is stained in blue, the activity of enhancers is
represented by the green colour.
Copyright: IMP

Genome sequences store the information about an organism’s development in the DNA’s four-letter alphabet. Genes carry the instruction for proteins, which are the building blocks of our bodies. However, genes make up only a minority of the entire genome sequence – roughly two percent in humans. The remainder was once dismissed as “junk”, mostly because its function remained elusive. “Dark matter” might be more appropriate, but gradually light is being shed on this part of the genome, too.

Far from being useless, the non-coding part of DNA contains so-called regulatory regions or enhancers that determine when and where each gene is expressed. This regulation ensures that each gene is only active in appropriate cell-types and tissues, e.g. haemoglobin in red blood cell precursors, digestive enzymes in the stomach, or ion channels in neurons. If gene regulation fails, cells express the wrong genes and acquire inappropriate functions such as the ability to divide and proliferate, leading to diseases such as cancer.

Despite the importance of gene regulatory regions, scientists have been limited in their ability to study them on a genome-wide scale. Their identification relied on indirect means, which were error prone and required tedious experiments for validating and quantifying enhancer activities..

Alexander Stark and his team at the IMP in Vienna now closed this gap with the development of a new technology called STARR-seq (self-transcribing active regulatory region sequencing), published online by Science this week. STARR-seq allows the direct identification of DNA sequences that function as enhancers and simultaneously measures their activity quantitatively in entire genomes. 

Applying their technology to Drosophila cells, the IMP-scientists surprisingly find that the strongest enhancers reside in both regulatory genes that determine the respective cell-types as well as in broadly active “housekeeping” genes that are required for basic cell survival in most or all cells. In addition, they find several enhancers for each active gene, which might provide redundancy to ensure robustness of gene regulation. 

The new method combines advanced sequencing technology and highly specialized know-how in bio-computing. It is a powerful tool which, according to Alexander Stark, will prove immensely valuable in the future. “STARR-seq is like a magic microscope that lets us zoom in on the regulatory regions of DNA. It will be crucial to study gene regulation and how it is encoded in the genome – both during normal development and when it goes wrong in disease.”

source: http://www.alphagalileo.org/ViewItem.aspx?ItemId=127648&CultureCode=en

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Molecular twist helps regulate the cellular message to make histone proteins

 Histone proteins are the proteins that package DNA into chromosomes.  Every time the cell replicates its DNA it must make large amounts of newly made histones to organize DNA within the nucleus.

An imbalance in the production of DNA and histones is usually lethal for the cell, which is why the levels of the messenger RNA (mRNA) encoding the histone proteins must be tightly controlled to ensure the proper amounts of histones (not too many and not too few) are made.

In a collaborative effort published online in the January 18, 2013 issue of the journal Science, researchers at the University of North Carolina and Columbia University show for the first time how two key proteins in messenger RNA communicate via a molecular twist to help maintain the balance of histones to DNA.

“This is one of the safeguards that our cells have evolved and it is part of the normal progression through cell division – all growing cells have to use this all of the time,” said study co-author William F. Marzluff, PhD, Kenan Distinguished Professor of biochemistry and biophysics at UNC’s School of Medicine.

The structure of Histone mRNA stem-loop (center) with
exonuclease (left) and SLBP (right). Arrow (top center) points to the twist.
 Credit: Marzluff lab, UNC School of Medicine

Every time a cell divides, Marzluff adds, it has to replicate both DNA and histone proteins and then package them together into chromosomes. “That way, each of the two cells resulting from division has one complete set of genes.”

In humans, the 23 chromosomes that house roughly 35,000 genes are made up of both DNA and histone proteins. The DNA for a histone protein is first transcribed into RNA, which then acts as a guide for building a histone protein. Because the RNA relays a message – in this case a blueprint for a histone protein, it is referred to as messenger RNA, or mRNA.

Histone mRNAs differ from all other mRNAs and end in a stem-loop [or hairpin] sequence that is required for proper regulation of histone mRNAs.  In this study, the Columbia team of Liang Tong, PhD, Professor of biological sciences and the corresponding author on this project, and graduate student Dazhi Tan used crystallography to reveal the structure of two important proteins near the end of the histone mRNA stem-loop. This molecular complex is required for regulating the levels of the histone mRNA.

One of these proteins, stem-loop binding protein (SLBP) is required for translation of histone mRNA into protein, and the other is an exonuclease, which is required to destroy the mRNA. Both were initially identified at UNC by Marzluff and colleague Zbigniew Dominski, PhD, Professor of biochemistry and biophysics, also a study co-author.

“We knew there was some interaction between SLBP and the exonuclease, so we asked Liang to explain how they bind and communicate,” Dominski said. “And the surprising thing was that the proteins do it not by binding to each other but by changing the RNA structure at the site.”

“From the science point of view, that was the most dramatic thing,” Marzluff said. “The way these proteins help each other is either one can twist the RNA so the other can recognize it easier, and they don’t have to touch each other to do that.”

This protein complex is a critical regulator of histone synthesis, and is an important component of cell growth, he adds.  “Interfering with it could provide a new method for interfering with cancer cell growth.”

source: http://news.unchealthcare.org/news/2013/january/moleculartwist

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Study Quantifies the Size of Holes Antibacterials Create in Cell Walls to Kill Bacteria

The rise of antibiotic-resistant bacteria has initiated a quest for alternatives to conventional antibiotics. One potential alternative is PlyC, a potent enzyme that kills the bacteria that causes strep throat and streptococcal toxic shock syndrome. PlyC operates by locking onto the surface of a bacteria cell and chewing a hole in the cell wall large enough for the bacteria’s inner membrane to protrude from the cell, ultimately causing the cell to burst and die.

Research has shown that alternative antimicrobials such as PlyC can effectively kill bacteria. However, fundamental questions remain about how bacteria respond to the holes that these therapeutics make in their cell wall and what size holes bacteria can withstand before breaking apart. Answering those questions could improve the effectiveness of current antibacterial drugs and initiate the development of new ones.

Researchers at the Georgia Institute of Technology and the University of Maryland recently conducted a study to try to answer those questions. The researchers created a biophysical model of the response of a Gram-positive bacterium to the formation of a hole in its cell wall. Then they used experimental measurements to validate the theory, which predicted that a hole in the bacteria cell wall larger than 15 to 24 nanometers in diameter would cause the cell to lyse, or burst. These small holes are approximately one-hundredth the diameter of a typical bacterial cell.

“Our model correctly predicted that the membrane and cell contents of Gram-positive bacteria cells explode out of holes in cell walls that exceed a few dozen nanometers. This critical hole size, validated by experiments, is much larger than the holes Gram-positive bacteria use to transport molecules necessary for their survival, which have been estimated to be less than 7 nanometers in diameter,” said Joshua Weitz, an associate professor in the School of Biology at Georgia Tech. Weitz also holds an adjunct appointment in the School of Physics at Georgia Tech.

The study was published online on Jan. 9, 2013 in the Journal of the Royal Society Interface. The work was supported by the James S. McDonnell Foundation and the Burroughs Wellcome Fund.
Common Gram-positive bacteria that infect humans include Streptococcus, which causes strep throat; Staphylococcus, which causes impetigo; and Clostridium, which causes botulism and tetanus. Gram-negative bacteria include Escherichia, which causes urinary tract infections; Vibrio, which causes cholera; and Neisseria, which causes gonorrhea.

Gram-positive bacteria differ from Gram-negative bacteria in the structure of their cell walls. The cell wall constitutes the outer layer of Gram-positive bacteria, whereas the cell wall lies between the inner and outer membrane of Gram-negative bacteria and is therefore protected from direct exposure to the environment.

Georgia Tech biology graduate student Gabriel Mitchell, Georgia Tech physics professor Kurt Wiesenfeld and Weitz developed a biophysical theory of the response of a Gram-positive bacterium to the formation of a hole in its cell wall. The model detailed the effect of pressure, bending and stretching forces on the changing configuration of the cell membrane due to a hole. The force associated with bending and stretching pulls the membrane inward, while the pressure from the inside of the cell pushes the membrane outward through the hole.

A transmission electron microscope image of a Streptococcus
 pyogenes cell experiencing lysis after exposure to the
highly active enzyme PlyC. (Credit: Daniel Nelson, UMD)

“We found that bending forces act to keep the membrane together and push it back inside, but a sufficiently large hole enables the bending forces to be overpowered by the internal pressure forces and the membrane begins to escape out and the cell contents follow,” said Weitz.
The balance between the bending and pressure forces led to the model prediction that holes 15 to 24 nanometers in diameter or larger would cause a bacteria cell to burst. To test the theory, Daniel Nelson, an assistant professor at the University of Maryland, used transmission electron microscopy images to measure the size of holes created in lysed Streptococcus pyogenes bacteria cells following PlyC exposure.

Nelson found holes in the lysed bacteria cells that ranged in diameter from 22 to 180 nanometers, with a mean diameter of 68 nanometers. These experimental measurements agreed with the researchers’ theoretical prediction of critical hole sizes that cause bacterial cell death.
According to the researchers, their theoretical model is the first to consider the effects of cell wall thickness on lysis.

“Because lysis events occur most often at thinner points in the cell wall, cell wall thickness may play a role in suppressing lysis by serving as a buffer against the formation of large holes,” said Mitchell.
The combination of theory and experiments used in this study provided insights into the effect of defects on a cell’s viability and the mechanisms used by enzymes to disrupt homeostasis and cause bacteria cell death. To further understand the mechanisms behind enzyme-induced lysis, the researchers plan to measure membrane dynamics as a function of hole geometry in the future.
source:http://www.gatech.edu/newsroom/release.html?nid=182231

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Cheating — and getting away with it

We would all like to believe that there is a kind of karma in life that guarantees those who cheat eventually pay for their bad behavior, if not immediately, then somewhere down the line. But a study of a new gene in the amoeba Dictyostelium discoideum suggests that, at least for amoebae, it is possible to cheat and get away with it.

The experimental work was conducted by then graduate student Lorenzo Santorelli as part of a collaboration between evolutionary biologists David C. Queller and Joan E. Strassmann of Rice University and Gadi Shaulsky and Adam Kuspa of Baylor College of Medicine. Santorelli has since moved to Oxford University and his advisors to Washington University in St. Louis, where Queller is the Spencer T. Olin Professor of Biology and Strassmann is a professor of biology, both in Arts & Sciences.
The cheat in question is putting more than your clone’s fair share of cells into a communal spore body, so that your genome dominates the next generation of amoebae. The idea has always been that cheating clones pay a price in the form of reduced evolutionary fitness in some other chapter of their lives.

A slice through a culture plates shows slugs (clumps) of the social amoebae D. discoideum (at left) on their way to becoming fruiting bodies (right). The photograph was shot in the lab of Joan Strassmann and David Queller by entomologist and photographer Alex Wild. For more of Wild’s photos, visit http://www.alexanderwild.com/.

In work described in the Jan. 9 issue of BMC Evolutionary Biology, the scientists tested the fitness of a knockout mutant (an amoeba with one disabled gene) called CheaterB. When mixed with equal parts of a wild-type clone, the cheater clone contributed almost 60 percent of the cells in the spore body, 10 percent more than its fair share.

The scientists ran CheaterB cells through exhaustive tests of their ability to grow, develop, form spores and germinate. CheaterB did just as well in these tests as its ancestor wild strain. Under laboratory conditions, at any rate, CheaterB didn’t seem to be paying a fitness cost for cheating.
The study raises important questions about the tension between cooperation and cheating. Why would breaking something that is presumably functional (by knocking out a gene) confer an advantage in the first place? And if cheating benefits the cheater and has no hidden cost, what holds cheating in check?

Cheating is surprisingly easy
D. discoideum spend most of their lives as predatory single cells hunting bacteria through the leaf litter and upper soil layers of forests in eastern North America. But when they can’t find bacteria and begin to starve, they gather to form fruiting bodies, a thin stalk of cells with a ball of spores at the top, like a miniature Space Needle. The amoebae that end up in the stalk die, giving up their lives to benefit the amoebae that become spores.
Importantly the cells that stream together to form the fruiting body can be clonal (genetically identical) or have two (or more) genetic makeups. If each clone in a two-clone fruiting body contributes half the cells to the spore body, both clones gain from cooperating because each must sacrifice fewer cells to the stalk.
But game theory suggests the clones should sometimes evolve strategies that allow them to gain the benefits of cooperation without paying the costs.
In 2008 Queller and Strassmann published a genome-wide screen of D. discoideum that found roughly 180 cooperation genes, genes that might produce cheaters if they mutated. The number of genes, and the number of different biological pathways they affected, suggested it might be easy to evolve cheating and difficult to control it fully.
At the time cheaters were believed to be held in check by mechanisms that made non-cooperation costly. The first D. discoideum cheater to be scrutinized, CheaterA, described in 2000, is not able to form fruiting bodies on its own. This is a crippling disability that would prevent it from surviving in the wild.
But the screen from 2008 selected only clones able to produce clonal fruiting bodies, thus passing a basic test of evolutionary fitness. These clones were what is called facultative cheaters, cheating only under favorable conditions, and not obligate cheaters, forced to cheat no matter what.
The overall robustness of knockout mutant CheaterB deepens the mystery. “No measurable laboratory trait revealed an Achilles heel,” Strassmann says, “but that doesn’t mean there isn’t one in natural environments. Otherwise, why would a naturally occurring mutation that duplicated the knockout not take over amobae populations?”
source:https://news.wustl.edu/news/Pages/24754.aspx

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Virus caught in the act of infecting a cell

The detailed changes in the structure of a virus as it infects an E. coli bacterium have been observed for the first time, report researchers from The University of Texas at Austin and The University of Texas Health Science Center at Houston (UT Health) Medical School this week in Science Express.
To infect a cell, a virus must be able to first find a suitable cell and then eject its genetic material into its host. This robot-like process has been observed in a virus called T7 and visualized by Ian Molineux, professor of biology at The University of Texas at Austin, and his colleagues.

Researchers found that the T7
virus has six tail fibers that
are folded back against its capsid.
 The fibers extend as the virus locates
 a suitable host and as it “walks”
 across its host cell surface to find
 a site to infect.

The researchers show that when searching for its prey, the virus briefly extends — like feelers — one or two of six ultra-thin fibers it normally keeps folded at the base of its head.
Once a suitable host has been located, the virus behaves a bit like a planetary rover, extending these fibers to walk randomly across the surface of the cell and find an optimal site for infection.
At the preferred infection site, the virus goes through a major change in structure in which it ejects some of its proteins through the bacterium's cell membrane, creating a path for the virus's genetic material to enter the host.
After the viral DNA has been ejected, the protein path collapses and the infected cell membrane reseals.

"Although many of these details are specific to T7," said Molineux, "the overall process completely changes our understanding of how a virus infects a cell."
For example, the researchers now know that most of the fibers are usually bound to the virus head rather than extended, as was previously thought. That those fibers are in a dynamic equilibrium between bound and extended states is also new.
Molineux said that the idea that phages "walk" over the cell surface was previously proposed, but their paper provides the first experimental evidence that this is the case.

The top images are tomograms of the virus in action. The illustrations show T7 using its fibers to “walk” across the cell surface and infect the cell.

This is also the first time that scientists have made actual images showing how the virus's tail extends into the host — the very action that allows it to infect a cell with its DNA.
"I first hypothesized that T7 made an extended tail more than 10 years ago," said Molineux, "but this is the first irrefutable experimental evidence for the idea and provides the first images of what it looks like."
The researchers used a combination of genetics and cryo-electron tomography to image the infection process. Cryo-electron tomography is a process similar to a CT scan, but it is scaled to study objects with a diameter a thousandth the thickness of a human hair.

source :http://www.eurekalert.org/pub_releases/2013-01/uota-vci011013.php

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Team Zone A

Team Under

Asif Raazaq, Co-Founder/Director

Shruti Thakur, Regional Head Delhi NCR
Stuti Mahajan, Regional Chief Editor Delhi NCR
Avantika Rawat, College Head Delhi NCR (JIIT)
Jahnavi Sharma, College Head Delhi NCR (JIIT)
Deepali Gupta, Regional Head- Research and Development Delhi NCR
Pawan Kushwaha, Regional Head-Tech and Operation U.P.
Divyanshi Yadav, Regional Head Research and Development U.P.
Ambuj Mishra, Regional Head External Relations, U.P.
Abhishek Singh, Regional Head Media and Advertising, U.P.
Wasi Syed, Regional Head Research and Development, Punjab
Sanjana Vig, Volunteer
Kalyani Verma, Volunteer

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Research opportunities at TIFR

Research Opportunities for exceptionally talented and strongly motivated students.

The Tata Institute of Fundamental Research is India's premier institution for advanced research in fundamental sciences. The Institute runs a graduate programme leading to the award of Ph.D. degree, as well as M.Sc. and Integrated Ph.D. in certain subjects. With its distinguished faculty, world class facilities and stimulating research environment, it is an ideal place for aspiring scientists to initiate their career.

The Graduate Programme at TIFR is classified into the following Subjects - Mathematics, Physics, Chemistry, Biology, Computer & Systems Sciences (including Communications and Math. Finance) and Science Education. It is conducted at the Mumbai campus and various National Centres of TIFR.

Graduate School Admissions (GS-2013)

Application Procedure

Students can apply online.  Please follow appropriate link on this website for filling up the application form.  Read the instructions carefully before you start filling up the online application form.

Manual Applications: Students from remote areas who do not have access to internet may apply manually.   They may send a request for application form (without DD) along with a self-addressed stamped (Rs 20/-) envelope (size 25cm x 17cm) superscribed "GS-2013 (Subject)" to :
For Biology: Admissions Section, NCBS, Bangalore  .
For other subjects, except Science Education: Universvity Cell , TIFR, Mumbai.
The filled-in application form should be sent along with DD and two passport size photographs (one pasted on the application and one stapled to it).

Students may appear for the written test in multiple subjects if the timings do not clash.  Please send a separate application (including Demand Draft) for each subject. In case of online applicants, students will have to re-register with a different email id.

Students who wish to apply online and make payment by Demand Draft may send the Demand Draft with their name, reference code and telephone number written behind it.  Alternately, students can make online payment through internet banking or by Debit/Credit Card. 

Eligibilty:

For Ph.D.: Masters in Basic Science or Bachelors in Applied Science.  These include M.Sc. (Agriculture), B.Tech., B.E., B.V.Sc., B.Pharma. (4 year course), MBBS, BDS, M.Pharma. Candidates will be shortlisted for interview based on written test marks, CV and Scientific write-up. For Integrated Ph.D./M.Sc.: Bachelors in any Basic Science. 
For Ph.D. Program in TCIS: M.Sc. in Physics, Chemistry or Biology.

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Masters and Ph.D at IISc Bangalore

INFORMATION AT A GLANCE

Indian Institute of Science (IISc) also referred to as ‘the Institute’ at certain places in this document announce Admissions to the following:

Research programmes - Doctoral (Ph D) and Master’s (M Sc [Engg])

Course programmes - (ME/M Tech/M Des/M.Mgt)

Integrated Ph D programmes

Candidates should go through the requirement of basic qualifications carefully and satisfy themselves that they fulfill all the eligibility criteria. 

1.    Candidates applying for :

Research programmes may indicate preferences for a maximum of 3 departments / centers / units.

Course programmes (ME /M Tech /M Des) may indicate preferences for a maximum of 5 disciplines.

Course programme (M.Mgt) have only one option under Management Studies.

Integrated Ph D programmes may indicate preferences for a maximum of 2 disciplines.

Application Forms with incomplete / incorrect information are liable to be rejected.

2.    The print out of the online Application Form should reach the

Assistant Registrar (Academic)

Admissions Unit

Indian Institute of Science

Bangalore 560012

on or before March 15,  2012 for the Sponsored candidates and March 26,  2012 for others.  The last date prescribed for the receipt of Application Forms cannot be extended for any reason.

3.    Please note that the receipt of an Admit Card for the Entrance Test 2012 or call letter for interview does not confer any right upon the applicant for admission to the Institute. 

4.    Please note that concealing or misrepresenting information of any sort will lead to automatic cancellation of admission even after selection/admission.

5.    Any claim or dispute arising in respect of admissions 2012 must be notified in writing on or before 30.9.2012. It is hereby made absolutely clear that the Courts and Tribunals in Bangalore, and Bangalore alone, shall have the exclusive jurisdiction to entertain and settle all such dispute or claim.

Online Application for Admission - 2013 (August Session) is open only during 1 Feb 2013 to 30 Apr 2013.

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Team Zone N

North Team under

Nimish Gopal, Co-Founder/Director

Tushar Kant, Chief Designer (Former)

Abin Ghosh, Regional Head-Technology and Maintenance

Mohd Tayyab, Regional Head-Editor

Rajat Yadav, Regional Head-External Relations

Naveen Nagar, Regional Head-Research and Development

Harsh Patodia, Regional Head-Finance

Teena Mehlawat, Regional Head-Rajasthan

Tanvi Das, Editor-GBioFin

Anurag Tiwari, Student Head-Haryana

Designer team- Manohar, Arun, Saurabh, Akshay, Moinak, 

Subhranshu

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In Epigenomics, Location is Everything

In a novel use of gene knockout technology, researchers at the University of California, San Diego School of Medicine tested the same gene inserted into 90 different locations in a yeast chromosome – and discovered that while the inserted gene never altered its surrounding chromatin landscape, differences in that immediate landscape measurably affected gene activity.
The findings, published online in the Jan. 3 issue of Cell Reports, demonstrate that regulation of chromatin – the combination of DNA and proteins that comprise a cell’s nucleus – is not governed by a uniform “histone code” but by specific interactions between chromatin and genetic factors.

An x-ray micrograph of a yeast cell, Saccharomyces
cerevisiae, as it buds before dividing. Courtesy of
 Carolyn Larabell, UC San Francisco, Lawrence
Berkeley National Laboratory and the National
Institute of General Medical Sciences.

“One of the main challenges of epigenetics has been to get a handle on how the position of a gene in chromatin affects its expression,” said senior author Trey Ideker, PhD, chief of the Division of Genetics in the School of Medicine and professor of bioengineering in UC San Diego’s Jacobs School of Engineering. “And one of the major elements of that research has been to look for a histone code, a general set of rules by which histones (proteins that fold and structure DNA inside the nucleus) bind to and affect genes.”
The Cell Reports findings indicate that there is no singular universal code, according to Ideker. Rather, the effect of epigenetics on gene expression or activity depends not only on the particular mix of histones and other epigenetic material, but also on the identity of the gene being expressed.
To show this, the researchers exploited an overlooked feature of an existing resource. The widely-used gene knockout library for yeast, originally created to see what happens when a particular gene is missing, was built by systematically inserting the same reporter gene into different locations. Ideker and colleagues focused on this reporter gene and observed what happens to gene expression at different locations along yeast chromosome 1.
“If epigenetics didn’t matter – the state of histones and DNA surrounding the gene – the expression of a gene would be the same regardless of where on the chromosome that gene is positioned,” said Ideker. But in every case, gene expression was measurably influenced by interaction with nearby epigenetic players.
Ideker said the work provides a new tool for more deeply exploring how and why genes function, particularly in relation to their location.
source http://ucsdnews.ucsd.edu/pressrelease/in_epigenomics_location_is_everything

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Rare Form of Active 'Jumping Genes' Found In Mammals

Little brown bat (Myotis lucifugus)

J.N. Stuart

Much of the DNA that makes up our genomes can be traced back to strange rogue sequences known as transposable elements, or jumping genes, which are largely idle in mammals. But Johns Hopkins researchers report they have identified a new DNA sequence moving around in bats — the first member of its class found to be active in mammals. The discovery, described in a report published in December on the website of the Proceedings of the National Academy of Sciences, offers a new means of studying evolution, and may help in developing tools for gene therapy, the research team says.

“Transposable elements are virtually everywhere in nature, from bacteria to humans,” says Nancy Craig, Ph.D., a Howard Hughes investigator and professor in the Johns Hopkins University School of Medicine’s Department of Molecular Biology and Genetics. “They’re often seen as parasites, replicating themselves and passing from generation to generation without doing anything for their hosts. But in fact they play an important role in fueling adaptation and evolution by adding variability to the genome.”

As their name suggests, jumping genes can move from place to place in the genome, sometimes even inserting themselves into the middle of another gene. Some work by replicating themselves and inserting the copies into new places in the genome — retroviruses such as HIV are comprised of this type of jumping gene, which enables the host cell to be hijacked to make more virus particles. Another class of jumping genes, known as “DNA cut-and-paste,” doesn’t make copies, but instead cuts itself out of one site in the genome before hopping into another. Craig explains that in mammal genomes, most jumping genes are of the copy-and-paste variety, and most of these are fossils, mutated to the point where they can no longer move about. Although some remnants of cut-and-paste jumping genes have been unearthed in mammals, until now, all of them have been inactive.

Craig’s team made its discovery while studying piggyBac, an active cut-and-paste jumping gene from insects. PiggyBac got its name because it hitched a ride from one host to another on a virus. While studying how the jumping gene works, the researchers also used computational methods to search for piggyBac-like DNA sequences in the genomes of some species, including that of the little brown bat. There they found a sequence similar to piggyBac, one that didn’t appear to have collected mutations that would make it inactive. Sure enough, near-identical copies were sprinkled throughout the genome, indicating that the sequence had jumped relatively recently. Craig named the find piggyBat. Her team also found that piggyBat can move within bat cells, other mammalian cells and yeast, showing that it is indeed a still-active DNA element.

Many organisms have developed systems to decrease the frequency at which jumping genes move, Craig says. Such systems are a component of immunity, protecting mammals from retroviruses, as well as from the risk that jumping genes will wreak havoc by interrupting an important gene.

Over time, the protective systems have made most mammalian jumping genes inactive. The finding that a bat species is host to an exception, combined with the fact that bats are particularly susceptible to viruses, may indicate that the systems that protect us from dangerous genetic material are not as well-developed in bats, Craig says. But whatever the reason for its presence, piggyBat “opens up a window for studying jumping gene regulation in a mammal where the element is still active,” she says.

This future research should yield insights on the workings of jumping genes themselves, as well as on the protective systems that keep them in check, Craig says. Ultimately, her group hopes to custom-design jumping genes that can be used for targeted, safe and effective gene therapy, delivering genes needed to treat disease.
source: www.hopkinsmedicine.org/news/media/releases/rare_form_of_active_jumping_genes_found_in_mammals

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