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Tuesday, October 19, 2010

Some useful books for CSIR


Hi every one,
Some useful books for CSIR
I found some useful books given as reference for CSIR and these books can help us to prepare for all exams including DBT, BARC, ICMR also...

Lehninger- Biochemistry,
Cooper/ Benjamin- Molecular Biology,
Wilson and Walker- Calculations in Biochem/ Practical Chemistry,and also for biophysics,
Kuby- Immunology,
Animal Physiology- Wikipedia notes,
Prescott- Microbiogy,
Pelzar- Microbiology
Whittaker- Bioprocess
NCERT books- 11, 12 (Biology, Physics, Maths)
Gupta- Statistics,
Ecology- Odum,
General Biology- Campbell and reece,
Gardner- Genetics (especially for the problems of mendelian genetics, quantitative genetics)
Life book
Zoology- Reece,
Invertebrates- Agarwal

Also try solving the model question papers given in the website, and try to solve almost problems given at the end of each chapter.

Different approach needed for preparing section-A of paper-I, which is a general paper and only a thorough knowledge of CBSE books will siffice ot answer atleast 25 questions.

some logical questions are asked in paperI, for that Rastogi books are available for conveying basics of logical reasoning and verbal ability

Try to watch animations of Benjamin to understand some tough topics of molecular biology, as they are very understandable and concepots are given clearly.

Also many informations and quizzes are available in online of the book of Biology- Campbell as it will be useful fo paperI of subject, these covers basic concepts and remembering is easier, pls make use of it!


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Sunday, October 17, 2010

Fwd: Bioinformatics






Escape analysis and lock coarsening in JAVA 6.0

Posted: 16 Oct 2010 12:37 AM PDT


The popularity of the Java programming language has made escape analysis a target of interest. Java's combination of heap-only object allocation, built-in threading, and the Sun HotSpot dynamic compiler creates a candidate platform for escape analysis related optimizations. Escape analysis is implemented in Java Standard Edition 6.


Example (Java)

class A {
final int finalValue;

public A( B b ) {
super();
b.doSomething( this ); // this escapes!
finalValue = 23;
}

int getTheValue() {
return finalValue;
}
}

class B {
void doSomething( A a ) {
System.out.println( a.getTheValue() );
}
}
In this example, the constructor for class A passes the new instance of A to B.doSomething. As a result, the instance of A—and all of its fields—escapes the scope of the constructor.

Java is able to manage multithreading at the language level. Multithreading is a technique that allows programs to operate faster on computer system that have multiple CPUs. Also, a multithreaded application has the ability to remain responsive to input, even when it is performing long running tasks.
However, programs that use multithreading need to take extra care of objects shared between threads, locking access to shared methods or blocks when they are used by one of the threads. Locking a block or an object is a time-consuming operation due to the nature of the underlying operating system-level operation involved .
As the Java library does not know which methods will be used by more than one thread, the standard library always locks blocks when necessary in a multithreaded environment.
Prior to Java 6, the virtual machine always locked objects and blocks when asked to by the program even if there was no risk of an object being modified by two different threads at the same time. For example, in this case, a local Vector was locked before each of the add operations to ensure that it would not be modified by other threads (Vector is synchronized), but because it is strictly local to the method this is not necessary:
public String getNames() {
Vector v = new Vector();
v.add("Me");
v.add("You");
v.add("Her");
return v.toString();
}
Starting with Java 6, code blocks and objects are locked only when necessary , so in the above case, the virtual machine would not lock the Vector object at all







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Cockroach brains, coming to a pharmacy near you -Insect tissue extracts show antibacterial activity

Cockroaches may be nasty bugs, but they could help fight even nastier ones. New research finds that the rudimentary brains of cockroaches and locusts teem with antimicrobial compounds that slay harmful E. coli and MRSA, the antibiotic-resistant staph bacterium. The work could lead to new compounds for fighting infectious diseases in humans.

Extracts of ground-up brain and other nerve tissue from the American cockroach, Periplaneta americana, and desert locust, Schistocerca gregaria, killed more than 90 percent of a type of E. coli that causes meningitis, and also killed methicillin-resistant staph, microbiologist Simon Lee reported September 7 at the Society for General Microbiology meeting at the University of Nottingham in England.

"Some of these insects live in the filthiest places ever known to man," says Naveed Khan, coauthor of the new study. "These insects crawl on dead tissue, in sewage, in drainage areas. We thought, 'How do they cope with all the bacteria and parasites?'"

Khan and his colleagues became intrigued by insect antimicrobials when they noticed that many soldiers were returning from the Middle East with unusual infections, yet locusts living in the same areas were unperturbed. So the researchers, all from the University of Nottingham, began investigating how the insects ward off disease.

The team ground up various body parts from both cockroaches and locusts that had been reared in the lab and incubated them for two hours with different bacteria. Leaving these mixtures overnight on petri dishes revealed that the extracts from brains and from locust thorax nerve tissue killed nearly 100 percent of the bacteria.

Yet the insect brain extracts didn't seem to bother human kidney or epithelial cells when grown with them in a lab dish.

Curiously, extracts of insect fat, muscle and blood didn't bother the bacteria at all. Cockroaches and locusts often eat stuff loaded with microbes, says parasitologist Carl Lowenberger of Simon Fraser University in Burnaby, Canada, so you would think insect guts and blood, which bathes the organs, would have similar antimicrobial activity.

Nine molecules appear to be responsible for the antimicrobial activity in locust tissue, although they have yet to be identified. The team is also still working out the details of the cockroach compounds.

The compounds may work together as a cocktail, Lowenberger says. Insects make hundreds of antimicrobial compounds, and it may be that very high concentrations of those molecules would be required for fighting an infection in humans. But the research "is pretty neat stuff," he says. And perhaps down the road, the yet-unidentified molecules will prove useful in fighting infections in people.



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Doggy Genes: Newly Sequenced Genome Could Shed Light on Human Diseases

Molecular biologists have completely sequenced the first dog genome. Understanding how genetics plays a role in canine diseases could lead to new treatments for diseases shared by humans, such as diabetes, epilepsy and cancer. Breeders could also soon be able to check the purity of pedigrees by sending dogs' cheek swabs to the lab.

We may be more like dogs than we think. Now, a complete map of dog genes not only helps explain what gives dogs their unique set of traits, behaviors, and diseases -- it could help identify human diseases, too. Why are some dogs excellent ball chasers and others perfect for your lap? The answer to dog differences is hidden in specific sequences of DNA called genes. A standard poodle, named Shadow, was the first dog to have its genes mapped, but it was only about 80-percent complete. For the first time, molecular biologists have completely mapped out the genes of a boxer.

"The boxer genome will help us get at the genes responsible for diseases and traits in dogs," says Ewen Kirkness, a molecular biologist at The Institute for Genomic Research in Rockville, Md. Dogs and humans share many of the same diseases, like diabetes, epilepsy and cancer. Mapping dog genes could be the chief tool in finding disease-causing genes in people, because Kirkness says the same genes will be responsible for similar diseases in humans. Genes that cause disease in dogs are easier to find than in people. Mutations in a dozen different genes can cause human disease, almost impossible to find. In dogs, only one gene mutation can cause a disease, and that same mutated gene causes an identical disease in humans. "Then we have a better handle on what is causing the disease in humans, also," Kirkness says.

Studying dog families also helps get a better handle on their own health and help eliminate dog diseases.

"Testing can be done by breeders to limit the passage of these mutations into future generations." Having a genetic map may also mean owners of pure-bred dogs and mutts may soon be able to document which breeds their dogs come from by simply sending a cheek swab or blood sample to a genetics lab. BACKGROUND: For the first time ever, scientists have successfully sequenced the entire genomic structures of two dog breeds: the boxer and the poodle. This is a major step forward for research in such fields as veterinary medicine. Extending this work to the human genome could help doctors better understand and fight human diseases and illnesses, including cancer research. THE

STUDY: In a new study, scientists at the Institute for Genomic Research found distinct genetic differences between boxer and poodle dog breeds, and went on to compare those variations in the genomes from nine other breeds, as well as the genomes from four types of wolves and a coyote. They did this by tracking short stretches of DNA that occur randomly, called short interspersed elements (SINEs), which often turn the expression of those genes up, down or even off. Ultimately they found that the overall dog population contains at least 20,000 differences. THE

IMPLICATIONS: For genomics researchers, variable SINEs can act as signposts for specific genes linked to a disease or traits. Identifying those genes is easier to do in dogs because they have been selectively bred for so long, creating the highest degree of physical and behavioral differences seen within a species. A dog genome is estimated to include 19,300 genes, and nearly all of them correspond to similar human genes. Specific breeds are predisposed, for instance, to heart disease, cancer, blindness, deafness, and other common disorders. A second study documented many of those disease-related differences.



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Better Marker for Breast Cancer May Reduce Need for Second Surgeries

A new material could help surgeons more accurately locate breast cancers, reduce the need for second surgeries and minimize pre-surgical discomfort for patients. Microscopic gas-filled spheres of silica, a porous glass, can mark the location of early-stage tumors to show their position using ultrasound imaging in the operating room.

A team of chemists, radiologists and surgeons at the University of California, San Diego, created the new material, which they describe in a forthcoming issue of the journal MedChemComm.
The X-rays used to make mammograms reveal calcium deposits associated with breast cancer even in tumors too small to be felt. But surgeons can't use X-rays while operating. Instead, radiologists place guide wires into tumors hours or even the day before surgery. The wires don't mark depth well and can shift. Patients find them both uncomfortable and unsettling.

As an alternative, the researchers created spheres of silica and filled them with perfluoropentane, a gas that has been used before in short-lived contrast materials for medical imaging. The rigid silica shells help the new material last longer.

"These little gas-filled microbubbles stick to human breast tissue for days and can be seen with ultrasound," said William Trogler, professor chemistry. "If doctors placed them in early stage breast cancer, which is difficult to see during surgery, they could help surgeons remove all of it in the first operation."

In the past few years, radiologists have tried implanting radioactive "seeds" instead of wires to mark tumors, but the seeds last only a few hours and must be inserted with a large-bore needle, which is painful. In addition, only one abnormal region can be marked, but patients with a form of breast cancer called ductal in situ carcinoma often have several. The seeds also expose both patient and staff to radiation, can't been imaged in three dimensions and create radioactive medical waste.

At just two micrometers in diameter - half the width of a strand of spider silk - small silica microbubbles can be precisely injected into clusters of abnormal cells using a thin needle. Radiologists would be able to inject the durable material days before surgery. And ultrasound scans reveal the position of the bubble in three dimensions on the operating table.

"Instead of just using a Geiger-counterlike device to say you're getting closer to the radioactive seed, you could actually see where to carve," said Andrew Kummel, professor of chemistry. The increased precision should help surgeons avoid the need for second surgeries.

"By outlining the tumor more completely in multiple directions, the particles could potentially help surgeons remove non-palpable tumors in a single operation," said Sarah Blair, a surgeon at Moores UCSD Cancer Center. "They will definitely make the operation more comfortable for patients."

The researchers think the ultrasound pressure waves burst the microbubbles. "They're thin, fragile balls of porous glass, like Christmas tree ornaments," Kummel said. "The shell is just one two-hundredth of the diameter of the ball. When it breaks, the gas squirts out. Doppler ultrasound detects that movement."
Nano-scale silica microbubbles, which the team reports in this paper as well, are too small to remain in place, but might drain from a cancerous site to help identify which lymph nodes are most likely to contain stray cells that could help the cancer spread.
The current study demonstrates the feasibility of the technology in tissue samples. Tests in animal models are underway, and toxicology studies must also be completed before clinical trials in humans could begin.

Chemists Bill Trogler, and Andy Kummel, of UCSD's Division of Physical Sciences, and radiologist Robert Mattrey and surgeon Sarah Blair of the Moores UCSD Cancer Center led the project. Additional co-authors include radiologist Yuko Kono, and Sergio Sandoval, Moores UCSD Cancer Center; Paul Martinez of the Department of Chemistry and Biochemistry; and Jessica Wang-Rodriguez of the Department of Pathology.

The National Cancer Institute provided financial support for this study.



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Thursday, October 14, 2010

Biophysicists Grow Pretty Bacteria In Petri Dishes To Find Antibiotics

Biophysicists are growing Petri dishes of different species of bacteria in order to develop new antibiotics. The bacteria are subjected to different temperatures and have limited food sources inside the dish. Despite these conditions, most colonies tend to communicate and reproduce. Their growth results in unique patterns of varying colors--a sort of "bacteria painting." Researchers are hoping to learn more about the strategies the bacteria use to thrive, in order to find weaknesses that new drugs could exploit.

There was a time when doctors thought antibiotics could cure all. It's a different story today as drug-resistant bacteria emerge in places like hospitals and schools. To keep up with changes in bacterial behavior, scientists are fighting bacteria using an artistic approach.

Biophysicist Herbert Levine's Petri dishes look like an exhibit at a modern art museum. His beautiful images are actually made from bacteria similar to the ones that cause deadly diseases. Dr. Levine uses bacteria in Petri dishes in his quest to discover the next super drug. He's fighting a new generation of bacterial infections that includes MRSA, a flesh-eating disease resistant to antibiotics.

"We thought we had a whole arsenal of antibiotics and these would always work ý but the bacteria are smarter than we used to give them credit for being," said Dr. Levine, who works at the University of California in San Diego.

Dr. Levine and his team have gone back to the basics of biology. They have created bacteria patterns by changing the temperature and limiting the food sources inside Petri dishes. Despite harsh conditions, the colonies find ways to communicate and reproduce.

"If we can understand what strategies they're using, we can devise methods to defeat those strategies," Dr. Levine said.

Through Dr. Levine's work, scientists have learned bacteria are very resourceful. They enclose themselves in areas antibiotics can't find. They also soak up antibiotics to keep the rest of their colony safe and transform themselves into new strains that are less sensitive to the drugs.

"If that basic understanding of nature leads to better life for humanity, then, of course, that makes us even more excited," Dr. Levine said.

Along the way, scientists turned the study of bacteria into an art form.

Dr. Levine and his colleague, Eshel Ben-Jacob, use the patterns to create computer models. One day those models could be the basis for new medicines that fight all types of bacteria.

WHAT IS MRSA: MRSA is a common cause of skin infections; it can also cause pneumonia, ear infections and sinusitis. MRSA bacteria are sometimes dubbed 'superbugs' because they are highly resistant to common antibiotics like penicillin, making infections difficult to treat effectively. Bacteria are highly adaptive, and over time they naturally develop resistance, protecting them from incoming germs (and antibiotics) and making them harder to kill. If MRSA enters the body through the skin, it can cause irritating skin infections, but if it enters the lungs or bloodstream, it can cause serious blood infections, pneumonia, even death. MRSA infection rates in the US have been increasing since 1970, largely because surveillance programs to monitor its spread are not effective. Other countries, such as the Netherlands, Sweden and Denmark have all but eliminated MRSA from their hospitals through such surveillance programs, which focus on screening patients for MRSA at admission and isolating any carriers.

DRUG RESISTANCE: Bacteria are highly adaptive, and over time they naturally develop resistance, protecting them from incoming germs (and antibiotics), which makes them more difficult to kill. If someone has strep throat, for example, repeated exposure to penicillin and amoxicillin can result in a throat full of bacteria that can shield strep germs from the older drugs. The surviving bacteria then reproduce more and become more dominant. Sometimes parents discontinue antibiotic medication prematurely when they or their children begin to feel better, so the strep germ isn't entirely killed off, leading to much more severe infections requiring the use of even stronger drugs later on. This can also happen with many other infections inside the body and on the skin.


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Blocking an Oncogene in Liver Cancer Could Be Potential Therapy Option

Scientists have found that a synthetic molecule they designed can block activation of a gene in liver cancer cells, halting a process that allows some of those cancer cells to survive chemotherapy.

Without the interference of this gene's function, certain liver cancer cells appear to be protected from the toxic effects of chemotherapy drugs.

Blocking the oncogene, called STAT3, prevents a protein from protecting the cells, the research suggests. As a result, more liver cancer cells succumb to treatment.

Researchers hope an anti-cancer drug based on the molecule's design eventually will be developed for use in patients, after the required animal and clinical testing is completed.

The scientists have seen similar results in studies using this experimental molecule, called LLL12, to block STAT3 as a way to induce cell death in breast and pancreatic cancer cells.

"For patients, it would be easy to use an intravenous drug based on this small molecule, which is relatively cheap and easy to manufacture," said Jiayuh Lin, senior author of the study and an associate professor of pediatrics at Ohio State University.

"We also have seen signs that blocking STAT3 could block other downstream targets, and could affect other STAT3-regulated genes that can turn normal cells into cancer cells. We believe this molecule has a lot of potential for cancer therapy."

Lin led the team of scientists who designed LLL12 using powerful computers and a computational method called structure-based design. The group reported on its creation earlier this year.

This new study is published in a recent issue of the Journal of Biological Chemistry.

The protein in this process is called interleukin-6, or IL-6. It is a cytokine, a chemical messenger that causes inflammation, and can have both beneficial and damaging effects in the body. Previous research by other scientists has shown that high levels of IL-6 in the blood are associated with hepatocellular carcinoma, the most common type of liver cancer.

The fifth most common cancer in humans, liver cancer remains one of the most difficult to successfully treat. Patients' overall five-year survival rate is about 10 percent, according to the American Cancer Society.

In this study, the researchers observed that liver cancer cells known to be resistant to a common chemotherapy drug, doxorubicin, had higher levels of IL-6 than did other liver cancer cells -- an indication that the protein likely fosters the drug resistance. Subsequent tests showed that these resistant cells with high IL-6 also had higher levels of STAT3 phosphorylation than did other cells.

To further demonstrate this relationship between the protein and cell survival, Lin and colleagues pretreated liver cancer cells with the chemotherapy drug and then followed with different doses of IL-6. The addition of IL-6 rescued these cells from chemo-induced death.

Alternately, when the scientists introduced an antibody to inhibit IL-6 in drug-resistant cancer cells and then followed with doses of doxorubicin, 70 percent more of the cells treated with the IL-6 inhibitor died compared to cells treated with the chemo drug alone -- a sign that the loss of IL-6 lowers survival in these particular cancer cells.

After determining in cell cultures that IL-6 activates STAT3 to help perform this cell survival function, the researchers focused on testing the effects of blocking the gene alone.

They first used silencing RNA, or siRNA, to prevent activation of the STAT3. More of the siRNA-treated cells died than did cells in which the STAT3 was not blocked.

"At this point, we know that STAT3 plays an important role, and that IL-6 depends on STAT3 to protect cells from dying," said Lin, also an investigator in Ohio State's Comprehensive Cancer Center and the Center for Childhood Cancer at Nationwide Children's Hospital.

The scientists then turned to the synthetic molecule, LLL12, which was designed specifically to tuck itself into a gap in STAT3's two-part structure and disable its activation.

The researchers introduced LLL12 to four types of liver cancer cells and followed with a dose of IL-6. The IL-6 protein had no protective effect on cells treated with the molecule, meaning it could not turn on STAT3, a required step in protecting the cells from death.

To be sure, they also tested how cells with and without LLL12 treatment responded to chemotherapy. The small molecule treatment completely blocked resistance to the drug, Lin said, even in the types of liver cancer cells that express the highest IL-6 levels and are most resistant to doxorubicin.

Importantly, the researchers were able to determine that inhibiting STAT3 activation did not affect other proteins that are induced by IL-6 for potentially beneficial reasons. The small molecule also did not exacerbate the effects of chemotherapy on normal liver cells.

Lin and colleagues are currently testing the effects of LLL12 in multiple myeloma, breast and colon cancer cells, in which the IL-6/STAT3 pathway also plays an important role.

This work was supported by the grants from the National Institutes of Health, the Pancreatic Cancer Action Network -- American Association of Cancer Research, and the National Foundation for Cancer Research.

Co-authors of the study include Yan Liu of the Department of Pediatrics, and Pui-Kai Li and Chenglong Li of the Division of Medicinal Chemistry and Pharmacognosy, all at Ohio State.


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Ancient Viral Invasion Shaped Human Genome

Scientists at the Genome Institute of Singapore (GIS), a biomedical research institute of the Agency for Science, Technology and Research 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.

Scientists at the Genome Institute of Singapore (GIS), a biomedical research institute of the Agency for Science, Technology and Research 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."


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Hope for a New Treatment for Bone Cancer: Can 'Friendly' Bacteria Kill Cancer Cells?

The Bone Cancer Research Trust has launched Bone Cancer Awareness Week and has funded a new project at the University which is testing a theory that 'friendly bacteria' can be used to kill bone cancer cells.

Researchers at the School of Clinical Sciences' Division of Pre-Clinical Oncology are investigating whether modifying a harmless type of the bacterium, Salmonella typhimurium, can produce molecules which kill cancer cells in osteosarcoma, a primary bone cancer. The scientists are using a clinically safe form of the bacterium which has been found to localise to tumour tissue rather than healthy tissue.

Osteosarcoma (OS) is the most common type of primary bone cancer and although rare, can be particularly distressing because it affects mostly children and adolescents. Cases tend to have a poor outlook because the cancer often does not respond well to the treatments currently available. There have been few new treatments for OS in the past 20 years and more research and techniques to fight it are urgently needed as more than 2,000 children and young people are diagnosed with the disease every year in the UK.

A main challenge in developing better treatments for bone cancer is finding a much more effective way of targeting anti-cancer drugs at the tumour. Many drugs are given by intravenous injection and use the body's venous system to reach their target, but tumours in bone tend to have a low blood supply.

Dr Coughlan's aim is to modify the Salmonella bacteria to act as a vehicle for cancer-killing agents. It's believed special molecules, called RNA interference molecules, when produced in the bacteria will be more effectively released into malignant cells destroying the levels of cancer-causing molecules there.

It's hoped this research will eventually lead to a treatment for bone cancer that is better targeted at tumours and doesn't affect normal, healthy tissue.


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Tuesday, October 12, 2010

Virtual Research Institute Needed to Unlock RNA’s

Ten years on from the human genome project, RNA (ribonucleic acid) has stolen some of DNA's limelight. The basic ingredient of our genes, DNA long outshone the other form of genetic material in our cells, RNA. RNA was seen as a simple stepping stone in the cell's gene-reading activities.
Research over the last decade has shown RNA to be a remarkable molecule and a multi-talented actor in heredity. It is thought to be a major participant in the chemical reactions that led to the origins of life on Earth -- the 'RNA World' hypothesis. RNA also controls genes in a way that was only recently discovered: a process called RNA interference, or RNAi. Medical researchers are currently testing new types of RNAi-based drugs for treating conditions such as macular degeneration, the leading cause of blindness, and various infections, including those caused by HIV and the herpes virus.
"RNA could bring significant advances to the diagnosis, treatment and prevention of many human diseases," said Professor Jörg Vogel from the University of Würzburg, Germany, who co-chaired the report. "In the global context, it's surprising that Europe doesn't have many centres specifically funded for and dedicated to it, particularly in comparison to the US. We strongly recommend creating a network of RNA centres, linked together as a Europe-wide 'virtual institute'. A first step could involve calls through the European Commission and national funders. "
The virtual RNA institute would be made up of locally-funded, multidisciplinary centres with a critical mass of strong research groups in disciplines such as biology, biochemistry, chemistry, genetics, bioinformatics, biophysics, structural analysis, microbiology, plant sciences and clinical medicine. This environment could be well-suited to promoting superior training of a generation of young scientists, PhD students and postdoctoral researchers. They could also help deliver dedicated education programmes for RNA research, which are currently lacking.
A particular area where an increasing demand in the future can be foreseen is, as in almost all other areas of life science, bioinformatics. "A new generation of bioinformaticians needs to be trained to meet future demand, in RNA research and in many other areas of the life sciences," continues Professor Vogel.
New models for public funding of infrastructure and resources for promising compounds to be used in the clinic should be developed. The financial burden for taking basic compounds and developing them into drugs could be shared by academic-industrial partnerships.
'RNA World: a new frontier in biomedical research' reviews the high pace of discovery in RNA research and gives a 5-10 year outlook of how both basic RNA research and its use in clinical practice should develop. Nine thematic priority areas were identified to address new and promising opportunities for biomedical, biotechnological, pharmaceutical and clinical RNA research


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Rare Hybrid Cell Key to Regulating the Immune System

"This is actually the first cell we know of that has this type of appearance in nature," Dr. Andrew Mellor, molecular geneticist and immunologist who co-directs MCG's Immunotherapy Discovery Institute, said of the cell that looks like a dendritic cell and a B cell but isn't really either.
The discovery of this rare hybrid could have implications for the efficacy of new therapies that manipulate these two cell types to treat diseases such as cancer and rheumatoid arthritis.
When MCG scientists first reported the human equivalent of this cell in Science in 2002, they called it a subset of the dendritic cell that clusters in high exposure areas such as the gut but also roams the body, looking for invaders like a virus or cancer. Dendritic cells show their find to T cells, telling them to ignore or attack by bringing trash-eating macrophages, natural killer cells and the like into the fight.
What seemed most unique about the subset is its ability to express indoleamine 2,3 dioxygenase, or IDO, to turn off T cells. IDO is an enzyme used by fetuses and tumors alike to escape the immune response.
The new studies show that is only part of the cells' distinctiveness. The cells also have the identifying markings of B cells, known for their ability to make antibodies against invaders. In fact, they found the IDO-presenting cells came from the same precursor cell as B cells. But, when the scientists looked at mice missing B cells, they still found the IDO-producing cells. Hence, the cell didn't need to produce antibodies to turn off T cells.
In reality, IDO-expressing cells have properties of both cells, said Burles A. Johnson III, an MCG M.D.-Ph.D. student and first author of the paper published in the Proceedings of the National Academy of Sciences. "It looks like a B cell and it's not. It looks like a dendritic cell and it is and it isn't," Johnson said.
While their studies are in mice, the cells also are in humans, showing up in some unfortunate places such as the drainage system for tumors, melanoma or even HIV where they likely help the diseases survive.
They also may be showing up in new dendritic cell therapies designed to strengthen the immune response to cancer. If the therapies happen to include some IDO-expressing cells, those could end up helping the cancer, said Mellor, the paper's corresponding author. "All you need is a few of these cells in your dendritic cell vaccine and you don't get stimulation any more, you get suppression," Mellor said.
Their confusing face could also cause hybrids to be lost in B cell-depleting therapies designed to lessen the immune system's attack on joints in rheumatoid arthritis. "These therapies may also deplete IDO-expressing cells and decrease therapy effectiveness because you are eliminating cells that are there to help you," Johnson said.
"This gives us new insight into why these therapies might not be working as well as we think they might," Mellor added. Long-term goals include figuring out how to manipulate the hybrid's activity to benefit patients.
The research was funded by the National Institutes of Health and the Germany-based pharmaceutical company Boehringer-Ingelheim. Mellor is a Georgia Research Alliance Eminent Scholar in Molecular Immunogenetics.


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Cell Survival Protein Discovery Rewrites Immune System Story

A discovery by Walter and Eliza Hall Institute researchers in Melbourne, Australia, reported in the journal Science, is set to rewrite a long-held belief about how the body's immune system establishes its memory.

The findings of Dr Ingela Vikstrom and Associate Professor David Tarlinton, from the institute's Immunology division, centre on immune cells called B cells that produce the antibodies which fight infection.

"B cells and antibody production are the key to the success of all currently used vaccines for immunity in humans," said Associate Professor Tarlinton. "It is therefore critical that we continue to develop our knowledge of the molecular interactions that lead to immune function, which are still only vaguely understood."

Memory B cells are essential for the long-lived immunity that arises after immunisation. To develop into memory cells, B cells have to survive the natural process of apoptosis, or programmed cell death, that occurs following a large immune response.

Associate Professor Tarlinton and Dr Vikstrom study the so-called pro-survival proteins that regulate B cell survival and are therefore responsible for instructing these cells whether to live or die.

Dr Vikstrom said that B cell memory arises in temporary cellular structures called germinal centres that develop in response to activation of the immune system.

"We used genetic and pharmacological methods to identify which pro-survival molecules were essential for the process of 'instructing' these cells to establish germinal centres, as well as instructing activated B cells to proliferate and differentiate into memory B cells," Dr Vikstrom said.

"We studied two well-known pro-survival proteins called Bcl-xL and Mcl-1, which we knew were involved in the process. It surprised us to find that, contrary to popular belief, Mcl-1 is the essential pro-survival protein required for creation and maintenance of B cell memory."

The finding contradicts the widely accepted theory in immunology circles that Bcl-xL is the major pro-survival protein responsible for sustaining the development of memory B cells.

The findings build on a paper Associate Professor Tarlinton and Dr Vikstrom published earlier this year in Proceedings of the National Academy of the Sciences, with institute researchers Dr Andrew Lew and Dr Emma Carrington. Using a molecule that blocked the action of Bcl-xL, the study revealed that Bcl-xL was not necessary for the development of germinal centres and memory B cells, indicating that another pro-survival protein -- now shown to be Mcl-1 -- was the key to survival.

Mcl-1 is known to be an important survival protein for cancers. Associate Professor Tarlinton said the discovery could have repercussions for cancer treatment, as cancerous cells often arise from unregulated cell growth caused by defects in the apoptotic pathway. It could also have implications for the treatment of autoimmune disease and inhibiting transplant rejection.

"All cells have the potential to undergo apoptosis, so developing our understanding of the major proteins responsible for this process will have applications to all cell types in the body," he said.

The work was supported by the National Health and Medical Research Council, the Leukaemia and Lymphoma Society, and the US National Institutes of Health.


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Clue to Unusual Drug-Resistant Breast Cancers Found

Researchers at the University of Illinois at Chicago College of Medicine have found how gene expression that may contribute to drug resistance is ramped up in unusual types of breast tumors. Their findings may offer new therapy targets.

 

The study is published in the Oct. 8 issue of the Journal of Biological Chemistry, where it is designated a paper of the week.

Approximately 70 percent of breast cancers express the estrogen receptor. These "ER-positive" tumors usually respond to hormone-related therapies, such as tamoxifen or aromatase inhibitors. But not always.

"We were interested in a subset of ER-positive tumors that are unusually aggressive and also drug-resistant," said Jonna Frasor, assistant professor of physiology and biophysics at the UIC College of Medicine and principal investigator of the study.

Following up on earlier observations that these aggressive ER-positive tumors express genes that respond both to estrogen and inflammatory factors called cytokines, Frasor and her colleagues focused on the gene for a drug-transporter protein which is believed to pump chemotherapy drugs out of tumor cells, making them resistant.

It is unexpected to find estrogen and inflammatory proteins seemingly working together to drive the cancer's aggressiveness, says Madhumita Pradhan, a student in Frasor's lab and first author of the paper. In many cases, estrogen is known to be protective against inflammatory processes, Pradhan said.

The researchers showed that in breast cancer cells, an inflammatory protein called NFĸB and the estrogen receptor act together to increase expression of the transporter gene. And they were able to show how.

An area on a gene called a promoter acts as an on/off switch that determines whether the gene is transcribed and the protein it encodes is produced. The promoter has spaces called response elements, where molecules can attach and help to turn the switch on or off.

"We found that the estrogen receptor gets recruited to the promoter of this gene," Frasor said. "Once there, the ER allows NFĸB to be recruited to its own response element. Once the second molecule binds, it actually stabilizes the ER and the gene is turned on to a much greater extent than with the ER alone."

This novel mechanism could have important implications in the treatment of breast cancers in which inflammation and estrogen can promote cancer progression, Frasor said.


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Scientists Trick Bacteria Into Embedding Small Molecules in Cell Wall

The finding, described online in the journal ACS Chemical Biology this week, represents the first time scientists have engineered the cell wall of a pathogenic "Gram-positive" bacteria -- organisms responsible not only for Staph infections but also pneumonia, strep throat and many others. The discovery could pave the way for new methods of combating the bacteria responsible for many of the most infectious diseases.

The team engineered one end of their small molecules to contain a peptide sequence that would be recognized by the bacteria. In Staphylococcus aureus, an enzyme called sortase A is responsible for attaching proteins to the cell wall.

"We sort of tricked the bacteria into incorporating something into its cell wall that it didn't actually make," said David Spiegel, a Yale chemist who led the study. "It's as if the cell thought the molecules were its own proteins rather than recognizing them as something foreign."

The scientists focused specifically on the cell wall because it contains many of the components the cell uses to relate to its environment, Spiegel said. "By being able to manipulate the cell wall, we can in theory perturb the bacteria's ability to interact with human tissues and host cells."

The team used three different small molecules in their experiment -- including biotin, fluorescein and azide -- but the technique could be used with other molecules, Spiegel said, as well as with other types of bacteria. Another advantage to the new technique is that the scientists did not have to first genetically modify the bacteria in any way in order for them to incorporate the small molecules, meaning the method should work on naturally occurring bacteria in the human body.

Staph infections, such as the drug-resistant MRSA, have plagued hospitals in recent years. More Americans die each year from Staphylococcus aureus infections alone than from HIV/AIDS, Parkinson's disease or emphysema.

Being able to engineer the cell walls of not only Staphylococcus aureus but a whole family of bacteria could have widespread use in combating these illnesses, Spiegel said, adding that any number of small molecules could be used with their technique. "For example, if we tag these bacteria with small fluorescent tracer molecules, we could watch the progression of disease in the human body in real time." The molecules could also be used to help recruit antibodies that occur naturally in the bloodstream, boosting the body's own immune response to diseases that tend to go undetected, such as HIV/AIDS or cancer.

"This technique has the potential to help illuminate basic biological processes as well as lead to novel therapeutics from some of the most common and deadly diseases affecting us today," Spiegel said.

Other authors of the paper include James Nelson, Alexander Chamessian, Patrick McEnaney, Ryan Murelli and Barbara Kazmiercak (all of Yale University).


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Transgenic Corn Suppresses European Corn Borer, Saves Farmers Billions

Transgenic corn's suppression of the European corn borer has saved Midwest farmers billions of dollars in the past decade, reports a new study in Science.

Research conducted by several Midwest universities shows that suppression of this pest has saved $3.2 billion for corn growers in Illinois, Minnesota, and Wisconsin over the past 14 years with more than $2.4 billion of this total benefiting non-Bt corn growers. Comparable estimates for Iowa and Nebraska are $3.6 billion in total, with $1.9 billion accruing for non-Bt corn growers.

Transgenic corn is engineered to express insecticidal proteins from the bacterium Bacillus thuringiensis (Bt). Bt corn has become widely adopted in U.S. agriculture since its commercialization in 1996. In 2009, Bt corn constituted 63 percent of the U.S. crop.
Corn borer moths can't distinguish between Bt and non-Bt corn, so females lay eggs in both types of fields. Once eggs hatch in Bt corn, young borer larvae feed and die within 24 to 48 hours.

The major benefit of planting Bt corn is reduced yield losses, and Bt acres received this benefit after the growers paid Bt corn technology fees. But as a result of areawide pest suppression, non-Bt acres also experienced yield savings without the cost of Bt technology fees, and thus received more than half of the benefits from growing Bt corn in the region.

"We've assumed for some time that economic benefits were accruing, even among producers who opted not to plant Bt hybrids," said co-author of the study Mike Gray, University of Illinois Extension entomologist and professor in the Department of Crop Sciences. "However, once quantified, the magnitude of this benefit was even more impressive."

Over the past several years, entomologists and corn producers have noticed very low densities of European corn borers in Illinois. In fact, Illinois densities have reached historic lows to the point where many are questioning its pest status, Gray said.

"Since the introduction of Bt corn, initially targeted primarily at the European corn borer, many entomologists and ecologists have wondered if population suppression over a large area would eventually occur," Gray said. "As this research shows, areawide suppression has occurred and dramatically reduced the estimated $1 billion in annual losses caused previously by the European corn borer."

This information also provides incentives for growers to plant non-Bt corn in addition to Bt corn.

"Sustained economic and environmental benefits of this technology will depend on continued stewardship by producers to maintain non-Bt maize refuges to minimize the risk of evolution of Bt resistance in crop pest species," Gray said.

This study titled, "Areawide Suppression of European Corn Borer with Bt Maize Reaps Savings to Non-Bt Maize Growers," will appear in the October 8 edition of Science. The lead researcher is Bill Hutchison of the University of Minnesota. Collaborating authors include Eric Burkness and Roger Moon of the University of Minnesota, Paul Mitchell of the University of Wisconsin, Tim Leslie of Long Island University, Shelby Fleischer of Pennsylvania State University, Mark Abrahamson of the Minnesota Department of Agriculture, Krista Hamilton of the Wisconsin Department of Agriculture, Trade and Consumer Protection, Kevin Steffey and Mike Gray of the University of Illinois, Rick Hellmich of USDA-ARS, Von Kaster of Syngenta Seeds Inc., Tom Hunt and Bob Wright of the University of Nebraska, Ken Pecinovsky of Iowa State University, Tom Rabaey of General Mills Inc., Brian Flood of Del Monte Foods and the late Earl Raun of Pest Management Company.


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HUMAN-LIKE BRAIN FOUND IN WORM

Brain structures directly related to the human brain have just been identified in a marine ragworm, according to a paper published in the latest issue of the journal Cell.

The discovery means that the origins of the human brain can now be traced back at least 600 million years, when we last shared a common ancestor with this species,Platynereis dumerilii, a relative of the common earthworm.

"This worm lives in self-made tubes, explores its environment actively for food, and shows signs of learning behavior," lead author Raju Tomer told Discovery News. "Therefore, we thought this ragworm would be the ideal candidate to look for the counterparts of vertebrate higher brain centers in invertebrates."

Tomer, a scientist at the European Molecular Biology Laboratory (EMBL), and his colleagues suspect that other invertebrates, such as insects, spiders, crustaceans and velvet worms likely also possess the brain structures, called "mushroom bodies," which correspond to our cerebral cortex. The cerebral cortex is a part of the human brain involved in memory, learning, thought, language, consciousness and more.

Tomer and his team used a new technique they developed, called "cellular profiling by image registration," to investigate a large number of genes in the marine ragworm's compact brain. The method enabled the scientists to determine each cell's molecular fingerprint, and to define cell types according to the genes they express, rather than just based on their shape and location, as was done before.

"The development and patterning mechanisms of annelid mushroom bodies and vertebrate brains are too similar to be explained by independent origins," Tomer said. "They must share a common evolutionary precursor, though less complex, which evolved in the last common ancestor more than 600 million years ago."

Co-author Detlev Arendt, also at EMBL, told Discovery News that the sea floor at that time must have been covered with various food sources. In order for organisms to explore these foods, it would have been "advantageous to evolve a brain center that was able to integrate the different smells and ultimately learn what is good and what is bad food."

This first pre-brain probably then consisted of a group of densely packed cells that received and processed very basic information about food and the environment. The structure may have enabled our ancestors crawling over the sea floor to identify food sources, move towards them, and then later to integrate previous experiences into learning.

When French biologist Felix Dujardin first observed the mushroom bodies in invertebrates in 1850, he proposed that these structures bestowed insects with a certain degree of free will control over their instinctive actions. Dujardin's theories have since been largely validated.

Subsequent research has established that the mushroom bodies, which look a bit like mushrooms, serve as a center for associative learning and memory formation, activities that are very similar to those of the cerebral cortex.

"Our cerebral cortex functions by associating sensory information, such as smell, sound and vision, with events, and by storing these associations as memories by modifying the connection strength of neurons," Tomer explained.

"These stored memories then form the basis for making right decisions in the future. Similar mechanisms are found in invertebrates as well, where mushroom bodies are known to be largely responsible for associative learning."

He doubts, however, that invertebrates think and feel just as we do, since their brains are small and lack the "immensely large number of neurons" present in the human brain.

In the future, the scientists hope to further investigate worm brains, and those of other invertebrates, to better determine how they work and to help figure out what the brain of the last common ancestor of vertebrates and these worms might have looked like.

"Our ultimate goal is to reconstruct and understand the evolution of brains in animals, to trace their neuronal composition and their function from the very beginning of animal evolution to something as complex as today's human brain," Arendt said.


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New twists in double helix discovery story are uncovered

Cold Spring Harbor, NY -- The story of the double helix's discovery has a few new twists. A new primary source -- a never-before-read stack of letters to and from Francis Crick, and other historical materials dating from the years 1950-76 -- has been uncovered by two professors at the Watson School of Biological Sciences at Cold Spring Harbor Laboratory (CSHL).

The letters both confirm and extend current knowledge of the circumstances surrounding the epoch-making discovery of DNA's elegant double-helical structure, for which Crick, James D. Watson (now CSHL's chancellor emeritus) and Maurice Wilkins were awarded the Nobel Prize in 1962. Unlike the structure itself, which amazed even its discoverers in its simplicity, the story of the discovery has revealed a complex tangle of people, ambitions and institutional politics behind the process of scientific investigation.

"It's primarily the insights these new letters provide about the personalities of the discoverers that people will find most fascinating," says Alex Gann, Ph.D., who along with Jan Witkowski, Ph.D., uncovered the new Crick materials and co-authored a paper on them that appears in the journal Nature Sept. 30.

Following the publication of landmark works including Watson's confessional The Double Helix in 1968 and Horace Freeland Judson's The Eighth Day of Creation 11 years later, most historians have been content to believe that the archives had been fully explored and would not reveal much more about the double helix story. But 34 of the newfound letters are between Crick and Wilkins and draw attention to what Gann and Witkowski have described as Wilkins' "tortured soul" during the critical period 1951-53, when Watson and Crick were alternately put on, taken off and then restored to an effort to discover DNA's structure.

"We are really between forces which may grind all of us into little pieces," Wilkins wrote to Crick in one letter. As Witkowski explains, "Maurice Wilkins on the one hand wanted to be open - he believed science should be open and was all in favor of cooperation, the exchange of ideas and data; but on the other hand, he was also mindful of his own career: he knew he had to get results and publish papers." As the upstarts Watson and Crick, then unknowns, jockeyed for permission at Cambridge to explore the DNA structure problem, Wilkins, at King's College, was already well engaged in experimentation that would prove vital in determination of the solution. Wilkins' boss at King's, John Randall, hired Rosalind Franklin and had, unknown to Wilkins, assured her that she was in "sole charge" of the DNA work at King's. This led to conflicts between Franklin and Wilkins, who assumed he and Franklin would be partners.

This was but the beginning of a series of now historic misunderstandings. Between the lines of the newly discovered Crick letters with Wilkins, one grasps, on Wilkins' end, the anguish, and on Crick's, what at times comes across as the self-assurance and jocularity of the player possessing superior position.

This is but a fraction of the newly found letters, which were uncovered unexpectedly in the midst of an archival collection of materials donated to Cold Spring Harbor by Sydney Brenner, the distinguished molecular biologist and Nobel laureate, who worked alongside Crick following discovery of the double helix. The two shared an office at Cambridge from 1956 to 1977. Coincidentally, the CSHL Press has just released a new biography of Brenner by Errol Friedberg.

Among the new letters there are some 30 between Crick and George Gamow, dating to 1953-64. Other of his correspondents included Leo Szilard, C.P. Snow, and J. Robert Oppenheimer, among many others. The most important of the new letters, cited in the Gann-Witkowski paper, are now in the process of being digitized at the CSHL Archives (http://library.cshl.edu) to facilitate public access. Mila Pollock, Executive Director of the CSHL Library and Archives, says it is her hope that digitization will proceed so that the Crick correspondence in its entirety will be accessible to all via the Internet. The greater part of the collection resides at the Wellcome Library (http://library.wellcome.ac.uk)


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