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Wednesday, November 10, 2010

Cleaning Infected Blood - Biologists Develop Machine To Remove Viruses From Blood

infectious disease experts designed a machine called the hemopurifier. It works much like a dialysis machine, using thin fibers to capture and remove viruses from the blood it filters. The machine requires the drawing of blood through an artery, which is sent through a tube into the machine, then back into the body. It can treat a number of illnesses.

Every day, 14,000 people are infected with HIV, the virus that leads to AIDs. There's no cure, but now a breakthrough -- a machine that could clean blood, keeping more and more people alive longer.

"I remember lying in bed thinking, 'I am going to die. I'm going to die. I feel so sick.' And I remember thinking laying in that bed, 'And I know exactly what it is,'" HIV patient John Paul Womble, told Ivanhoe. HIV could kill Womble. He watched his father die from the virus and now he is living



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Mumbai Boy won a reality TV show to fund his dream stem cell research

Caezaan Keshvani is currently enrolled in university in New York, USA. Before he began his PhD programme at SUNY Upstate Medical University in Syracuse, he studied at University of Sheffield, UK. What made this all possible for this bright young man who had all but given up hope of ever studying abroad? Winning a reality television show.

Raised in Mumbai, Caezaan's story is a little different from the thousands of Indian students who head abroad each year. After completing his CIE A levels, he planned to head abroad to study. As he planned his next step, tragedy struck. His father, a doctor, was seriously injured in the train bomb blasts in Mumbai in 2006 and most of the family savings were used up for the multiple surgeries he had to undergo. As his study abroad hopes gradually dwindled, Caezaan learned of a reality show that offered the winner a 100-per cent



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Antibodies with More “Hang Time” May Give Researchers a Jump on New HIV Vaccine Strategy

Researchers are inching their way toward a new HIV vaccine strategy by studying the cells of people who have naturally—and bafflingly—strong immune defenses against the virus.

Last year, Howard Hughes Medical Institute investigator Michel C. Nussenzweig's team figured out how to isolate key immune cells from rare individuals who are HIV-positive but carry very low levels of the virus in their blood and have only mild, if any, symptoms.

That study found that these individuals produce a diverse army of antibodies—blood proteins that go after foreign invaders—to target HIV particles from multiple angles.

Now, the team has discovered that some of these so-called 'broadly neutralizing antibodies' are versatile in another way: a single antibody can bind to two structurally distinct sites on an HIV particle at once. The findings are published in the September 29, 2010 issue of the journal Nature.

Although neutralizing antibodies cannot cure HIV once an individual is infected, experiments in primates



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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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