Scientists Discover How Immune Cells Die During HIV Infection; Identify Potential Drug to Block AIDS

Research led by scientists at the Gladstone Institutes has identified the precise chain of molecular events in the human body that drives the death of most of the immune system's CD4 T cells as an HIV infection leads to AIDS. Further, they have identified an existing anti-inflammatory drug that in laboratory tests blocks the death of these cells -- and now are planning a Phase 2 clinical trial to determine if this drug or a similar drug can prevent HIV-infected people from developing AIDS and related conditions.

Two separate journal articles, published simultaneously today in Nature and Science, detail the research from the laboratory of Warner C. Greene, MD, PhD, who directs virology and immunology research at Gladstone, an independent biomedical-research nonprofit. His lab's Science paper reveals how, during an HIV infection, a protein known as IFI16 senses fragments of HIV DNA in abortively infected immune cells. This triggers the activation of the human enzyme caspase-1 and leads to pyroptosis, a fiery and highly inflammatory form of cell death. As revealed in the Nature paper, this repetitive cycle of abortive infection, cell death, inflammation and recruitment of additional CD4 T cells to the infection "hot zone" ultimately destroys the immune system and causes AIDS. The Nature paper further describes laboratory tests in which an existing anti-inflammatory inhibits caspase-1, thereby preventing pyroptosis and breaking the cycle of cell death and inflammation.
"Gladstone has made two important discoveries, first by showing how the body's own immune response to HIV causes CD4 T cell death via a pathway triggering inflammation, and secondly by identifying the host DNA sensor that detects the viral DNA and triggers this death response," said Robert F. Siliciano, MD, PhD, a professor of medicine at Johns Hopkins University, and a Howard Hughes Medical Institute investigator. "This one-two punch of discoveries underscores the critical value of basic science -- by uncovering the major cause of CD4 T cell depletion in AIDS, Dr. Greene's lab has been able to identify a potential new therapy for blocking the disease's progression and improving on current antiretroviral medications."
The research comes at a critical time, as so-called AIDS fatigue leads many to think that HIV/AIDS is solved. In fact, HIV infected an additional 2.3 million people last year, according to UNAIDS estimates, bringing the global total of HIV-positive people to 35.3 million. Antiretroviral medications (ARVs) can prevent HIV infections from causing AIDS, but they do not cure AIDS. Further, those taking ARVs risk both a latent version of the virus, which can rebound if ARVs are discontinued, and the premature onset of diseases that normally occur in aging populations. Plus, some 16 million people who carry the virus do not have access to ARVs, according to World Health Organization estimates.
Seeking solutions for all these challenges, the new Gladstone discovery builds on earlier research from Dr. Greene's lab, published in Cell in 2010. This study showed how HIV attempts, but fails, to productively infect most of the immune system's CD4 T cells. In an attempt to protect the body from the spreading virus, these immune cells then commit "cellular suicide," leading to the collapse of the immune system -- and AIDS.
After that research, the Gladstone scientists began to look for ways to prevent this process by studying exactly how the suicidal response is initiated. Working in the laboratory with human spleen and tonsil tissue, as well as lymph-node tissue from HIV-infected patients, the researchers found that these so-called abortive infections leave fragments of HIV's DNA in the immune cells. As described in Nature, pyroptosis ensues as immune cells rupture and release inflammatory signals that attract still more cells to repeat the death cycle.
"Our studies have investigated and identified the root cause of AIDS -- how CD4 T cells die," said Gladstone Staff Research Investigator Gilad Doitsh, PhD, who is the Nature paper's lead author, along with Nicole Galloway and Xin Geng, PhD. "Despite some 30 years of HIV research, this key HIV/AIDS process has remained pretty much a black box."
Once the scientists discovered this key process, as described in Nature, they began to investigate how the body senses the fragments of HIV's DNA in the first place, before alerting the enzyme caspase-1 to launch an immune response in the CD4 T cells. To identify the so-called DNA sensor, the scientists found a way to genetically manipulate CD4 T cells in spleen and tonsil tissue. In doing so, they discovered that reducing the activity of a protein known as IFI16 inhibited pyroptosis, explained Zhiyuan Yang, PhD, a Gladstone postdoctoral fellow who is one of the paper's two lead authors.
"This identified IFI16 as the DNA sensor, which then sends signals to caspase-1 and triggers pyroptosis," says Kathryn M. Monroe, PhD, the Science paper's other lead author, who completed the research while a postdoctoral fellow at Gladstone. "We can't block a process until we understand all of its steps -- so this discovery is critical to devising ways to inhibit the body's own destructive response to HIV. We have high hopes for the upcoming clinical trial."
The Phase 2 trial -- which will test an existing anti-inflammatory's ability to block inflammation and pyroptosis in HIV-infected people -- promises to validate a variety of expected advantages to this therapy. For example, by targeting the human body, or host, instead of the virus, the drug is likely to avoid the rapid emergence of drug resistance that often plagues the use of ARVs. The anti-inflammatory may also provide a bridge therapy for the millions without access to ARVs, while also reducing persistent inflammation in HIV-infected people already on ARVs. Many suspect this inflammation drives the early onset of aging-related conditions such as dementia and cardiovascular disease. By reducing inflammation, the drug might also prevent expansion of a reservoir of latent virus that hides in the body where it thwarts a cure for HIV/AIDS.
"This has been an absolutely fascinating voyage of discovery," said Dr. Greene, who is also a professor of medicine, microbiology and immunology at the University of California, San Francisco, with which Gladstone is affiliated. "Every time we turned over an 'experimental rock' in the studies, a new surprise jumped out."
 

Journal References:

1. Gilad Doitsh, Nicole L. K. Galloway, Xin Geng, Zhiyuan Yang, Kathryn M. Monroe, Orlando Zepeda, Peter W. Hunt, Hiroyu Hatano, Stefanie Sowinski, Isa Muñoz-Arias, Warner C. Greene. Cell death by pyroptosis drives CD4 T-cell depletion in HIV-1 infection. Nature, 2013; DOI: 10.1038/nature12940
2. K. M. Monroe, Z. Yang, J. R. Johnson, X. Geng, G. Doitsh, N. J. Krogan, W. C. Greene. IFI16 DNA Sensor Is Required for Death of Lymphoid CD4 T Cells Abortively Infected with HIV. Science, 2013; DOI: 10.1126/science.1243640

Courtesy: ScienceDaily
 

TB Bacteria Mask Their Identity to Intrude Into Deeper Regions of Lungs

TB-causing bacteria appear to mask their identity to avoid recognition by infection-killing cells in the upper airways. The bacteria call up more permissive white blood cells in the deeper regions of the lungs and hitch a ride inside them to get into the host's body.

Flying under the radar: tuberculosis-causing mycobacteria initiate infection in the lower lung to evade pathogen-killing cells. (Credit: Ramakrishnan Lab/University of Washington)

Details on this finding are reported Dec. 16 in the advanced online edition of the journal Nature. The research was a collaboration between the University of Washington and the Seattle Biomedical Research Institute.
Dr. Lalita Ramakrishan, who studies how TB evades the body's immune system and manipulates the body's defenses for its own ends, is the senior author. She is a UW professor of microbiology, medicine and immunology. The lead author is C.J. Cambier of the UW Department of Immunology.
Ramakrishnan noted that the recent study also suggests an explanation for the longstanding observation that tuberculosis infections begin in the comparatively sterile lower lungs. In the upper respiratory tract, resident microbes and inhaled microbes of a variety of species signal their presence.
These tip-offs alert and attract many infection-fighting cells to the upper airways. The presence of other microbes in the upper airway may thereby help to keep TB infections at bay by creating a hostile environment.
Their presence may explain why TB is a less contagious disease than those caused by several other respiratory pathogens.
To cause disease, TB bacteria must sneak through this well-patrolled area and head for parts of the lungs where fewer microbiocidal cells are policing.
Almost like intruders wearing a stocking over their faces to keep surveillance cameras from clearly recording their features, the TB pathogens produce particular types of fatty substances, or lipids, on their cell surfaces.
These lipids, abbreviated as PDIM, are already known to be associated with bacterial virulence. The researchers showed that PDIM lipids function by masking the underlying molecular patterns that would reveal their dangerous nature to macrophages, a first-line defense of infection-fighting cells.
At the same time, a related lipid -- called PGL -- on the bacterium's cell surface promotes the recruitment of cells described as permissive macrophages. These clean-up cells engulf but don't kill the TB pathogens. Instead, they take them across the lung lining, deep into the lung tissue where the bacteria can establish an infection.
According to the researchers on this study, these mechanisms appear to allow certain TB pathogens to avoid detection by the pattern recognition receptors that enable some infection-fighting cells to spot a variety of different disease microbes through the pathogen-associated molecular patterns on or near their cell surface.
Like most other bacteria, TB pathogens have many of these telltale molecular patterns that should activate an immune response. However, TB pathogens have evolved mechanisms to circumvent tripping the alarm, in this case by physically masking the otherwise detectable pattern. This cover-up allows them to infect the airway initially by avoiding the infection-fighting cell populations that are detrimental to their survival, the researchers noted.
The TB pathogens then use the other lipid molecule, PGL, to co-opt a host chemical pathway that triggers the recruitment of the permissive macrophages.
The present study expands on earlier work in the Ramakrishan and collaborative labs, which helped describe the strategies by which TB pathogens manipulate host pathways for their own purposes after they enter certain host cells.
These include the secretion of proteins that help expand the niche for TB by recruiting macrophages to the early lung tubercles characteristic of the disease. The present study describes earlier stages in infection, when the pathogens first come in contact with their potential host at the surface of the lining of the lung.
"The current study suggests the manner in which the TB pathogens manipulate recruitment of the first responding macrophages to gain access to their preferred niche," the researchers noted.
"The choreographed entry involves two related TB cell lipids acting in concert to avoid one host pathway while inducing another," they wrote. The findings link the previously known, absolutely essential virulence factor on the surface of TB cells, PDIM, to the evasion of immune cell detection. They also might explain why a certain pathogen molecular pattern recognition system is dispensable in protecting against TB. On the other hand, PGL is not required on the surface of TB cells for them to infect the body.
Ramakrishnan noted that globally, a lot of samples of TB taken from infected patients do not have PGL. "However," she and her research team noted, "the importance of PGL in mediating TB virulence or transmission is underscored by its presence in many of the W-Beijing strains" of TB which are starting to rapidly appear in more patient samples, and which have predominated in outbreaks in North America.
Ramakrishnan explains that their findings suggest how PGL may play an important role in increasing TB's infectivity.
"The presence of PGL in ancestral strains of TB suggest it played an integral role in the evolution of TB infectivity," the researchers noted. "TB is an ancient disease and the enhanced infectivity conferred by PGL may have been essential for most of its history before human crowding, with its increased opportunity for transmission, made it dispensable."
The study findings, and previous work on TB, might also explain why smaller droplets of TB are more infectious than larger ones. Only the smaller droplets can make their way down into the lower airways. On the flip side, all it takes is 3 or fewer TB mycobacteria with PGL-producing ability to enter the lower lungs and start an infection.
 

Journal Reference:

1. C. J. Cambier, Kevin K. Takaki, Ryan P. Larson, Rafael E. Hernandez, David M. Tobin, Kevin B. Urdahl, Christine L. Cosma, Lalita Ramakrishnan. Mycobacteria manipulate macrophage recruitment through coordinated use of membrane lipids. Nature, 2013; DOI: 10.1038/nature12799

Courtesy: ScienceDaily
 

New -- And Reversible -- Cause of Aging: Naturally Produced Compound Rewinds Aspects of Age-Related Demise in Mice

Researchers have discovered a cause of aging in mammals that may be reversible.

Sirt1 protein, red, circles the cell's chromosomes, blue. (Credit: Ana Gomes)

The essence of this finding is a series of molecular events that enable communication inside cells between the nucleus and mitochondria. As communication breaks down, aging accelerates. By administering a molecule naturally produced by the human body, scientists restored the communication network in older mice. Subsequent tissue samples showed key biological hallmarks that were comparable to those of much younger animals.
"The aging process we discovered is like a married couple -- when they are young, they communicate well, but over time, living in close quarters for many years, communication breaks down," said Harvard Medical School Professor of Genetics David Sinclair, senior author on the study. "And just like with a couple, restoring communication solved the problem."
This study was a joint project between Harvard Medical School, the National Institute on Aging, and the University of New South Wales, Sydney, Australia, where Sinclair also holds a position.
The findings are published Dec. 19 in Cell.
Communication breakdown
Mitochondria are often referred to as the cell's "powerhouse," generating chemical energy to carry out essential biological functions. These self-contained organelles, which live inside our cells and house their own small genomes, have long been identified as key biological players in aging. As they become increasingly dysfunctional over time, many age-related conditions such as Alzheimer's disease and diabetes gradually set in.
Researchers have generally been skeptical of the idea that aging can be reversed, due mainly to the prevailing theory that age-related ills are the result of mutations in mitochondrial DNA -- and mutations cannot be reversed.
Sinclair and his group have been studying the fundamental science of aging -- which is broadly defined as the gradual decline in function with time -- for many years, primarily focusing on a group of genes called sirtuins. Previous studies from his lab showed that one of these genes, SIRT1, was activated by the compound resveratrol, which is found in grapes, red wine and certain nuts.
Ana Gomes, a postdoctoral scientist in the Sinclair lab, had been studying mice in which this SIRT1 gene had been removed. While they accurately predicted that these mice would show signs of aging, including mitochondrial dysfunction, the researchers were surprised to find that most mitochondrial proteins coming from the cell's nucleus were at normal levels; only those encoded by the mitochondrial genome were reduced.
"This was at odds with what the literature suggested," said Gomes.
As Gomes and her colleagues investigated potential causes for this, they discovered an intricate cascade of events that begins with a chemical called NAD and concludes with a key molecule that shuttles information and coordinates activities between the cell's nuclear genome and the mitochondrial genome. Cells stay healthy as long as coordination between the genomes remains fluid. SIRT1's role is intermediary, akin to a security guard; it assures that a meddlesome molecule called HIF-1 does not interfere with communication.
For reasons still unclear, as we age, levels of the initial chemical NAD decline. Without sufficient NAD, SIRT1 loses its ability to keep tabs on HIF-1. Levels of HIF-1 escalate and begin wreaking havoc on the otherwise smooth cross-genome communication. Over time, the research team found, this loss of communication reduces the cell's ability to make energy, and signs of aging and disease become apparent.
"This particular component of the aging process had never before been described," said Gomes.
While the breakdown of this process causes a rapid decline in mitochondrial function, other signs of aging take longer to occur. Gomes found that by administering an endogenous compound that cells transform into NAD, she could repair the broken network and rapidly restore communication and mitochondrial function. If the compound was given early enough -- prior to excessive mutation accumulation -- within days, some aspects of the aging process could be reversed.
Cancer connection
Examining muscle from two-year-old mice that had been given the NAD-producing compound for just one week, the researchers looked for indicators of insulin resistance, inflammation and muscle wasting. In all three instances, tissue from the mice resembled that of six-month-old mice. In human years, this would be like a 60-year-old converting to a 20-year-old in these specific areas.
One particularly important aspect of this finding involves HIF-1. More than just an intrusive molecule that foils communication, HIF-1 normally switches on when the body is deprived of oxygen. Otherwise, it remains silent. Cancer, however, is known to activate and hijack HIF-1. Researchers have been investigating the precise role HIF-1 plays in cancer growth.
"It's certainly significant to find that a molecule that switches on in many cancers also switches on during aging," said Gomes. "We're starting to see now that the physiology of cancer is in certain ways similar to the physiology of aging. Perhaps this can explain why the greatest risk of cancer is age. "
"There's clearly much more work to be done here, but if these results stand, then many aspects of aging may be reversible if caught early," said Sinclair.
The researchers are now looking at the longer-term outcomes of the NAD-producing compound in mice and how it affects the mouse as a whole. They are also exploring whether the compound can be used to safely treat rare mitochondrial diseases or more common diseases such as Type 1 and Type 2 diabetes. Longer term, Sinclair plans to test if the compound will give mice a healthier, longer life.
 

Journal Reference:

1. Ana P. Gomes, Nathan L. Price, Alvin J.Y. Ling, Javid J. Moslehi, Magdalene K. Montgomery, Luis Rajman, James P. White, João S. Teodoro, Christiane D. Wrann, Basil P. Hubbard, Evi M. Mercken, Carlos M. Palmeira, Rafael de Cabo, Anabela P. Rolo, Nigel Turner, Eric L. Bell, David A. Sinclair. Declining NAD Induces a Pseudohypoxic State Disrupting Nuclear-Mitochondrial Communication during Aging. Cell, 2013; 155 (7): 1624 DOI: 10.1016/j.cell.2013.11.037

Courtesy: ScienceDaily
 

First Step of Metastasis Halted in Mice With Breast Cancer

Cell biologists at Johns Hopkins have identified a unique class of breast cancer cells that lead the process of invasion into surrounding tissues. Because invasion is the first step in the deadly process of cancer metastasis, the researchers say they may have found a weak link in cancer's armor and a possible new target for therapy. A summary of their results will be published online in the journal Cell on Dec. 12.

A breast tumor (blue) uses leader cells (green) to invade muscle tissue (red) in a mouse. (Credit: Kevin Cheung, courtesy of Cell)

"Metastasis is what most threatens breast cancer patients, and we have found a way to stop the first part of the process in mice," says Andrew Ewald, Ph.D., assistant professor of cell biology at the Johns Hopkins School of Medicine.

Before metastasis occurs, single cells on the edge of a tumor, termed leader cells, form protrusions into the surrounding tissue, like someone dipping a toe in to test the water before deciding to venture farther, Ewald says. If the conditions are right, the leader cells act as guides, with many tumor cells following behind, as they escape the confines of the tumor into the healthy tissue beyond. Full metastasis occurs when the cells succeed in migrating to a new location -- the lungs, for example -- and set up shop, creating a new tumor.

Beginning with the idea that some cells in the tumor might be more invasive than others, Ewald's team grew mouse tumors in the laboratory in special 3-D gels that mimic the environment that surrounds breast tumors in human patients. Kevin Cheung, M.D., a medical oncology fellow in the Ewald lab, observed that the cancer cells infiltrated the gels in groups, with a few cells out in front and the rest following behind.

Looking for a molecular cause for the apparent "leadership" seen in the initiating cells, Cheung searched for proteins that were uniquely present in the leader cells. They identified one protein, cytokeratin 14, or K14, that was present in almost all leader cells but was very rare in the noninvasive parts of the tumor. When the team looked at tumors from mice that had other types of breast cancer -- some more prone to invasion and others less prone -- all had leader cells containing K14. The more invasive a tumor was, the more cells with K14 it had.

The team then grew breast tumors from 10 breast cancer patients in 3-D gels and found that the leader cells in these human tumors also contained K14. "Our research shows that the most invasive cells in breast tumors express K14 across all types of breast cancer," says Cheung. "Now we need to learn how to eliminate these leader cells from breast tumors in patients."

K14 is a protein that helps form the internal "skeleton" of many cell types, giving them structure and helping them to move. Although its presence in leader cells made its involvement in the invasion process seem likely, the investigators conducted further experiments to determine whether it was essential to the process or merely coincidental to it.

The researchers removed breast tumors from mice with breast cancer and divided them into an experimental group and a control group. Each group of tumors was exposed to viruses that had been reprogrammed to carry pieces of genetic material into the cells. The experimental group received genetic material designed to prevent the production of K14; the control group got genetic material that didn't affect the cells. The two groups of tumors were then transplanted into healthy mice, with experimental tumors on one side and control tumors on the other side of the same mouse.

After letting the tumors grow for some time, the team removed and examined them. As expected, in the control group, leader cells were present, contained K14 and were leading vigorous invasions into normal tissue. In the experimental tumors, whose cells had no K14, the tumor borders were smooth, with essentially no invasions occurring.

"We're still several years away from being able to use these insights to help patients with breast cancer, but we now know which tumor cells are the most dangerous, and we know some of the proteins they rely on to do their dirty work," says Ewald. "Just a few leader cells are sufficient to start the process of metastasis, and they require K14 to lead the invasion."

He also notes that K14 is present in cells within many other organs, so K14 may play a similar role in other types of cancer.

Journal Reference:

1. Kevin J. Cheung, Edward Gabrielson, Zena Werb, Andrew J. Ewald. Collective Invasion in Breast Cancer Requires a Conserved Basal Epithelial Program. Cell, 12 December 2013 DOI: 10.1016/j.cell.2013.11.029

Courtesy: ScienceDaily

Simple Mathematical Formula Describes Human Struggles

Would you believe that a broad range of human struggles can be understood by using a mathematical formula? From child-parent struggles to cyber-attacks and civil unrest, they can all be explained with a simple mathematical expression called a "power-law."

The manner in which a baby's cries escalate against its parent is comparable to the way riots in Poland escalated in the lead-up to the collapse of the Soviet Union. (Credit: © erllre / Fotolia)

In a sort of unified theory of human conflict, scientists have found a way to mathematically describe the severity and timing of human confrontations that affect us personally and as a society.

For example, the manner in which a baby's cries escalate against its parent is comparable to the way riots in Poland escalated in the lead-up to the collapse of the Soviet Union. It comes down to the fact that the perpetrator in both cases (e.g. baby, rioters) adapts quickly enough to escalate its attacks against the larger, but more sluggish entity (e.g. parent, government), who is unable, or unwilling, to respond quickly enough to satisfy the perpetrator, according to a new study published in Nature's Scientific Reports.

"By picking out a specific baby (and parent), and studying what actions of the parent make the child escalate or de-escalate its cries, we can understand better how to counteract cyber-attacks against a particular sector of U.S. cyber infrastructure, or how an outbreak of civil unrest in a given location (e.g. Syria) will play out, following particular government interventions," says Neil Johnson, professor of physics and the head of the interdisciplinary research group in Complexity, at the College of Arts and Sciences at the University of Miami (UM) and corresponding author of the study.

Respectively, the study finds some remarkable similarities between seemingly disconnected confrontations. For instance:

• The escalation of violent attacks in Magdalena, Colombia -- though completely cut off from the rest of the world -- is actually representative of all modern wars. Meanwhile, the conflict in Sierra Leone, Africa, has exactly the same dynamics as the narco-guerilla war in Antioquia, Colombia.
• The pattern of attacks by predatory traders against General Electric (GE) stock is equivalent to the pattern of cyber-attacks against the U.S. hi-tech electronics sector by foreign groups, which in turn mimics specific infants and parents.
• New insight into the controversial 'Bloody Sunday' attack by the British security forces, against civilians, on January 30,1972, reveals that Bloody Sunday appears to be the culmination of escalating Provisional Irish Republican Army attacks, not their trigger, hence raising new questions about its strategic importance.

The findings show that this mathematical formula of the form AB-C is a valuable tool that can be applied to make quantitative predictions concerning future attacks in a given confrontation. It can also be used to create an intervention strategy against the perpetrators and, more broadly, as a quantitative starting point for cross-disciplinary theorizing about human aggression, at the individual and group level, in both real and online worlds.

Journal Reference:

1. Neil F. Johnson, Pablo Medina, Guannan Zhao, Daniel S. Messinger, John Horgan, Paul Gill, Juan Camilo Bohorquez, Whitney Mattson, Devon Gangi, Hong Qi, Pedro Manrique, Nicolas Velasquez, Ana Morgenstern, Elvira Restrepo, Nicholas Johnson, Michael Spagat, Roberto Zarama. Simple mathematical law benchmarks human confrontations.Scientific Reports, 2013; 3 DOI: 10.1038/srep03463

Courtesy: ScienceDaily

New Strain of Bird Flu Packs a Punch Even After Becoming Drug-Resistant

 Researchers at the Icahn School of Medicine at Mount Sinai reported that a virulent new strain of influenza -- the virus that causes the flu -- appears to retain its ability to cause serious disease in humans even after it develops resistance to antiviral medications. The finding was included in a study that was published today in the journal Nature Communications.

This negatively-stained transmission electron micrograph (TEM) captured some of the ultrastructural details exhibited by the new influenza A (H7N9) virus. (Credit: CDC/Cynthia S. Goldsmith and Thomas Rowe)

It is not uncommon for influenza viruses to develop genetic mutations that make them less susceptible to anti-flu drugs. However, these mutations usually come at a cost to the virus, weakening its ability to replicate and to spread from one person to another.

Initial reports suggested that H7N9, an avian strain of influenza A that emerged in China last spring, could rapidly develop a mutation that made it resistant to treatment with the antiviral medication Tamiflu (oseltamivir). However, patients in whom drug resistance developed often had prolonged, severe infections and poor clinical outcomes. No vaccine is currently available to prevent H7N9, which infected at least 135 people and caused 44 deaths during the outbreak. In the absence of a vaccine, antiviral drugs are the only means of defense for patients who are infected with new strains of the flu.

"In this outbreak, we saw some differences in the behavior of H7N9 and other avian influenza strains that can infect humans, beginning with the rapid development of antiviral resistance in some people who were treated with oseltamivir and the persistence of high viral loads in those patients," said lead investigator Nicole Bouvier, MD, Assistant Professor of Medicine, Infectious Diseases at the Icahn School of Medicine at Mount Sinai.

Specifically, the investigators found that a drug-resistant H7N9 virus retained its ability to replicate in human respiratory cells and was comparable to a non-resistant form of the virus in producing severe illness in animal models. And although H7N9 appears to have a limited ability to spread readily from human to human, transmissibility in animal models was comparable between drug-susceptible and drug-resistant strains. "Transmission was inefficient for both of the H7N9 viruses that we tested in our experiments," said Dr. Bouvier. "But surprisingly, transmission of the drug-resistant virus was no less efficient than that of the drug-sensitive version."

"Many of the people infected with H7N9 during the outbreak in China were elderly or had other conditions that predisposed them to severe influenza illness," observed Dr. Bouvier. "Nevertheless, our study suggests that flu viruses can indeed develop drug-resistant mutations without suffering a penalty in terms of their own fitness."

Older antiviral drugs such as amantadine are no longer effective in treating most strains of the flu that infect humans. Newer antiviral drugs called neuraminidase inhibitors block an enzyme that helps the virus replicate. These drugs include Tamiflu, a pill, and Relenza (zanamivir), a powder that is inhaled. Both medications have drawbacks: flu viruses can develop resistance to the medications in people who take them, and, in many parts of the world, neither drug is available in an intravenous form to treat those with severe infections.

"Our study underscores the need to develop a bigger arsenal of antiviral drugs and vaccines, which will allow us to outsmart the influenza virus," said Dr. Bouvier. "Researchers at Mount Sinai are actively engaged in identifying new targets for drug therapy and are working to develop a universal vaccine that will prevent multiple strains of influenza."

Journal Reference:

1. Rong Hai, Mirco Schmolke, Victor H. Leyva-Grado, Rajagowthamee R. Thangavel, Irina Margine, Eric L. Jaffe, Florian Krammer, Alicia Solórzano, Adolfo García-Sastre, Peter Palese, Nicole M. Bouvier. Influenza A(H7N9) virus gains neuraminidase inhibitor resistance without loss of in vivo virulence or transmissibility. Nature Communications, 2013; 4 DOI: 10.1038/ncomms3854

Courtesy: ScienceDaily

Researchers Block Replication of AIDS Virus

A multidisciplinary team of scientists from Spanish universities and research centres, among which is the University of Valencia, has managed to design small synthetic molecules capable of joining to the genetic material of the AIDS virus and blocking its replication.

This achievement has been obtained for the first time in the world by a group of researcher led by José Gallego from Universidad Católica de Valencia "San Vicente Mártir." The University of Valencia, the Príncipe Felipe Research Centre, and the Instituto de Salud Carlos III have participated. The work has been recently published by Angewandte Chemie International Edition.
The newly designed synthetic molecules inhibit the output of genetic material of the virus from the infected cell nucleus to the cytoplasm, thus the virus replication is blocked and avoids the infection of other cells.
The genetic material of the AIDS virus, or HIV-1, is formed by ribonucleic acid (RNA), and encodes several proteins that allow it to penetrate the human cells and reproduce within them. The new virus inhibitors, called terphenyls, developed by this group of scientists, were designed by computer to reproduce the interactions of one of the proteins encoded by the virus, the viral protein Rev.
In this way, the terphenyls join Rev's receptor in the viral RNA, preventing the interaction between the protein and its RNA receptor. This interaction is necessary for the virus genetic material to leave the infected cell nucleus and, thus, it is essential for the survival of HIV-1. The fact that the terphenyls block the virus genetic material output of the cell prevents the infection of other cells.
This discovery is the result of a close collaboration between three research groups throughout several years. Thus, the scientists of the Universitat Católica de Valencia were in charge of the computational design and verified experimentally that the terphenyls were capable of joining the Rev receptor in the viral RNA and inhibit the interaction between this RNA and the protein.
For its part, the molecules were synthesised in professor Santos Fustero's organic Chemistry laboratory in the Príncipe Felipe Research Centre and the University of Valencia. Also, through experiments with cells infected by the virus, the group of José Alcamí in the Instituto de Salud Carlos III demonstrated that the inhibitors block the replication of the HIV-1 and inhibit the function of the Rev protein, confirming this way the validity of the models generated by computer.
Traditionally, pharmaceutical companies have focused on the development of medicines that act on target proteins, as the approach to the receptors made out of RNA is considerably complex.
Although several natural antibiotics act at the bacterial ribosomal RNA level, up to now designing by computer a new synthetic chemical entity capable of joining RNA target and have a relevant pharmacological effect was not possible. The terphenyl structures identified in this research could open new ways to approach other therapeutic targets formed by nucleic acids.
On the other hand, the infection by HIV affected 34 million people worldwide in 2010, according to the World Health Organisation (WHO). The emergence of resistance to the current antiretroviral therapies and the lack of an effective vaccine highlight the necessity of identifying the new medicines that act on other virus targets. Rev protein constitutes one of this alternative targets, but so far they it has not been possible to develop antiviral agents based in their inhibition.
The results of this research have been the objectives of a patent application, and the three laboratories involved in the research keep their collaboration with the objective of improving the pharmacological properties of new Rev inhibitors.
 

 Journal Reference:

1. Luis González-Bulnes, Ignacio Ibáñez, Luis M. Bedoya, Manuela Beltrán, Silvia Catalán, José Alcamí, Santos Fustero, José Gallego. Structure-Based Design of an RNA-Bindingp-Terphenylene Scaffold that Inhibits HIV-1 Rev Protein Function. Angewandte Chemie International Edition, 2013; DOI: 10.1002/anie.201309856

Courtesy: ScienceDaily
 

Methylation Signaling Controls Cancer Growth

A study led by researchers at Boston University School of Medicine (BUSM) demonstrates a new mechanism involving a signaling protein and its receptor that may block the formation of new blood vessels and cancer growth. The findings are published in the December issue of Science Signaling.

gnaling protein produced by damaged cells, which binds to one of its receptors VEGFR-2, located on the surface of blood vessel cells. Once VEGF is bound to its receptor, it is activated and sends a biochemical signal to the inside of the blood vessel cell to initiate angiogenesis. There are currently multiple Federal Drug Administration-approved medications that target this process. However these medications are limited by insufficient efficacy and the development of resistance.

The researchers demonstrated that a biochemical process called methylation, which can regulate gene expression, also affects VEGFR-2, and this can lead to angiogenesis. Using multiple methods, the researchers were able to interfere with the methylation process of VEGFR-2 and subsequently block angiogenesis and tumor growth.

"The study points to the methylation of VEGFR-2 as an exciting, yet unexplored drug target for cancer and ocular angiogenesis, ushering in a new paradigm in anti-angiogenesis therapy," said Nader Rahimi, PhD, associate professor of pathology, BUSM, who served as the study's senior investigator.

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The above story is based on materials provided by Boston University Medical Center, via EurekAlert!, a service of AAAS. 

Courtesy: ScienceDaily

Gene Mutation for Excessive Alcohol Drinking Found

Researchers have discovered a gene that regulates alcohol consumption and when faulty can cause excessive drinking. They have also identified the mechanism underlying this phenomenon.

The study showed that normal mice show no interest in alcohol and drink little or no alcohol when offered a free choice between a bottle of water and a bottle of diluted alcohol.
However, mice with a genetic mutation to the gene Gabrb1 overwhelmingly preferred drinking alcohol over water, choosing to consume almost 85% of their daily fluid as drinks containing alcohol -- about the strength of wine.
The consortium of researchers from five UK universities -- Newcastle University, Imperial College London, Sussex University, University College London and University of Dundee -- and the MRC Mammalian Genetics Unit at Harwell, funded by the Medical Research Council (MRC), Wellcome Trust and ERAB, publish their findings today in Nature Communications.
Dr Quentin Anstee, Consultant Hepatologist at Newcastle University, joint lead author said: "It's amazing to think that a small change in the code for just one gene can have such profound effects on complex behaviours like alcohol consumption.
"We are continuing our work to establish whether the gene has a similar influence in humans, though we know that in people alcoholism is much more complicated as environmental factors come into play. But there is the real potential for this to guide development of better treatments for alcoholism in the future."
Identifying the gene for alcohol preference
Working at the MRC Mammalian Genetics Unit, a team led by Professor Howard Thomas from Imperial College London introduced subtle mutations into the genetic code at random throughout the genome and tested mice for alcohol preference. This led the researchers to identify the gene Gabrb1 which changes alcohol preference so strongly that mice carrying either of two single base-pair point mutations in this gene preferred drinking alcohol (10% ethanol v/v -- about the strength of wine), over water.
The group showed that mice carrying this mutation were willing to work to obtain the alcohol-containing drink by pushing a lever and, unlike normal mice, continued to do so even over long periods. They would voluntarily consume sufficient alcohol in an hour to become intoxicated and even have difficulty in coordinating their movements.
The cause of the excessive drinking was tracked down to single base-pair point mutations in the gene Gabrb1, which codes for the beta 1 subunit, an important component of the GABA_A receptor in the brain. This receptor responds to the brain's most important inhibitory chemical messenger (GABA) to regulate brain activity. The researchers found that the gene mutation caused the receptor to activate spontaneously even when the usual GABA trigger was not present.
These changes were particularly strong in the region of the brain that controls pleasurable emotions and reward, the nucleus accumbens, as Dr Anstee explains: "The mutation of the beta1 containing receptor is altering its structure and creating spontaneous electrical activity in the brain in this pleasure zone, the nucleus accumbens. As the electrical signal from these receptors increases, so does the desire to drink to such an extent that mice will actually work to get the alcohol, for much longer than we would have expected."
Professor Howard Thomas said: "We know from previous human studies that the GABA system is involved in controlling alcohol intake. Our studies in mice show that a particular subunit of GABA_A receptor has a significant effect and most importantly the existence of these mice has allowed our collaborative group to investigate the mechanism involved. This is important when we come to try to modify this process first in mice and then in man."
Huge burden of alcohol addiction
Initially funded by the MRC, the 10-year project aimed to find genes affecting alcohol consumption. Professor Hugh Perry, Chair of the MRC's Neurosciences and Mental Health Board, said: "Alcohol addiction places a huge burden on the individual, their family and wider society. There's still a great deal we don't understand about how and why consumption progresses into addiction, but the results of this long-running project suggest that, in some individuals, there may be a genetic component. If further research confirms that a similar mechanism is present in humans, it could help us to identify those most at risk of developing an addiction and ensure they receive the most effective treatment."
The project was led by Professor Howard Thomas from Imperial College London and initiated at the MRC Mammalian Genetics Unit. The consortium now involves researchers at five UK universities -- Imperial College London, Newcastle University, Sussex University, University College London and the University of Dundee. Senior investigators are Dr Quentin Anstee at Newcastle University and Dr Susanne Knapp at Imperial College London (joint lead authors); Professor Dai Stephens at Sussex University; Professor Trevor Smart at University College London; Professor Jeremy Lambert and Dr Delia Belelli at the University of Dundee; and Professor Steve Brown at the MRC Mammalian Genetics Unit.
 

Journal Reference:

1. Quentin M. Anstee, Susanne Knapp, Edward P. Maguire, Alastair M. Hosie, Philip Thomas, Martin Mortensen, Rohan Bhome, Alonso Martinez, Sophie E. Walker, Claire I. Dixon, Kush Ruparelia, Sara Montagnese, Yu-Ting Kuo, Amy Herlihy, Jimmy D. Bell, Iain Robinson, Irene Guerrini, Andrew McQuillin, Elizabeth M.C. Fisher, Mark A. Ungless, Hugh M.D. Gurling, Marsha Y. Morgan, Steve D.M. Brown, David N. Stephens, Delia Belelli, Jeremy J. Lambert, Trevor G. Smart, Howard C. Thomas. Mutations in the Gabrb1 gene promote alcohol consumption through increased tonic inhibition. Nature Communications, 2013; 4 DOI: 10.1038/ncomms3816

Courtesy: ScienceDaily
 

Stuck On Flu

Researchers at the University of California, San Diego School of Medicine have shown for the first time how influenza A viruses snip through a protective mucus net to both infect respiratory cells and later cut their way out to infect other cells.

 

In this cartoon, experimental magnetic beads are coated with human or pig mucins (grey mesh), which are proteins containing sialic acids (red or blue diamonds), part of a protective mucus net secreted by respiratory cells. Humans and pigs have different sialic acids on their mucins, as indicated by the bottom molecular structures. The flu virus (green stars) bind to and cleave off sialic acids, snipping through the host mucus net to infect cells. (Credit: UC San Diego Health System)

 

The findings, published online in Virology Journal by principal investigator Pascal Gagneux, PhD, associate professor in the Department of Cellular and Molecular Medicine, and colleagues, could point the way to new drugs or therapies that more effectively inhibit viral activity, and perhaps prevent some flu infections altogether.
Scientists have long known that common strains of influenza specifically seek and exploit sialic acids, a class of signaling sugar molecules that cover the surfaces of all animal cells. The ubiquitous H1N1 and H3N2 flu strains, for example, use the protein hemagglutinin (H) to bind to matching sialic acid receptors on the surface of a cell before penetrating it, and then use the enzyme neuraminidase (N) to cleave or split these sialic acids when viral particles are ready to exit and spread the infection.
Mucous membrane cells, such as those that line the internal airways of the lungs, nose and throat, defend themselves against such pathogens by secreting a mucus rich in sialic acids -- a gooey trap intended to bog down viral particles before they can infect vulnerable cells.
"The sialic acids in the secreted mucus act like a sticky spider's web, drawing viruses in and holding them by their hemagglutinin proteins," said Gagneux.
Using a novel technique that presented viral particles with magnetic beads coated with different forms of mucin (the glycoproteins that comprise mucus) and varying known amounts of sialic acids, Gagneux and colleagues demonstrated that flu viruses counteract the natural barrier by also using neuraminidase to cut themselves free from binding mucosal sialic acids.
More notably, he said that by blocking neuraminidase activity in the mucus, the viruses remain stuck. "They can't release themselves from the mucus decoy and thus can't infect."
The discovery is likely to alter the way researchers and pharmaceutical companies think about how viruses and flu therapies function. Existing drugs like Tamiflu and Relenza inhibit neuraminidase activity and presumably dampen the ability of the flu virus to spread among cells. The work by Gagneux and colleagues suggests inhibiting neuraminidase activity in mucus may reduce the initial risk of infection.
The challenge will be to restrict neuraminidase inhibition to the mucus. Many types of cells in the human body produce neuraminidases, each performing vital cellular functions, particularly in the brain. Limiting neuraminidase inhibition to relevant mucus-secreting cells is necessary to reducing potential side effects.
"The airway's mucus layer is constantly being shed and renewed, within a couple of hours the entire layer is replaced by a new layer," said first author Miriam Cohen, PhD, an assistant project scientist in Gagneux's lab. "A drug or compound that slows down neuraminidase activity rather than completely inhibit its activity will suffice to enhance the natural protective effect of mucus and prevent infection."
 

Journal Reference:

1. Miriam Cohen, Xing-Quan Zhang, Hooman P Senaati, Hui-Wen Chen, Nissi M Varki, Robert T Schooley, Pascal Gagneux. Influenza A penetrates host mucus by cleaving sialic acids with neuraminidase. Virology Journal, 2013; 10 (1): 321 DOI: 10.1186/1743-422X-10-321

Courtesy: ScienceDaily
 

How Flu Evolves to Escape Immunity

Scientists have identified a potential way to improve future flu vaccines after discovering that seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution. Additionally, they found these single amino acid changes occur at only seven places on its surface -- not the 130 places previously believed. The research was published today, 21 November, in the journal Science.

 Family with the flu. Scientists have identified a potential way to improve future flu vaccines after discovering that seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution. (Credit: © Creativa / Fotolia)

"This work is a major step forward in our understanding of the evolution of flu viruses, and could possibly enable us to predict that evolution. If we can do that, then we can make flu vaccines that would be even more effective than the current vaccine," said Professor Derek Smith from the University of Cambridge, one of the two leaders of the research, together with Professor Ron Fouchier from Erasmus Medical Center in The Netherlands.

The flu vaccine works by exposing the body to parts of inactivated flu from the three major different types of flu that infect humans, prompting the immune system to develop antibodies against these viruses. When exposed to the actual flu, these antibodies can eliminate the flu virus.

However, every two or three years the outer coat of seasonal flu (made up of amino acids) evolves, preventing antibodies that would fight the older strains of flu from recognising the new strain. As a result, the new strain of virus escapes the immunity that has been acquired as a result of earlier infections or vaccinations. Because the flu virus is constantly evolving in this way, the World Health Organisation meets twice a year to determine whether the strains of flu included in the vaccine should be changed.

For this study, the researchers created viruses which had a variety of amino acid substitutions as well as different combinations of amino acid substitutions. They then tested these viruses to see which substitutions and combinations of substitutions caused new strains to develop.

They found that seasonal flu escapes immunity and develops into new strains typically by just a single amino acid substitution. Until now, it was widely believed that in order for seasonal flu to escape the immunity individuals acquire from previous infections or vaccinations, it would take at least four amino acid substitutions.

They also found that such single amino acid changes occurred at only seven places on its surface -- all located near the receptor binding site (the area where the flu virus binds to and infects host cells). The location is significant because the virus would not change so close to the site unless it had to, as that area is important for the virus to conserve.

"The virus needs to conserve this, its binding site, as it uses this site to recognize the cells that it infects in our throats," said Bjorn Koel, from Erasmus Medical Center in The Netherlands and lead author of the paper.

Seasonal flu is responsible for half a million deaths and many more hospitalizations and severe illnesses worldwide every year.

Journal Reference:

1. Björn F. Koel, David F. Burke, Theo M. Bestebroer, Stefan Van Der Vliet, Gerben C. M. Zondag, Gaby Vervaet, Eugene Skepner, Nicola S. Lewis, Monique I. J. Spronken, Colin A. Russell, Mikhail Y. Eropkin, Aeron C. Hurt, Ian G. Barr, Jan C. De Jong, Guus F. Rimmelzwaan, Albert D. M. E. Osterhaus, Ron A. M. Fouchier, Derek J. Smith. Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution. Science, 22 November 2013: Vol. 342 no. 6161 pp. 976-979 DOI: 10.1126/science.1244730

Courtesy: ScienceDaily

Neanderthal Viruses Found in Modern Humans

Ancient viruses from Neanderthals have been found in modern human DNA by researchers at Oxford University and Plymouth University.

Scanning electron micrograph showing human immunodeficiency virus (spherical) on human lymphocytes. Researchers hope to further investigate ancient endogenous retroviruses, belonging to the HML2 family of viruses, for possible links with cancer and HIV. (Credit: CDC/C. Goldsmith, P. Feorino, E. L. Palmer, W. R. McManus)

The researchers compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients. They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.
This latest finding, reported in Current Biology, will enable scientists to further investigate possible links between ancient viruses and modern diseases including HIV and cancer, and was supported by the Wellcome Trust and Medical Research Council (MRC).
Around 8% of human DNA is made up of 'endogenous retroviruses' (ERVs), DNA sequences from viruses which pass from generation to generation. This is part of the 90% of our DNA with no known function, sometimes called 'junk' DNA.
'I wouldn't write it off as "junk" just because we don't know what it does yet,' said Dr Gkikas Magiorkinis, an MRC Fellow at Oxford University's Department of Zoology. 'Under certain circumstances, two "junk" viruses can combine to cause disease -- we've seen this many times in animals already. ERVs have been shown to cause cancer when activated by bacteria in mice with weakened immune systems.'
Dr Gkikas and colleagues are now looking to further investigate these ancient viruses, belonging to the HML2 family of viruses, for possible links with cancer and HIV.
'How HIV patients respond to HML2 is related to how fast a patient will progress to AIDS, so there is clearly a connection there,' said Dr Magiorkinis, co-author of the latest study. 'HIV patients are also at much higher risk of developing cancer, for reasons that are poorly-understood. It is possible that some of the risk factors are genetic, and may be shared with HML2. They also become reactivated in cancer and HIV infection, so might prove useful as a therapy target in the future.'
The team are now investigating whether these ancient viruses affect a person's risk of developing diseases such as cancer. Combining evolutionary theory and population genetics with cutting-edge genetic sequencing technology, they will test if these viruses are still active or cause disease in modern humans.
'Using modern DNA sequencing of 300 patients, we should be able to see how widespread these viruses are in the modern population. We would expect viruses with no negative effects to have spread throughout most of the modern population, as there would be no evolutionary pressure against it. If we find that these viruses are less common than expected, this may indicate that the viruses have been inactivated by chance or that they increase mortality, for example through increased cancer risk,' said Dr Robert Belshaw, formerly of Oxford University and now a lecturer at Plymouth University, who led the research.
'Last year, this research wouldn't have been possible. There were some huge technological breakthroughs made this summer, and I expect we'll see even greater advances in 2014. Within the next 5 years, we should be able to say for sure whether these ancient viruses play a role in modern human diseases.'

Journal Reference:

1. Emanuele Marchi, Alex Kanapin, Matthew Byott, Gkikas Magiorkinis and Robert Belshaw. Neanderthal and Denisovan retroviruses in modern humans. Current Biology, 2013 DOI: 10.1016/j.cub.2013.10.028

Courtesy: ScienceDaily
 

Rare New Microbe Found in Two Spacecraft Clean Rooms

A rare, recently discovered microbe that survives on very little to eat has been found in two places on Earth: spacecraft clean rooms in Florida and South America.

 This microscopic image shows dozens of individual bacterial cells of the recently discovered species Tersicoccus phoenicis. This species has been found in only two places: clean rooms in Florida and South America where spacecraft are assembled for launch. Spacecraft clean rooms are one of the most thoroughly checked environments on Earth for what microbes are present. The monitoring provides an indication of what species might get into space aboard a spacecraft. The image includes a scale bar showing that each of the bacterial cells is about one micrometer, or micron, across (about 0.00004 inch). (Credit: NASA/JPL-Caltech)

Microbiologists often do thorough surveys of bacteria and other microbes in spacecraft clean rooms. Fewer microbes live there than in almost any other environment on Earth, but the surveys are important for knowing what might hitch a ride into space. If extraterrestrial life is ever found, it would be readily checked against the census of a few hundred types of microbes detected in spacecraft clean rooms.
The work to keep clean rooms extremely clean knocks total microbe numbers way down. It also can select for microbes that withstand stresses such as drying, chemical cleaning, ultraviolet treatments and lack of nutrients. Perversely, microbes that withstand these stressors often also show elevated resistance to spacecraft sterilization methodologies such as heating and peroxide treatment.
"We want to have a better understanding of these bugs, because the capabilities that adapt them for surviving in clean rooms might also let them survive on a spacecraft," said microbiologist Parag Vaishampayan of NASA's Jet Propulsion Laboratory, Pasadena, Calif., lead author of the 2013 paper about the microbe. "This particular bug survives with almost no nutrients."
This population of berry-shaped bacteria is so different from any other known bacteria, it has been classified as not only a new species, but also a new genus, the next level of classifying the diversity of life. Its discoverers named it Tersicoccus phoenicis. Tersi is from Latin for clean, like the room. Coccus, from Greek for berry, describes the bacterium's shape. The phoenicis part is for NASA's Phoenix Mars Lander, the spacecraft being prepared for launch in 2007 when the bacterium was first collected by test-swabbing the floor in the Florida clean room.
Some other microbes have been discovered in a spacecraft clean room and found nowhere else, but none previously had been found in two different clean rooms and nowhere else. Home grounds of the new one are about 2,500 miles (4,000 kilometers) apart, in a NASA facility at Kennedy Space Center and a European Space Agency facility in Kourou, French Guiana.
A bacterial DNA database shared by microbiologists worldwide led Vaishampayan to find the match. The South American detection had been listed on the database by a former JPL colleague, Christine Moissl-Eichinger, now with the University of Regensburg in Germany. She is first co-author of the paper published this year in the International Journal of Systematic and Evolutionary Microbiology identifying the new genus.
The same global database showed no other location where this strain of bacteria has been detected. That did not surprise Vaishampayan. He said, "We find a lot of bugs in clean rooms because we are looking so hard to find them there. The same bug might be in the soil outside the clean room but we wouldn't necessarily identify it there because it would be hidden by the overwhelming numbers of other bugs."
A teaspoon of typical soil would have thousands more types of microbes and billions more total microbes than an entire cleanroom. More than 99 percent of bacterial strains, as identified from DNA sequences, have never been cultivated in laboratories, a necessary step for the various types of characterization required to identify a strain as a new species.
Microbes that are tolerant of harsh conditions become more evident in clean room environments that remove the rest of the crowd.
"Tersicoccus phoenicis might be found in some natural environment with extremely low nutrient levels, such as a cave or desert," Vaishampayan speculated. This is the case for another species of bacterium (Paenibacillus phoenicis) identified by JPL researchers and currently found in only two places on Earth: a spacecraft clean room in Florida and a bore hole more than 1.3 miles (2.1 kilometers) deep at a Colorado molybdenum mine.
Ongoing research with Tersicoccus phoenicis is aimed at understanding possible ways to control it in spacecraft clean rooms and fully sequencing its DNA. Students from California State University, Los Angeles, have participated in the research to characterize the newly discovered species.
The California Institute of Technology, Pasadena, operates JPL for NASA.
 

Journal Reference:

1. P. Vaishampayan, C. Moissl-Eichinger, R. Pukall, P. Schumann, C. Sproer, A. Augustus, A. H. Roberts, G. Namba, J. Cisneros, T. Salmassi, K. Venkateswaran. Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments. International Journal of Systematic and Evolutionary Microbiology, 2012; 63 (Pt 7): 2463 DOI: 10.1099/ijs.0.047134-0

Courtesy: ScienceDaily
 

Researchers Regrow Hair, Cartilage, Bone, Soft Tissues: Enhancing Cell Metabolism Key to Tissue Repair

Young animals are known to repair their tissues effortlessly, but can this capacity be recaptured in adults? A new study from researchers at the Stem Cell Program at Boston Children's Hospital suggests that it can. By reactivating a dormant gene called Lin28a, which is active in embryonic stem cells, researchers were able to regrow hair and repair cartilage, bone, skin and other soft tissues in a mouse model.

This image shows tissue regrowth in adult mice (reactivated Lin28a gene). (Credit: Cell, Shyh-Chang et al.)

The study also found that Lin28a promotes tissue repair in part by enhancing metabolism in mitochondria -- the energy-producing engines in cells -- suggesting that a mundane cellular "housekeeping" function could open new avenues for developing regenerative treatments. Findings were published online by the journal Cell on November 7.
"Efforts to improve wound healing and tissue repair have mostly failed, but altering metabolism provides a new strategy which we hope will prove successful," says the study's senior investigator George Q. Daley, MD, PhD, director of Boston Children's Stem Cell Transplantation Program and an investigator with the Howard Hughes Medical Institute.
"Most people would naturally think that growth factors are the major players in wound healing, but we found that the core metabolism of cells is rate-limiting in terms of tissue repair," adds PhD candidate Shyh-Chang Ng, co-first author on the paper with Hao Zhu, MD, both scientists in the Daley Lab. "The enhanced metabolic rate we saw when we reactivated Lin28a is typical of embryos during their rapid growth phase."
Lin28, first discovered in worms, functions in all complex organisms. It is abundant in embryonic stem cells, expressed strongly during early embryo formation and has been used to reprogram skin cells into stem cells. It acts by binding to RNA and regulating how genes are translated into proteins.
To better understand how Lin28a promotes tissue repair, the researchers systematically looked at what specific RNAs it binds to. They initially had their sights on a tiny RNA called Let-7, which is known to promote cell maturation and aging.
"We were confident that Let-7 would be the mechanism," says Shyh-Chang. "But there was something else involved."
Specifically, the researchers found that Lin28a also enhances the production of metabolic enzymes in mitochondria, the structures that produce energy for the cell. By revving up a cell's bioenergetics, they found, Lin28a helps generate the energy needed to stimulate and grow new tissues.
"We already know that accumulated defects in mitochondrial metabolism can lead to aging in many cells and tissues," says Shyh-Chang. "We are showing the converse -- that enhancement of mitochondrial metabolism can boost tissue repair and regeneration, recapturing the remarkable repair capacity of juvenile animals."
Further experiments showed that bypassing Lin28a and directly activating mitochondrial metabolism with a small-molecule compound also had the effect of enhancing wound healing. This suggests the possibility of inducing regeneration and promoting tissue repair with drugs.
"Since Lin28 itself is difficult to introduce into cells, the fact that we were able to activate mitochondrial metabolism pharmacologically gives us hope," Shyh-Chang says.
Lin28A didn't universally induce regeneration in all tissues. Heart tissue showed little effect, and while the researchers were able to enhance the regrowth of finger tips in newborn mice, they could not in adults.
"Lin28a could be a key factor in constituting a healing cocktail," says Shyh-Chang, "but there are other embryonic factors that remain to be found."
 

Journal Reference:

1. Ng Shyh-Chang, Hao Zhu, T. Yvanka de Soysa, Gen Shinoda, Marc T. Seligson, Kaloyan M. Tsanov, Liem Nguyen, John M. Asara, Lewis C. Cantley, George Q. Daley. Lin28 Enhances Tissue Repair by Reprogramming Cellular Metabolism. Cell, 2013; 155 (4): 778 DOI: 10.1016/j.cell.2013.09.059

Courtesy: ScienceDaily
 

Novel Genetic Patterns May Make Us Rethink Biology and Individuality

Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth's Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest -- resulting in several different genotypes in one individual -- and second, some of the same genetic mutations occur in unrelated people. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams' surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought.

Concept image. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human. (Credit: © WavebreakMediaMicro / Fotolia)

His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal on November 7, 2013.
Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or "somatic" mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.
"We are in reality diverse beings in that a single person is genetically not a single entity -- to be philosophical in ways I do not yet understand -- what does it mean to be a person if we are variable within?" says Williams, the study's senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. "What makes you a person? Is it your memory? Your genes?" He continues, "We have always thought, 'your genome is your genome.' The data suggest that it is not completely true."
In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. "This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences." says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.
Having multiple genotypes from mutations within one's own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and child -- or twins -- exchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body). Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that "proved" that she was unrelated to two of her three biological sons.
Williams says that, although this was a small study, "there is a lot more going on than we thought, and the results are, in some ways, astoundingly weird."
Because somatic changes are thought to happen at random, scientists do not expect unrelated people to exhibit the same mutations. Williams and colleagues analyzed the same 10 tissue samples in two unrelated people. They found several identical mutations, and detected these repeated mutations only in kidney, liver and skeletal body tissues. Their research examined "mitochondrial DNA" (mtDNA) -- a part of DNA that is only inherited from the mother. Technically all women would share mtDNA from one common female ancestor, but mutations have resulted in differences. The importance of Williams' finding is that these tissue-specific, recurrent, common mutations in mtDNA among unrelated study subjects -- only detected in three body tissues -- are "not likely being developed and maintained through purely random processes," according to Williams. They indicate "a completely different model …. a decidedly non-random process that results in particular mutations, but only in specific tissues."
If our human DNA changes, or mutates, in patterns, rather than randomly; if such mutations "match" among unrelated people; or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don't yet know, but ongoing research may help reveal the answers.
Christopher Amos, PhD, Director of the Center for Genomic Medicine and Associate Director for Population Sciences at the Cancer Center, says, "This paper identifies mutations that develop in multiple tissues, and provides novel insights that are relevant to aging. Mutations are noticed in several tissues in common across individuals, and the aging process is the most likely contributor. The theory would be that selected mutations confer a selective advantage to mitochondria, and these accumulate as we age." Amos, who is also a Professor of Community and Family Medicine at Geisel, says, "To confirm whether aging is to blame, we would need to study tissues from multiple individuals at different ages." Williams concurs, saying, "Clearly these do accumulate with age, but how and why is unknown -- and needs to be determined."
As more and better data become available from high-throughput genetic analyses and high-powered computers, researchers are identifying an increasing number of medical conditions that result from somatic mutations, including neurological, hematological, and immune-related disorders. Williams and colleagues are conducting further research to examine how diseases, other than cancer or even benign conditions, may result from somatic changes. Williams, Moore and Amos will employ iQBS's Discovery supercomputer for next-generation sequencing to process subjects' DNA data. Future analyses will include large, whole-genome sequencing of the data for the two individuals studied in the current report.
Williams explains, "We know that cancer is caused by mutations that cause a tumor. But in this work, we chose to study mutations in people without any cancer. Knowing how we accumulate mutations may make it easier to separate genetic signals that may cause cancer from those that accumulate normally without affecting disease. It may also allow us to see that many changes that we thought caused cancer do not in many situations, if we find the same mutations in normal tissues."
Just as our bodies' immune systems have evolved to fight disease, interestingly, they can also stave off the effects of some genetic mutations. Williams states that, "Most genetic changes don't cause disease, and if they did, we'd be in big trouble. Fortunately, it appears our systems filter a lot of that out."
Mark Israel, MD, Director of Norris Cotton Cancer Center and Professor of Pediatrics and Genetics at Geisel, says, "The fact that somatic mutation occurs in mitochondrial DNA apparently non-randomly provides a new working hypothesis for the rest of the genome. If this non-randomness is general, it may affect cancer risks in ways we could not have previously predicted. This can have real impact in understanding and changing disease susceptibility."

Journal Reference:

1. David C. Samuels, Chun Li, Bingshan Li, Zhuo Song, Eric Torstenson, Hayley Boyd Clay, Antonis Rokas, Tricia A. Thornton-Wells, Jason H. Moore, Tia M. Hughes, Robert D. Hoffman, Jonathan L. Haines, Deborah G. Murdock, Douglas P. Mortlock, Scott M. Williams. Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans. PLoS Genetics, 2013; 9 (11): e1003929 DOI: 10.1371/journal.pgen.1003929

Courtesy: ScienceDaily

Yeast, Human Stem Cells Drive Discovery of New Parkinson's Disease Drug Targets

Using a discovery platform whose components range from yeast cells to human stem cells, Whitehead Institute scientists have identified a novel Parkinson's disease drug target and a compound capable of repairing neurons derived from Parkinson's patients.

A dual yeast and human stem cell discovery platform for Parkinson's disease: Investigations in simple baker's yeast cells brought to light abnormalities in Parkinson's patient neurons and identified genes and small molecules that correct them. Yeast chemical genetics identified the targeted pathway, conserved from yeast to human cells, of one such molecule. (Credit: Tom DiCesare/Whitehead Institute)

The platform -- whose effectiveness is described in dual papers published online this week in the journal Science -- could accelerate the discovery of drug candidates that address the underlying pathology of Parkinson's and other neurodegenerative diseases. Today, no such drugs exist.
Parkinson's disease (PD) and such neurodegenerative diseases as Huntington's and Alzheimer's are characterized by protein misfolding, resulting in toxic accumulations of proteins in the cells of the central nervous system. Cellular buildup of the protein alpha-synuclein, for example, has long been associated with PD, making this protein a seemingly appropriate target for therapeutic intervention.
In the search for compounds that might alter a protein's behavior or function -- such as that of alpha-synuclein -- drug companies often rely on so-called target-based screens that test the effect large numbers of compounds have on the protein in question in rapid, automated fashion. Though efficient, such an approach is limited by the fact that it essentially occurs in a test tube. Seemingly promising compounds emerging from a target-based screen may act quite differently when they're moved from the in vitro environment into a living setting.
To overcome this limitation, the lab of Whitehead Member Susan Lindquist has turned to phenotypic screens in which candidate compounds are studied within a living system. In Lindquist's lab, yeast cells -- which share the core cell biology of human cells -- serve as living test tubes in which to study the problem of protein misfolding and to identify possible solutions. Yeast cells genetically modified to overproduce alpha-synuclein serve as robust models for the toxicity of this protein that underlies PD.
"Phenotypic screens are probably underutilized for identifying drug targets and potential compounds," says Daniel Tardiff, a scientist in the Lindquist lab and lead author of one of the Science papers. "Here, we let the yeast tell us what is a good target. We let a living cell tell us what's critical for reversing alpha-synuclein toxicity."
In a screen of nearly 200,000 compounds, Tardiff and collaborators identified one chemical entity that not only reversed alpha-synuclein toxicity in yeast cells, but also partially rescued neurons in the model nematode C. elegans and in rat neurons. Significantly, cellular pathologies including impaired cellular trafficking and an increase in oxidative stress, were reduced by treatment with the identified compound. Enabled by the chemistry provided by Nate Jui in the Buchwald lab at MIT, Tardiff found that the compound was working by restoring functions mediated by a cellular protein critical for trafficking that was previously thought to be "undruggable."
But would these findings apply in human cells? To answer that question, husband-and-wife team Chee-Yeun Chung and Vikram Khurana led the second study published in Science to examine neurons derived from induced pluripotent stem (iPS) cells generated from Parkinson's patients. The cells and differentiated neurons (of a type damaged by the disease) were derived from patients that carried alpha-synuclein mutations and develop aggressive forms of the disease. To ensure that any pathology developed in the cultured neurons could be attributed solely to the genetic defect, the researchers also derived control neurons from iPS cells in which the mutation had been corrected.
Chung and Khurana used the wealth of data from the yeast alpha-synuclein toxicity model to clue them in on key cellular processes that became perturbed as patient neurons aged in the dish. Strikingly, exposure to the compound identified via yeast screens in Tardiff's study reversed the damage in these neurons.
"It was remarkable that the compound rescued yeast cells and patient neurons in similar ways and through the same target -- a target we would not have identified without yeast genetics to guide us," says Khurana, a postdoctoral scientist in the Lindquist lab and a neurologist at Massachusetts General Hospital who recruited patients for participation in this research. Khurana believes that the abnormalities discovered occur in the early stages of disease. If so, successful manipulation of the targets identified here might help slow or even prevent disease progression.
For the researchers involved, these findings are a bit of surprise. Because neurodegenerative disorders like PD are largely diseases of aging, modeling them in a culture dish using neurons grown from iPS cells has been thought to be exceedingly difficult, if not impossible.
"Many, ourselves included, were skeptical that we could find any important pathologies for a neurodegenerative disorder by reprogramming patient cells," says Chung, a Senior Research Scientist in the Lindquist lab. "Critically, we also validated these pathologies in post-mortem brains, so we're quite confident these are relevant for the disease."
Next steps for these scientists include chemically optimizing the compound identified and testing it in animal models. Moreover, they are convinced that this yeast-human stem cell discovery platform could be applied to other neurodegenerative diseases for which yeast models have been developed.
"Using yeast genetics to identify a compound and its mechanism of action against the fundamental pathology of a disease illustrates the power of the system we've built," says Lindquist, who is also professor of biology at MIT and a Howard Hughes Medical Institute investigator. "It's critical that we continue to leverage this power because as we reduce the rate at which people are dying from cancer and heart disease, the burden of these dreaded neurodegenerative diseases is going to rise. It's inevitable."
This work was supported by the National Institutes of Health (grants 5R01GM069530, GM58160, K01 AG038546, 5 R01CA084198), Howard Hughes Medical Institute, the JPB Foundation, the Eleanor Schwartz Charitable Foundation, the Bachmann-Strauss Dystonia & Parkinson Foundation, the American Brain Foundation, and the Parkinson's Disease Foundation.
 

Journal Reference:

1. Daniel F. Tardiff, Nathan T. Jui, Vikram Khurana, Mitali A. Tambe, Michelle L. Thompson, Chee Yeun Chung, Hari B. Kamadurai, Hyoung Tae Kim, Alex K. Lancaster, Kim A. Caldwell, Guy A. Caldwell, Jean-Christophe Rochet, Stephen L. Buchwald, Susan Lindquist. Yeast Reveal a “Druggable” Rsp5/Nedd4 Network that Ameliorates α−Synuclein Toxicity in Neurons. Science, 2013 DOI: 10.1126/science.1245321

Courtesy: ScienceDaily