of course cancer is caused by bacteria..., told you so years ago

bytesizebio | Cancer and microbiology have been closely linked for over 100 years. Cancer patients are usually immunosuppressed due to chemotherapy, requiring special treatment and conditions to prevent bacterial infection. Bladder cancer is typically treated with inactivated tuberculosis bacteria to induce an inflammatory response which turns against remaining cancer cells, with remarkably effective results.  Also, viruses are known to cause cancer, including  papillomavirus (cervical cancer), Hepatitis B (liver cancer), and  HTLV (human T-lymphocyte virus, causing lymphoma). In 1982, the bacterium  Helicobacter pylori was discovered to be the main cause of gastric ulcers, and the first direct link between bacteria and cancer — stomach cancer — was established. The link between chronic ulcers and stomach cancer was already well known: what was not knows is that bacteria were the initial cause of stomach ulcers. Since then, several other suspects have been named, including links between Chlamydia and lung cancer, and  Salmonella and gallbladder cancer.

Inflammation changes the gut ecosystem 

There are two fields in which are not  generally thought of as being linked: microbial ecology and cancer research.  When we think of microbial ecology, we think of agricultural soil enrichment, marine ecology, air quality, nutrient recycling, species interaction,  diversity and all that jazz. Not of cancer though. But in the past five years we have amassed more genomic DNA data than we have in the 50 years preceding them, including data from cancer tissue and associated bacteria. These data are beginning to show us that that the links between microbial populations and cancer are more prevalent, complex and intimate than we thought. Bacteria, as microbiologists keep repeating ad nauseam, make up 90% of the cellular population of our bodies (the extra 10% are, well, us).  Following metagenomic sequencing, human microbial flora have been shown to affect conditions as varied as obesity, metabolic disease (including diabetes)  infant growth and colorectal cancer — all of which we have not associated with bacteria until recently. As a result the people who study bacteria, and the people who study cancer are working together more than ever before. Last year, a study in Science  led by a group from the University of North Carolina Chapel Hill, has shown a clear mechanistic link between microbial communities, inflammation, and colorectal cancer. In a nutshell, their study suggests that the following sequence of events takes place: 1) inflammation disturbs gut ecosystems; 2) this disturbance to conditions that allow pathogens to invade the gut; 3) the pathogens damage the host cells increasing the risk of the development of colorectal cancer. The study used mice that lacked the gene that makes Interleukin-10 (IL-10). IL-10 suppresses the inflammatory response, and IL10-deficient mice (IL10^-/-) are genetically prone to gut inflammation.  The team compared bacterial communities in the inflamed guts of IL10^-/- mice with those in healthy normal (“wild type”) mice. They found that the diversity of different kinds of bacteria was significantly lower in the IL10^-/- mice. But the team found little difference in microbial diversity between mice that simply had inflammation and those that had inflammation and cancer, indicating that the inflammation was the critical factor affecting bacterial populations, reducing the diversity of bacteria in the colon. In fact, one major species to shoot up and dominate the inflamed gut was E. coli, another was Enterobacter faecalis. But IL10^-/- mice that were inoculated with E. faecalis only rarely developed cancer, while 80% of the group with E. coli did. Specifically, E. coli strain NC101 was foind to be the culprit. The NC101 strain has a cluster of genes under the name of “pks island”. In 2010 a group from Toulouse found that pks island genes cause cellular replication and DNA damage in the host: the harbingers of cancer.  The UNC researchers colonized a mouse gut cell-line with E. coli that had the pks genes, and with E. coli lacking the pks genes. The inflammation remained, but the cells inoculated with E. coli without the pks developed fewer tumors. While mice take longer to develop tumors, the researchers saw 80% more DNA damaged cells in gut cells of IL10^-/- mice inoculated with E. coli that had pks genes, versus those that were associated with E. coli without the pks genes.

Bacterial DNA in Cancer Cells

But the link between bacteria and cancer may run deeper than a changing microbial community. A recent study by a group at the University of Maryland School of Medicine shows that bacteria DNA gets transferred to human cells, in a process known as lateral gene transfer, or LGT.  LGT is known to occur quite commonly between bacteria, including bacteria of different species. In fact, that is how antibiotic resistance is transferred so quickly. But findings of bacterial LGT to humans are generally treated as possible experimental artifacts, rather than true events. The UMSM team scanned data from from the 1,000 Genomes Project and found more than 7,000 instances of LGT from bacteria to human cells. When they analyzed sequences from the Cancer Genome Atlas, they discovered 691,000 more cases  of LGT, and an overwhelming majority of LGT findings came from tumor samples, not from healthy cells. They found that DNA from Acinetobacter , was integrated into the genome of acute myeloid leukemia cells, especially in the mitochondrial genome. Acinetobacter is a soil bacterium but some species are known to be oppotunitic pathogens. For unknown reasons, this bacterium’s DNA was found more frequently in the genome of myeloid leukemia cells. Fist tap Dale.

isn't smegma believed to cause cervical cancer?

thescientist | In what appears to be a novel form of bacterial gene transfer, or conjugation, the microbe Mycobacterium smegmatis can share multiple segments of DNA at once to fellow members of its species, according to a study published today (July 9) in PLOS Biology. The result: the generation of genetic diversity at a pace once believed to be reserved for sexual organisms.

“It is a very nice study providing clear evidence that, in Mycobacterium smegmatis at least, conjugation underlies much of species diversity,” said Richard Meyer, who studies conjugation at The University of Texas at Austin, in an email to The Scientist.

Traditionally, transfer of genetic material through conjugation has been considered an incremental process. Plasmids mediate the transfer of short segments of DNA, one at a time, between pairs of touching bacterial cells, often conferring such traits as antibiotic resistance.

But M. smegmatis, a harmless bacterium related to the pathogen M. tuberculosis, appears to use a more extensive method of gene shuffling, endowing each recipient cell with a different combination of new genes. The researchers dubbed this form of conjugation “distributive conjugal transfer.” “We can generate a million [hybrid bacteria] overnight, and each of those million will be different than each other,” said coauthor Todd Gray, a geneticist at the New York State Department of Health’s Wadsworth Center.

Coauthor Keith Derbyshire, also a geneticist at the Wadsworth Center, and colleagues had previously published data indicating that M. smegmatis used a novel form of conjugation, but the new study confirms and expands on their suspicions using genetic data. The researchers compared the whole genome sequences of donor and recipient bacteria before and after the massive gene transfers.

The researchers found that, after the transfers, up to a quarter of the recipient bacteria’s genomes were made up of donated DNA, scattered through the chromosomes in segments of varying lengths.

According to the authors, the diversity resulting from distributive conjugal transfer approaches that achieved by meiosis, the process of cell division that underlies sexual reproduction. “The progeny were like meiotic blends,” said Derbyshire. “The genomes are totally mosaic.”

the doe has a "joint genome institute" exploring uncharted reaches of the microcosmos...,

thescientist | The tree of life is dominated by microbes, but many large branches remain uncharted because scientists have been historically restricted to studying the small fraction of species that will grow in a lab. An international team of scientists has now begun to redress this bias, sequencing full genomes from single cells to bring the “uncultured majority” into view.

In total, the team identified more than 200 new microbial species belonging to 29 underrepresented or unknown lineages. And the results, published today (July 14) in Nature, were full of new metabolic abilities and genetic surprises.

“[There has been a] strong imperative to fill in the microbial tree of life,” said Philip Hugenholtz from the University of Queensland, one of the study’s leaders. “If you have an incomplete view of evolution—vastly incomplete in the case of microorganisms—you have a vastly incomplete understanding of biology.”

By sequencing DNA directly from environmental samples, geneticists have suggested that the two microbial domains of life—bacteria and archaea—include at least 60 major lineages (phyla), but just four of these account for more than 88 percent of cultivated microbes. Of the others, around half are “candidate phyla,” whose members have never been grown in lab cultures.

To fill these gaps, the team collected samples from nine diverse habitats, including industrial reactors, hot springs, and a gold mine. The researchers gravitated towards places that were low in oxygen since these tend to harbor a greater and more interesting spread of microbes than familiar sites like our bodies. 

From these samples, Tanja Woyke from the Department of Energy’s Joint Genome Institute in California isolated 9,600 individual cells and amplified the genomes of around a third of these. If any of these genomes looked like they came from new lineages, the team sequenced them completely.

They ended up with 201 full genomes representing 21 bacterial lineages and 8 archaeal ones. Some of these were candidate phyla known only by abstract codes, but the team has now given them descriptive names based on the biology of their members. For example, EM19 is now Calescamantes (“heat lovers”) because they hail from an extremely hot environment, and OD1 is now Parcubacteria (“thrifty bacteria”) for its streamlined metabolism. 

pandoraviruses hint at fourth domain of life...,

fauxnews | The discovery of two new jumbo-sized viruses is blurring the lines between viral and cellular life and could point to the existence of a new type of life, scientists suggest. 

The two large viruses, detailed in this week's issue of the journal Science, have been dubbed "Pandoraviruses" because of the surprises they may hold for biologists, in reference to the mythical Greek figure who opened a box and released evil into the world.

The discovery of Pandoraviruses is an indication that our knowledge of Earth's microbial biodiversity is still incomplete, explained study coauthor Jean-Michel Claverie, a virologist at the French National Research Agency at Aix-Marseille University.

"Huge discoveries remain to be made at the most fundamental level that may change our present conception about the origin of life and its evolution," Claverie said.

Eugene Koonin, a computational evolutionary biologist at the National Center for Biotechnology Information in Bethesda, Md., who was not involved in the study, called the Pandoraviruses a "wonderful discovery," but not a complete surprise.

"In a certain sense, it's something that we saw coming, and it's wonderful that it has come," Koonin said.

human breath analysis and individual metabolic phenotypes

plosone | The metabolic phenotype varies widely due to external factors such as diet and gut microbiome composition, among others. Despite these temporal fluctuations, urine metabolite profiling studies have suggested that there are highly individual phenotypes that persist over extended periods of time. This hypothesis was tested by analyzing the exhaled breath of a group of subjects during nine days by mass spectrometry. Consistent with previous metabolomic studies based on urine, we conclude that individual signatures of breath composition exist. The confirmation of the existence of stable and specific breathprints may contribute to strengthen the inclusion of breath as a biofluid of choice in metabolomic studies. In addition, the fact that the method is rapid and totally non-invasive, yet individualized profiles can be tracked, makes it an appealing approach.

energetic costs of cellular computations

pnas | Cells often perform computations in order to respond to environmental cues. A simple example is the classic problem, first considered by Berg and Purcell, of determining the concentration of a chemical ligand in the surrounding media. On general theoretical grounds, it is expected that such computations require cells to consume energy. In particular, Landauer’s principle states that energy must be consumed in order to erase the memory of past observations. Here, we explicitly calculate the energetic cost of steady-state computation of ligand concentration for a simple two-component cellular network that implements a noisy version of the Berg–Purcell strategy. We show that learning about external concentrations necessitates the breaking of detailed balance and consumption of energy, with greater learning requiring more energy. Our calculations suggest that the energetic costs of cellular computation may be an important constraint on networks designed to function in resource poor environments, such as the spore germination networks of bacteria.

lake vostok yields new bacterial life

RT | Russian researchers have found unidentified bacteria in waters of the unique sub-glacial Lake Vostok. However, this is not a sensational discovery since the microorganism was found in possible kerosene contaminated waters.

The finding from the water sample taken in May 2012 showed that the bacteria do not belong to any of the existing classes of bacteria. Before the latest discovery, science knew only one species of bacteria that can live under these conditions.

“The last analysis was completed a week ago - there will be another, but the results are unlikely to change anything. After exclusion of all known contaminants - extraneous organisms - bacterial DNA was detected, which does not coincide with any of the known species in the world,” RIA Novosti quotes Sergey Bulat of the St. Petersburg Nuclear Physics Institute in Russia.

However, the discovery turns out not to be that sensational.

“There has been one strain of bacteria which we did not find in drilling liquid, but these bacteria could in principal use kerosene as an energy source,” the head of the laboratory of the same institution, Vladimir Korolev said. "That is why we can’t say that a previously-unknown bacteria was found,” he stressed.

In February 2012 Russian researchers became the first in the world to reach the waters of Lake Vostok after more than decades of drilling work.

This year, on January 10, scientists came up with another record. They managed to reach the fresh ice at a depth of 3383 meters and took samples at 3,406 meters. Ice formed as the water from the lake rose into the hole due to upward-pressure in the crack researchers drilled last February.

Last year Russian scientists managed to drill through 3700 meters of ice, reach the surface of the lake and take 40 liters of prehistoric water. However, those samples, scientists said later, were not clean enough to prove the existence of any kind of life – the water contained some substances of drilling liquid, kerosene and Freon, used while getting through the thick ice.

As recently as March 1, Russian researchers successfully obtained fresh ice samples from the lake as the work continues there. They said it would take months to clarify whether life exists in the fossil water below the 3.5-km deep glacier.

All water samples will be brought to St. Petersburg in May on board the research ship Academic Fyodorov, which is currently working in the Antarctic.

afterlife...,

wired | Most people have pulled long-forgotten vegetables from their refrigerator's depths at least once, and just the memory is enough to make a stomach turn. But one man's fridge mold is another man's still life. Estonian artist Heikki Leis' Afterlife is a veritable rotting cornucopia of vegetables photographed long past their prime.

"I was inspired by some potatoes I had once left out in a pot for too long. They had started to mold and on closer examination the colors and textures looked interesting enough to take some photos," Leis wrote in an e-mail.

Leis then started experimenting with various fruits and vegetables. He sometimes let them decay for two months, keeping them covered so they wouldn't dry out. When Leis finished, he was truly finished. "I'm tempted to say I ate them, but the truth is I just threw them away," he said.

Leis said he'd be open to an expert's analysis of his rotting concoctions, so Wired invited mycologist Kathie Hodge of Cornell University, who's working on a book about food-decaying fungi, to look at the work.

There are thousands of molds out there, and "we see them all the time and yet we don't look at them. They live with us and we automatically throw these things out," said Hodge, who took Wired on a tour of Leis' moldy world, though not without a warning.

"Getting them to this level is probably not a good idea, so don't try this at home!" she said.

the next dimension in imaging: it's about time

Fist tap Big Don.

"told you so" moments stacking up like hotcakes now...,

NYTimes | IN recent years, scientists have made extraordinary advances in understanding the causes of autism, now estimated to afflict 1 in 88 children. But remarkably little of this understanding has percolated into popular awareness, which often remains fixated on vaccines.

So here’s the short of it: At least a subset of autism — perhaps one-third, and very likely more — looks like a type of inflammatory disease. And it begins in the womb.

It starts with what scientists call immune dysregulation. Ideally, your immune system should operate like an enlightened action hero, meting out inflammation precisely, accurately and with deadly force when necessary, but then quickly returning to a Zen-like calm. Doing so requires an optimal balance of pro- and anti-inflammatory muscle.

In autistic individuals, the immune system fails at this balancing act. Inflammatory signals dominate. Anti-inflammatory ones are inadequate. A state of chronic activation prevails. And the more skewed toward inflammation, the more acute the autistic symptoms.

Nowhere are the consequences of this dysregulation more evident than in the autistic brain. Spidery cells that help maintain neurons — called astroglia and microglia — are enlarged from chronic activation. Pro-inflammatory signaling molecules abound. Genes involved in inflammation are switched on.

These findings are important for many reasons, but perhaps the most noteworthy is that they provide evidence of an abnormal, continuing biological process. That means that there is finally a therapeutic target for a disorder defined by behavioral criteria like social impairments, difficulty communicating and repetitive behaviors.

But how to address it, and where to begin? That question has led scientists to the womb. A population-wide study from Denmark spanning two decades of births indicates that infection during pregnancy increases the risk of autism in the child. Hospitalization for a viral infection, like the flu, during the first trimester of pregnancy triples the odds. Bacterial infection, including of the urinary tract, during the second trimester increases chances by 40 percent.

The lesson here isn’t necessarily that viruses and bacteria directly damage the fetus. Rather, the mother’s attempt to repel invaders — her inflammatory response — seems at fault. Research by Paul Patterson, an expert in neuroimmunity at Caltech, demonstrates this important principle. Inflaming pregnant mice artificially — without a living infective agent — prompts behavioral problems in the young. In this model, autism results from collateral damage. It’s an unintended consequence of self-defense during pregnancy.

Yet to blame infections for the autism epidemic is folly. First, in the broadest sense, the epidemiology doesn’t jibe. Leo Kanner first described infantile autism in 1943. Diagnoses have increased tenfold, although a careful assessment suggests that the true increase in incidences is less than half that. But in that same period, viral and bacterial infections have generally declined. By many measures, we’re more infection-free than ever before in human history.

Better clues to the causes of the autism phenomenon come from parallel “epidemics.” The prevalence of inflammatory diseases in general has increased significantly in the past 60 years. As a group, they include asthma, now estimated to affect 1 in 10 children — at least double the prevalence of 1980 — and autoimmune disorders, which afflict 1 in 20.

but then I told you this a looooong time ago, right?

TheScientist | A usually benign strain of the gut microbe E. coli produces toxins in mice with inflammatory bowel disease, which can lead to DNA-damage and cancer in the host tissue. The results were reported last week in Science (August 16).

“They’re not exactly your flagship disease-causing bacteria,” lead researcher Christian Jobin, from the University of North Carolina at Chapel Hill, told Nature.

Individuals with inflammatory bowel disease are at higher risk of developing colorectal cancer than the general population. But researchers thought that the main culprit was the over-active immune cells, which released DNA-damaging molecules. The new work suggests that gut microbes may also contribute to the process, as inflammation appears to change the microbial composition of the gut to favor toxin-producing E. coli strains.

Experts think that the research could lead to methods of reducing the risk of cancer by altering the microbial community, though that strategy has to be tested.

medical ecology

NYTimes | For a century, doctors have waged war against bacteria, using antibiotics as their weapons. But that relationship is changing as scientists become more familiar with the 100 trillion microbes that call us home — collectively known as the microbiome.

“I would like to lose the language of warfare,” said Julie Segre, a senior investigator at the National Human Genome Research Institute. “It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.”

This new approach to health is known as medical ecology. Rather than conducting indiscriminate slaughter, Dr. Segre and like-minded scientists want to be microbial wildlife managers.

No one wants to abandon antibiotics outright. But by nurturing the invisible ecosystem in and on our bodies, doctors may be able to find other ways to fight infectious diseases, and with less harmful side effects. Tending the microbiome may also help in the treatment of disorders that may not seem to have anything to do with bacteria, including obesity and diabetes.

“I cannot wait for this to become a big area of science,” said Michael A. Fischbach, a microbiologist at the University of California, San Francisco, and an author of a medical ecology manifesto published this month in the journal Science Translational Medicine.

Judging from a flood of recent findings about our inner ecosystem, that appears to be happening. Last week, Dr. Segre and about 200 other scientists published the most ambitious survey of the human microbiome yet. Known as the Human Microbiome Project, it is based on examinations of 242 healthy people tracked over two years. The scientists sequenced the genetic material of bacteria recovered from 15 or more sites on their subjects’ bodies, recovering more than five million genes.

The project and other studies like it are revealing some of the ways in which our invisible residents shape our lives, from birth to death.

A number of recent reports shed light on how mothers promote the health of their children by shaping their microbiomes. In a study published last week in the journal PLoS One, Dr. Kjersti Aagaard-Tillery, an obstetrician at Baylor College of Medicine, and her colleagues described the vaginal microbiome in pregnant women. Before she started the study, Dr. Aagaard-Tillery expected this microbiome to be no different from that of women who weren’t pregnant.

“In fact, what we found is the exact opposite,” she said.

oops, they forgot the breastesses...,

kurzweilai | Some 200 members of the Human Microbiome Project (HMP) Consortium from nearly 80 universities and scientific institutions, organized by the National Institutes of Health, have mapped the normal microbial makeup of healthy humans, producing numerous insights and even a few surprises.

The report on on their five years of research was published Thusday June 14, 2012, in a series of coordinated scientific reports in Nature the PLoS.

Researchers found, for example, that nearly everyone routinely carries pathogens, microorganisms known to cause illnesses.

In healthy individuals, however, pathogens cause no disease; they simply coexist with their host and the rest of the human microbiome, the collection of all microorganisms living in the human body.

Researchers must now figure out why some pathogens turn deadly and under what conditions, likely revising current concepts of how microorganisms cause disease.

“Like 15th century explorers describing the outline of a new continent, HMP researchers employed a new technological strategy to define, for the first time, the normal microbial makeup of the human body,” said NIH Director Francis S. Collins, M.D., Ph.D.

“HMP created a remarkable reference database by using genome sequencing techniques to detect microbes in healthy volunteers. This lays the foundation for accelerating infectious disease research previously impossible without this community resource.”

To define the normal human microbiome, HMP researchers sampled 242 healthy U.S. volunteers (129 male, 113 female), collecting tissues from 15 body sites in men and 18 body sites in women.

Researchers collected up to three samples from each volunteer at sites such as the mouth, nose, skin (two behind each ear and each inner elbow), and lower intestine (stool), and three vaginal sites in women; each body site can be inhabited by organisms as different as those in the Amazon Rainforest and the Sahara Desert.

Historically, doctors studied microorganisms in their patients by isolating pathogens and growing them in culture. This painstaking process typically identifies only a few microbial species, as they are hard to grow in the laboratory. In HMP, researchers purified all human and microbial DNA in each of more than 5,000 samples and analyzed them with DNA sequencing machines.

the wonder of breasts

Guardian | We love breasts, yet can't quite take them seriously. Breasts embarrass us. They're unpredictable. They're goofy. They can turn babies and grown men into lunkheads.

They appear out of nowhere in puberty, they get bigger in pregnancy, they're capable of producing prodigious amounts of milk, and sometimes they get sick. But for such an enormously popular feature of the human race, it's remarkable how little we know about their basic biology.

The urgency to know and understand breasts has never been greater. Modern life has helped many of us live longer and more comfortably. It has also, however, taken a strange toll on our breasts. For one thing, they are bigger than ever. We are sprouting them at younger ages. We are filling them with saline and silicone and transplanted stem cells to change their shape. This year marks the 50th anniversary of the first silicone implant surgery in Houston, Texas.

More tumours form in the breast than in any other organ, making breast cancer the most common malignancy in women worldwide. Its incidence has almost doubled since the 1940s and is still rising.

But breasts are often overlooked, at least for non-cancer scientific research. The Human Microbiome Project, for example, is decoding the microbial genes of every major human gland, liquid and orifice, from the ears to the genitals. It neglected to include breast milk.

I wanted to know more, so I went to the 15th meeting of the International Society for Research in Human Milk and Lactation in Lima. Many attendees were molecular biologists, biochemists or geneticists who are deconstructing milk bit by bit. Until recently, it was thought breast milk had around 200 components. These could be divided into the major ingredients of fats, sugars, proteins and enzymes. But new technologies have allowed researchers to look deeper into each of these categories and discover new ones.

Scientists used to think breast milk was sterile, like urine. But it's more like cultured yoghurt, with lots of live bacteria doing who knows what. These organisms evolved for a reason, and somehow they're helping us out. One leading theory is they act as a vaccine, inoculating the infant gut. A milk sample has anywhere from one to 600 species of bacteria. Most are new to science.

Then there are the sugars. There's a class of them called oligosaccharides, which are long chains of complex sugars. Scientists have identified 140 of them so far, and estimate there are about 200. The human body is full of oligosaccharides, which ride on our cells attached to proteins and lipids. But a mother's mammary gland cooks up a unique batch of "free" or unattached ones and deposits them in milk. These are found nowhere else in nature, and not every mother produces the same ones, since they vary by blood type. Even though they're sugars, the oligosaccharides are, weirdly, not digestible by infants. Yet they are a main ingredient, present in milk in the same percentage as the proteins, and in higher amounts than the fats. So what are they doing there?

They don't feed us, but they do feed many types of beneficial bacteria that make a home in our guts and help us fight infections. In addition to recruiting the good bugs, these sugars prevent the bad bugs from hanging around. "The benefits of human milk are still underestimated," said Lars Bode, an immunobiologist at the University of California, San Diego. "We're still discovering functional components of breast milk."

what bugs are in your gut?

TheScientist | Humans from different cultures and geographic locations differ in the diversity of bacteria in their guts, but the metabolic functions that those microbial communities serve are similar, according to a report out in Nature today (May 9). The findings come from a large-scale sequencing project carried out on 531 samples of human excrement from Africa, South America, and the United States.

“It’s a humungous paper, with multiple key findings,” said food scientist David Mills of the University of California, Davis. “An impressive and complex piece of work,” agreed molecular biologist Jeremy Nicholson of Imperial College, London. Neither researcher participated in the study.

The scale and complexity stem from the research team’s aim of answering a multifaceted question—“What is the degree to which these microbial communities… vary within a person, as a function of postnatal development, physiological status, cultural tradition, and where a person lives,” said geneticist Jeffrey Gordon of the Washington University in St Louis, who led the study.

To this end, the researchers collected samples of feces from villagers in rural Malawi, Amerindians in Amazonian Venezuela, and metropolis-dwelling Americans. They then performed high-throughput sequencing on DNA taken from the samples to determine both the species and strains of microbes present and which microbial genes were most abundant.

The team found a common pattern for how the microbiomes of babies develop in the three countries. “It takes 6 to 9 months to get the first 6 or 700 bugs and then another couple of years to get the adult set,” explained Nicholson. “[Gordon] finds there is the same sort of developmental time span between countries,” he said, “but that the resulting microbiomes are nonetheless distinct between, let’s call it, a third-world population and a westernized population.”

One of the most striking differences was the degree of microbial diversity, with both the Amerindians and Malawians having far greater diversity than the Americans. “But, ironically, [Americans] might have more diversity in terms of the food eaten,” said Mills, which might have been expected to correlate with microbial diversity. Gordon suggested the Westerners’ lack of diversity could result from “our lifestyle, our degree of hygiene, [and] our use of antibiotics,” though further research is needed to test these possibilities.

Despite these differences between the gut microbiomes of the three cultures, there were also striking similarities, said Gordon. For example, “across all three populations, we see this age-dependent change in vitamin biosynthesis,” he said. In infants, gut bacteria tend to carry more copies of genes involved in folate biosynthesis, while the guts of older individuals harbor microbes carrying more genes for folate metabolism. Conversely, genes involved in vitamin B-12 synthesis became more prevalent in the gut microbiome with age.

“What’s really fascinating about those results,” said Mills, “is that it is reflecting what the host needs.”

oh, it's more than that...., but at least this is a start

guardian | Bacteria, viruses and parasites cause around 2m cases of cancer in the world each year, experts believe.

Of the 7.5m global deaths from cancer in 2008, an estimated 1.5m may have been due to potentially preventable or treatable infections.

Scientists carried out a statistical analysis of cancer incidence to calculate that around 16% of all cancers diagnosed in 2008 were infection-related. The proportion of cancers linked to infection was three times higher in developing countries than in developed ones.

Key cancer-causing infectious agents include human papillomavirus (HPV), the gastric bug Helicobacter pylori and the hepatitis B (HBV) and C viruses.

These four were together believed to be responsible for 1.9m cases of cancer, mostly gastric, liver and cervical cancers.

Cervical cancer accounted for around half of infection-related women's cancers. In men, more than 80% of infection-related cancers affected the liver, stomach and colon.

Dr Catherine de Martel and Dr Martyn Plummer, from the International Agency for Research on Cancer in Lyon, wrote in the Lancet Oncology journal: "Infections with certain viruses, bacteria, and parasites are one of the biggest and preventable causes of cancer worldwide … Application of existing public-health methods for infection prevention, such as vaccination, safer injection practice, or antimicrobial treatments, could have a substantial effect on future burden of cancer worldwide."

The researchers used information from a number of sources, including a cancer-incidence database covering 27 cancers from 184 countries.

a truly great loss indeed...,

The Scientist | Evolutionary biologist Lynn Margulis died last week (November 22) at the age of 73. She was best known for proposing the theory of endosymbiosis, which states that rather than evolving via genetic mutation, new species were more likely to have come about via parasitic or symbiotic relationships that became permanently inter-dependent over time.

“She was always stimulating; she always had a new idea, some new connection she had seen and she couldn’t wait to tell you about,” Steve Goodwin, Dean of the College of Natural Resources
 and the Environment told MassLive.com.

Margulis showed early aptitude in science, enrolling at the University of Chicago and earning her bachelor’s degree in zoology by the age of 18. Shortly thereafter she married her first husband, the astronomer Carl Sagan. The marriage ended by the time she got her doctorate in genetics from the University of California, Berkeley, in 1965.

She developed her ideas on symbiosis in the late 1960s, and tried to publish her ideas in 15 journals before finally being accepted by the Journal of Theoretical Biology, according to The New York Times. Though it was highly controversial at the time, serial symbiosis is widely accepted among evolutionary scientists today.

In the 1970s, she became a supporter of James Lovelock’s Gaia hypothesis, which proposed that the earth could be thought of as a complex system whose atmospheric and mineral components existed in symbiosis with living organisms, allowing biota as a whole to self-perpetuate.

She taught evolutionary biology for nearly 40 years, first at the Boston University and then at the University of Massachusetts, where I had the opportunity to experience her carefully crafted course. I came to the class expecting Margulis to expound on the theories that she had championed. Instead, she exposed our small seminar class to the experiments of many researchers whose work provided evidence for her ideas, and invited us to make own conclusions.

“If science doesn’t fit in with the cultural milieu, people dismiss science—they never reject their cultural milieu!” said Margulis in the book The Third Culture: Beyond the Scientific Revolution. In the same chapter, Richard Dawkins wrote: “I greatly admire Lynn Margulis’s sheer courage and stamina in sticking by the endosymbiosis theory, and carrying it through from being an unorthodoxy to an orthodoxy.”

According to The New York Times, Margulis died from a stroke. She is survived by a daughter Jennifer Margulis and three sons Dorion Sagan, Jeremy Sagan, Zachary Margulis-Ohnuma.

what is nanotechnology?

crnano | A basic definition: Nanotechnology is the engineering of functional systems at the molecular scale. This covers both current work and concepts that are more advanced.

In its original sense, 'nanotechnology' refers to the projected ability to construct items from the bottom up, using techniques and tools being developed today to make complete, high performance products.

The Meaning of Nanotechnology

When K. Eric Drexler popularized the word 'nanotechnology' in the 1980's, he was talking about building machines on the scale of molecules, a few nanometers wide—motors, robot arms, and even whole computers, far smaller than a cell. Drexler spent the next ten years describing and analyzing these incredible devices, and responding to accusations of science fiction. Meanwhile, mundane technology was developing the ability to build simple structures on a molecular scale. As nanotechnology became an accepted concept, the meaning of the word shifted to encompass the simpler kinds of nanometer-scale technology. The U.S. National Nanotechnology Initiative was created to fund this kind of nanotech: their definition includes anything smaller than 100 nanometers with novel properties.

Much of the work being done today that carries the name 'nanotechnology' is not nanotechnology in the original meaning of the word. Nanotechnology, in its traditional sense, means building things from the bottom up, with atomic precision. This theoretical capability was envisioned as early as 1959 by the renowned physicist Richard Feynman.

I want to build a billion tiny factories, models of each other, which are manufacturing simultaneously. . .The principles of physics, as far as I can see, do not speak against the possibility of maneuvering things atom by atom. It is not an attempt to violate any laws; it is something, in principle, that can be done; but in practice, it has not been done because we are too big. Richard Feynman, Nobel Prize winner in physics

Based on Feynman's vision of miniature factories using nanomachines to build complex products, advanced nanotechnology (sometimes referred to as molecular manufacturing
will make use of positionally-controlled mechanochemistry guided by molecular machine systems. Formulating a roadmap for development of this kind of nanotechnology is now an objective of a broadly based technology roadmap project led by Battelle (the manager of several U.S. National Laboratories) and the Foresight Nanotech Institute.

Shortly after this envisioned molecular machinery is created, it will result in a manufacturing revolution, probably causing severe disruption. It also has serious economic, social, environmental, and military implications.

Four Generations
Mihail (Mike) Roco of the U.S. National Nanotechnology Initiative has described four generations of nanotechnology development (see chart below). The current era, as Roco depicts it, is that of passive nanostructures, materials designed to perform one task. The second phase, which we are just entering, introduces active nanostructures for multitasking; for example, actuators, drug delivery devices, and sensors. The third generation is expected to begin emerging around 2010 and will feature nanosystems with thousands of interacting components. A few years after that, the first integrated nanosystems, functioning (according to Roco) much like a mammalian cell with hierarchical systems within systems, are expected to be developed.

neuroscience of the gut

Scientific American | People may advise you to listen to your gut instincts: now research suggests that your gut may have more impact on your thoughts than you ever realized. Scientists from the Karolinska Institute in Sweden and the Genome Institute of Singapore led by Sven Pettersson recently reported in the Proceedings of the National Academy of Sciences that normal gut flora, the bacteria that inhabit our intestines, have a significant impact on brain development and subsequent adult behavior.

We human beings may think of ourselves as a highly evolved species of conscious individuals, but we are all far less human than most of us appreciate. Scientists have long recognized that the bacterial cells inhabiting our skin and gut outnumber human cells by ten-to-one. Indeed, Princeton University scientist Bonnie Bassler compared the approximately 30,000 human genes found in the average human to the more than 3 million bacterial genes inhabiting us, concluding that we are at most one percent human. We are only beginning to understand the sort of impact our bacterial passengers have on our daily lives.

Moreover, these bacteria have been implicated in the development of neurological and behavioral disorders. For example, gut bacteria may have an influence on the body’s use of vitamin B6, which in turn has profound effects on the health of nerve and muscle cells. They modulate immune tolerance and, because of this, they may have an influence on autoimmune diseases, such as multiple sclerosis. They have been shown to influence anxiety-related behavior, although there is controversy regarding whether gut bacteria exacerbate or ameliorate stress related anxiety responses. In autism and other pervasive developmental disorders, there are reports that the specific bacterial species present in the gut are altered and that gastrointestinal problems exacerbate behavioral symptoms. A newly developed biochemical test for autism is based, in part, upon the end products of bacterial metabolism.

But this new study is the first to extensively evaluate the influence of gut bacteria on the biochemistry and development of the brain. The scientists raised mice lacking normal gut microflora, then compared their behavior, brain chemistry and brain development to mice having normal gut bacteria. The microbe-free animals were more active and, in specific behavioral tests, were less anxious than microbe-colonized mice. In one test of anxiety, animals were given the choice of staying in the relative safety of a dark box, or of venturing into a lighted box. Bacteria-free animals spent significantly more time in the light box than their bacterially colonized littermates. Similarly, in another test of anxiety, animals were given the choice of venturing out on an elevated and unprotected bar to explore their environment, or remain in the relative safety of a similar bar protected by enclosing walls. Once again, the microbe-free animals proved themselves bolder than their colonized kin.

Pettersson’s team next asked whether the influence of gut microbes on the brain was reversible and, since the gut is colonized by microbes soon after birth, whether there was evidence that gut microbes influenced the development of the brain. They found that colonizing an adult germ-free animal with normal gut bacteria had no effect on their behavior. However, if germ free animals were colonized early in life, these effects could be reversed. This suggests that there is a critical period in the development of the brain when the bacteria are influential. Fist tap Dorcas Daddy.

bacteria divide people into types

NYTimes | In the early 1900s, scientists discovered that each person belonged to one of four blood types. Now they have discovered a new way to classify humanity: by bacteria. Each human being is host to thousands of different species of microbes. Yet a group of scientists now report just three distinct ecosystems in the guts of people they have studied.

Blood type, meet bug type.

“It’s an important advance,” said Rob Knight, a biologist at the University of Colorado, who was not involved in the research. “It’s the first indication that human gut ecosystems may fall into distinct types.”

The researchers, led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, found no link between what they called enterotypes and the ethnic background of the European, American and Japanese subjects they studied.

Nor could they find a connection to sex, weight, health or age. They are now exploring other explanations. One possibility is that the guts, or intestines, of infants are randomly colonized by different pioneering species of microbes.

The microbes alter the gut so that only certain species can follow them.

Whatever the cause of the different enterotypes, they may end up having discrete effects on people’s health. Gut microbes aid in food digestion and synthesize vitamins, using enzymes our own cells cannot make.

Dr. Bork and his colleagues have found that each of the types makes a unique balance of these enzymes. Enterotype 1 produces more enzymes for making vitamin B7 (also known as biotin), for example, and Enterotype 2 more enzymes for vitamin B1 (thiamine).

The discovery of the blood types A, B, AB and O had a major effect on how doctors practice medicine. They could limit the chances that a patient’s body would reject a blood transfusion by making sure the donated blood was of a matching type. The discovery of enterotypes could someday lead to medical applications of its own, but they would be far down the road.

“Some things are pretty obvious already,” Dr. Bork said. Doctors might be able to tailor diets or drug prescriptions to suit people’s enterotypes, for example.

Or, he speculated, doctors might be able to use enterotypes to find alternatives to antibiotics, which are becoming increasingly ineffective. Instead of trying to wipe out disease-causing bacteria that have disrupted the ecological balance of the gut, they could try to provide reinforcements for the good bacteria. “You’d try to restore the type you had before,” he said.

Dr. Bork notes that more testing is necessary. Researchers will need to search for enterotypes in people from African, Chinese and other ethnic origins. He also notes that so far, all the subjects come from industrial nations, and thus eat similar foods. “This is a shortcoming,” he said. “We don’t have remote villages.”

The discovery of enterotypes follows on years of work mapping the diversity of microbes in the human body — the human microbiome, as it is known. The difficulty of the task has been staggering. Each person shelters about 100 trillion microbes.

(For comparison, the human body is made up of only around 10 trillion cells.) But scientists cannot rear a vast majority of these bacteria in their labs to identify them and learn their characteristics.