Escherichia coli

Anti-Bacterial, Generic Noroxin, Norfloxacin 400mg

NORFLOXACIN is a quinolone antibiotic. It can kill certain bacteria or stop their growth. This medicine is used to treat infections of the prostate and urinary tract. It is also used to treat some sexually transmitted diseases. It will not work for colds, flu, or other viral infections., September 15, 2010  —  Bacteria are famed for their ability to adapt to our toughest antibiotics. But resistance doesn’t spring up evenly across an entire colony. A new study suggests that a small cadre of hero bacteria are responsible for saving their peers. By shouldering the burden of resistance at a personal cost, these charitable cells ensure that the entire colony survives.

Henry Lee from the Howard Hughes Medical Centre assaulted a vat of Escherichia coli with increasingly strong waves of the drug norfloxacin, always using just enough to seriously impede their growth without killing them outright. As expected, the group became more resistant over time. By the end of the experiment, they were shrugging off doses of antibiotics that would have previously killed them.

But Lee found that not all the bacteria were equal. Most still remained vulnerable to the drug, and the group’s overall defences were bolstered by a small group of highly resistant individuals. The leaders of the resistance all had particularly high levels of a protein called tryptophanase. Tryptophanase breaks down the amino acid tryptophan and produces indole, a chemical that acts like a call to arms. It rallies the colony into action.

When bacteria detect indole, they start mass-producing molecular pumps that evict any drugs that have breached their walls. With these molecules, the beleaguered bacteria can pump out norfloxacin faster than it can kill them.

Indole also tells bacteria to start toughening up. In response, the cells tune down certain genes that norfloxacin would normally use to kill them and tune up genes that protect their insides from damage. By producing indole, the most resistant bacteria were prompting changes in their weaker neighbours that greatly increased the amount of norfloxacin they could withstand.

When Lee peered into the genes of the most resistant cells, he found that their own resistance was the result of several personal adaptations that averted death by norfloxacin. They had altered genes that would normally be targeted by the drug, removing its targets. They had switched on genes that protect them from chemical damage or that mass-produce produce drug-pumps. None of these mutations affect the production of indole; they just gave the mightiest cells the chance they needed to produce this rallying chemical.

When Lee challenged his bacteria with another drug called gentamicin, he found exactly the same thing – a resistant elite promoting the survival of the group by releasing waves of indole. This seems to be a general tactic, rather than a drug-specific one.

Producing indole isn’t easy; it takes energy to manufacture. Why should a small number of bacteria shoulder this burden to protect other members of the colony? Lee thinks that relationships are the answer. Having multiplied from common ancestors, the bacteria in the group are all related to one another and carry virtually the same genes. In this light, making a small sacrifice for the sake of genetically identical others is a good move.

Image from Nature

H.L. Lee, et al., “Bacterial charity work leads to population-wide resistance,” Nature, 467:82-6, 2010.  —  Antibiotics are meant to kill bacteria, so it might be disheartening to learn that some bacteria can literally eat antibiotics for breakfast. In fact, some species can thrive quite happily on nothing but antibiotics, even at high concentrations.

The rise of drug-resistant bacteria poses a significant threat to public health and many dangerous bugs seem to be developing resistance at an alarming rate. The headline-grabbing MRSA may be getting piggybacks from livestock to humans, while several strains of tuberculosis are virtually untreatable by standard drugs.

But a startling new study reveals just how widespread antibiotic resistance really is. Gautam Dantas from Harvard Medical School managed to culture antibiotic-eating bacteria from every one of 11 soil samples, taken from farmland and urban areas across the US. All eleven were positively loaded with a diverse group of bacteria that were extremely resistant to a wide range of antibiotics at high concentrations.

Soil super-bugs

In their natural environment, these soil bacteria are frequently exposed to a massive array of antibiotics from plants and other microbes, and have evolved ways of detecting and evading them. These resistant strains act as a living reservoir of innovative genetic means of resisting antibiotics, known as the ‘antibiotic resistome‘.

Dantas searched for resistant bacteria by culturing colonies that could grow in solutions where antibiotics were their only source of carbon. He tested 18 different antibiotics that are used to kill a variety of different bacterial species. Some of these were natural, others man-made; some were old, others new. But every single one managed to support at least one strain of bacteria. Six of them, including commonly used drugs like penicillin, vancomycin, ciprofloxacin and carbenicillin, even managed to feed bacteria from all 11 soils.

The degree of resistance in the soil bacteria was nothing short of extraordinary. Dantas cultured a representative set of 75 resistant strains and found that on average, they resisted 17 of the 18 antibiotics at low concentrations of 20 milligrams per litre (full bars in image below). But even at higher concentrations of 1 gram per litre (filled bars in image below), each strain managed to stand firm against an average of 14 out of 18 drugs.

When Dantas studied some of these strains more closely, he found that they nullified the drugs using similar techniques to the drug-resistant versions of disease-causing bacteria. Some shunted the antibiotics out of their cells with molecular pumps, others used enzymes to cut up the drugs, and yet others reprogrammed their own genetic code to deprive antibiotics of their targets.

Reservoir of resistance

The real danger is that the soil-living species could provide new defences that more dangerous ones can draw on to shrug off our best drugs.  Bacteria are capable of passing genetic material between one another as easily as two humans might swap business cards, making it trivial for the soil super-bugs to pass their crucial genes on to more dangerous species. To see how easily this could happen, have a look at this earlier post about how the food poisoning bug Salmonella has passed a resistance gene on to the Black Death bacterium. 

In principle, bacteria should be more able to successfully take up resistance genes from other closely related species. It’s worrying then that Dantas’s antibiotic-eaters belonged to such diverse groups.  By establishing a family tree of the different strains, he found that they were members of at least 11 different bacterial groups, although over half of them came from just two orders – the Burkholderiales and the Pseudomonadales. These include a wide variety of species that are known to infect hospital patients with weakened immune systems.

They are known for their large genome sizes (well, large for bacteria anyway) and some groups have suggested that these sizeable genomes allow them to metabolise a wide range of chemicals, antibiotics included. This unusual diet will come as no surprise to many a microbiologist. Bacteria can colonise some of the most extreme environments on the planet and can survive on the most unlikely to food sources, from crude oil to toxic waste. Now, it seems that they can also survive solely on chemicals that are meant to kill them.

Images from Science

Reference: doi:10.1126/science.1155157

The New York Times, by Nicholas Wade, September 15, 2010  —  Under Mendel’s laws of inheritance, you could thank mom and dad equally for all the outstanding qualities you inherited.

But there’s long been some fine print suggesting that a mother’s and father’s genes do not play exactly equal roles. Research published last month now suggests the asymmetry could be far more substantial than supposed. The asymmetry, based on a genetic mechanism called imprinting, could account for some of the differences between male and female brains and for differences in a mother’s and father’s contributions to social behavior.

A person gets one set of genes from each parent. Apart from the sex chromosomes, the two sets are equivalent, and in principle it should not matter if a gene comes from mother or father. The first sign that this is not always true came from experiments in which mouse embryos were engineered to carry two male genomes, or two female genomes. The double male and double female mice all died in the womb. Nature evidently requires one genome from each parent.

Biologists then made the embryos viable by mixing in some normal cells. The surprising outcome was that mice with two male genomes had large bodies and small brains. With the double female genome mice, it was the other way around. Evidently the maternal and paternal genomes have opposite effects on the size of the brain.

The root of the asymmetry is a procedure called imprinting in which either the mother’s or the father’s copy of a particular gene is inactivated. The best worked out example concerns a gene called insulinlike growth factor-2, which promotes the growth of the fetus. The IGF-2 gene is active in the paternal genome but imprinted or inactivated in the genome the fetus receives from its mother.

The leading explanation for imprinting is a theory that invokes conflict between relatives. Developed by David Haig, an evolutionary biologist at Harvard, the theory holds that there is a clash of interests between the fetus, whose purpose is to extract as much nutrition as possible, and the mother, whose interests lie in allocating her resources evenly to all the other children she may bear in the future.

Over the course of evolution this conflict has come to be mediated at a genetic level, Dr. Haig’s explanation goes, because the mother and the father have different interests. Speaking of mammals in general, the conflict is driven by female promiscuity. The mother wants to share her resources among progeny who may have different fathers, whereas the father is interested in the survival of only his own child. So the father always confers the IGF-2 gene in active form and the mother always bequeaths it in imprinted or silent form. The gene is imprinted in mice, humans and many other mammals.

It may seem strange to have a genetic tug of war within the fetus, with the paternal copy of the IGF-2 gene always asking for more, and the maternal copy refusing to ask at all, but presumably over the course of evolution the individuals who carried these two warring copies of the gene left more offspring than those with the gene in any other form.

Until last month only a hundred imprinted genes were known, and the mechanism seemed just an interesting deviation from Mendelian genetics. Research led by Christopher Gregg and Catherine Dulac of Harvard has shown that imprinting is far more common and more intricate than supposed.

Working in mice, the Harvard team showed that around 1,300 genes are imprinted. Dr. Dulac said that she expects a substantial, though lesser, proportion to be imprinted in people — maybe some 1 percent of the genome — because humans are more monogamous than mice and so the parents’ interests are more closely aligned.

Dr. Dulac was able to detect so many new imprinted genes by taking advantage of the ease with which genes can now be decoded. She cross-bred two very different strains of mice, thus ensuring that the maternal and paternal versions of each gene would have recognizably different sequences of DNA.

When a gene is activated, the cell transcribes it into RNA, DNA’s close chemical cousin. By decoding all the RNA transcripts in the mouse’s cells, Dr. Dulac could pick out those genes in which the paternal version was being transcribed much more than maternal version, and vice versa.

Besides finding far more imprinted genes than expected, Dr. Dulac’s team also picked up unexpected patterns in the way the genes were expressed. Maternal genes were more active in the embryo’s brain, but paternal genes became more active in the adult.

In another novel pattern, she found sex differences in imprinted genes in different region of the brain, particularly those concerned with feeding and with mating behavior. A gene called interleukin-18 is activated from the mother’s version in two important regions of the brain. This asymmetry is of interest because the gene in people has been linked with multiple sclerosis, a disease that predominates in women.

Altogether Dr. Dulac found 347 genes where either the mother’s or the father’s copy was more actively expressed in certain regions of the brain. Sex differences in the brain are usually attributed to the influence of hormones, but sex-based differences in imprinting may be another mechanism by which nature spins male and female brains out of the same genome.

“In your brain, your mom and your dad keep telling you what to do — I keep laughing when I think about it,” Dr. Dulac said.

In the cortex of the brain, Dr. Dulac discovered another unexpected asymmetry. Women have two X chromosomes, one from the mother and one from the father. The usual rule is that in each cell either the mother’s or the father’s copy is chosen at random to be switched off. But in the neurons of the cortex, there is a much greater chance that the paternal X chromosome will be switched off. “So again, it’s the conflict between mom and dad — each tries to use different chromosomes to influence you,” Dr. Dulac said.

Dr. Haig says that his theory of imprinting explains not only the tug of war between mother and fetus but also why there are imprinted genes in the brain.

It all has to do with the different interests of the mother’s family and the father’s family, which tug the individual in different directions. Relatives get into the argument because they share varying proportions of an individual’s genes.

Evolutionary fitness depends on passing one’s genes on to the next generation. But it also counts to pass on the identical genes that have been co-inherited by one’s siblings, uncles and aunts. The doctrine, known as inclusive fitness, was proposed by the biologist William Hamilton in the 1960s and is widely accepted, though is not without critics. It was challenged last month in the journal Nature by the Harvard biologist E. O. Wilson and two colleagues.

Under inclusive fitness, Dr. Haig has pointed out, a conflict of interest between the mother’s and father’s relatives would have arisen because of the different dispersal patterns of men and women. Most often it has been the woman who leaves her ancestral village and goes to live with her husband’s family.

The maternal genes stand to gain if the woman is as selfish as possible and focuses just on her and her children’s welfare. But since the father is related to everyone else in the village, the father’s genes will gain from altruistic behavior. Such a conflict will result in imprinted genes, just like the battle between the mother and fetus over the mother’s resources, in Dr. Haig’s view.

Two evolutionary biologists, Francisco Ubeda of the University of Tennessee and Andy Gardner of the University of Oxford in England, have devised a mathematical model for assessing the consequences of a woman living in her husband’s village, among people to whom she is not related. Natural selection, they say in an article in the current issue of Evolution, will favor the activation of paternal genes that underlie altruistic behavior and maternal genes that promote selfishness. “Your paternal genes want you to be nicer to your neighbors than your maternal genes do,” Dr. Gardner said in an interview.

In most people the altruistic and selfish motives operate in some reasonable kind of balance. But the imprinted genes carry a serious vulnerability: since they are silenced, a mutation to the other copy can be disastrous. Diseases like autism may be connected with disruptions to imprinted genes, Dr. Gardner said.

Imprinting, far from being a genetic curiosity, may play a central role in sexual differences and in psychiatric disease, if Dr. Haig’s explanation is correct. Much of the available evidence comes from mice, and people may to some extent have emancipated themselves from imprinting when they evolved the pair bond system of mating about a million years ago. But the pair bond does not mean perfect monogamy, and in its deviations from perfection there is plenty of room for imprinting to thrive.

A monkeypox patient in Lomela, Congo.The patient,who was examined by
epidemiologist Anne Rimoin, eventually died from monkeypox-related
complications.   Photo:  courtesy of Anne Rimoin, September 15, 2010, by Bob Grant  —  Cases of monkeypox, a disease caused by a DNA virus closely related to smallpox and cowpox, have increased dramatically in rural villages in the heart of the Democratic Republic of Congo (DRC), according to researchers working in the war-ravaged African country.

Reporting their results online at PNAS, an international team of scientists found that within one area the average annual incidence of monkeypox between November 2006 and November 2007 increased by about 20 times compared to the average annual incidence recorded in the 5 years between 1981 and 1986, the last time scientists actively monitored the study population.

Though monkeypox is seldom fatal, the alarming increase in the DRC, where monitoring is sporadic at best, means that the disease has the potential to emerge as one that is more deadly and spreads faster, according to Anne Rimoin, the University of California, Los Angeles, epidemiologist who led the research team. “Each infection gives the virus the opportunity to evolve into a more virulent variant,” Rimoin told The Scientist. “We’re worried about what could happen. This study is a warning bell.”

Anecdotal evidence has indicated for years that when global smallpox vaccination campaigns halted in the late 1970s, human monkeypox — to which the smallpox vaccine lends cross protection — was rare.

Rimoin’s data strongly suggests that since smallpox vaccinations stopped, the incidence of monkeypox has been creeping back up, thanks in part to several species of wild animals serving as reservoirs. “The data do tell us that it appears that when smallpox immunization was common, monkeypox was acquired less often and transmitted less often,” Don Burke, director of the University of Pittsburgh’s Center for Vaccine Research who was not involved in the study, told The Scientist. Indeed, Rimoin’s team found that people vaccinated for smallpox living in the study area had more than a 5-fold lower risk of monkeypox than unvaccinated individuals.

Monkeys are a common food source and are easily found in local villages. But they
may harbor infectious diseases.  Photo:  courtesy of Anne Rimoin


Though the original animal host of the virus that causes monkeypox is unknown, African squirrel, rat, mice, shrew, dormouse, and primate species are reservoirs. Transmission from animal to human likely occurs when people are bitten or come into contact with the blood or other body fluids of an infected animal. The human populations that Rimoin and her colleagues studied live near the tropical forest habitats of these animals and frequently eat them. With more migration from the countryside into cities and more so-called “bushmeat” starting to appear in markets in larger urban centers, such as DRC’s capital Kinshasa, the monkeypox virus could spread beyond rural populations, Rimoin said. “It’s only a matter of time that infected rodents are sold and distributed in larger cities.”

In 2003, almost 100 people in the US contracted monkeypox after prairie dogs sold as pets came in contact with an infected shipment of African rodents, according to the US Centers for Disease Control and Prevention. None of the infected Americans died, but the incident “showed that the virus is capable of spreading to new animal reservoirs outside of central Africa,” Rimoin noted.

But infection spreading from animals to humans is only part of the problem. The more worrying aspect of the disease’s spread is human-to-human, or secondary, transmission, according to Burke. Rimoin said that her team wasn’t able to track the rise in secondary transmission, but that she plans to conduct these studies soon. “When we see an increase that is so great, it suggests that human to human transmission may have also increased.”

Rimoin discusses the dangers of bushmeat hunting with local hunters in the Sankuru district.
Photo:  courtesy of Anne Rimoin


In addition, Rimoin said she plans sequence the virus samples she collected in DRC and compare them to samples collected in the 1980s to see if the monkeypox virus has been evolving in the last thirty years into become more transmissible or more virulent.

In the meantime, Rimoin suggested that the best way to stem the spread of the virus within the DRC is to launch educational campaigns that address proper handling of potential reservoir species and healthcare practices that prevent human-to-human transmission in the country. Though revisiting a widespread smallpox vaccination effort would almost certainly curb infection rates, she said that this would be virtually impossible. “At present the logistics of this are great and the expense would also be great,” Rimoin said.

For now, monitoring of the situation is essential, agree Burke and Rimoin. “This is a perfect example of positioning ourselves to be able to predict and prevent at an early stage rather than waiting for a full blown epidemic,” said Burke.

A. Rimoin, et al., “Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo,” PNAS, doi: 10.1073/pnas.1005769107, 2010., September 14, 2010  —  Unhappy meals: American doctors’ TV ad features a corpse holding a hamburger and the line ‘I was lovin’ it’. McDonald’s, which has thrived in the recession, isn’t laughing

McDonald’s fast food is graphically linked to health problems in this ad from a doctors’ group urging viewers: ‘Tonight, make it vegetarian ‘

It is an image to sap the flabbiest of appetites. An overweight, middle-aged man lies dead on a mortuary trolley, with a woman weeping over his body. The corpse’s cold hand still clutches a half-eaten McDonald’s hamburger.

A hard-hitting US television commercial bankrolled by a Washington-based medical group has infuriated McDonald’s by taking an unusually direct shot at the world’s biggest fast-food chain this week, using a scene filmed in a mortuary followed by a shot of the brand’s golden arches logo and a strapline declaring: “I was lovin’ it.”

The line is a provocative twist on McDonald’s long-standing advertising slogan, “I’m lovin’ it” and a voiceover intones: “High cholesterol, high blood pressure, heart attacks. Tonight, make it vegetarian.”

The commercial, bankrolled by the Physicians Committee for Responsible Medicine (PCRM), goes further than most non-profit advertising and has drawn an angry reaction from both the Chicago-based hamburger multinational and the broader restaurant industry.

The National Restaurant Association criticized it as “irresponsible” and said it was an attempt to scare the public with a “limited” view of nutrition. A McDonald’s spokesman said: “This commercial is outrageous, misleading and unfair to all consumers. McDonald’s trusts our customers to put such outlandish propaganda in perspective, and to make food and lifestyle choices that are right for them.”

The commercial, to be aired initially in the Washington area but potentially in further US cities, comes amid an increasingly lively debate in the US about healthy eating. The first lady, Michelle Obama, has made nutrition a signature issue and is leading a campaign to encourage physical fitness and improved diets – particularly among American children, a third of whom are overweight.

The recession has hardly helped the healthy eating cause. McDonald’s has enjoyed a relatively prosperous financial crisis as diners opt for its affordable offerings in place of more expensive high-street restaurants. Its global profits for the six months to June were up 12% to $2.3bn, powered by sales rises both in the United States and Britain.

The PCRM’s director of nutrition education, Susan Levin, made no apologies for singling out the golden arches: “McDonald’s is one of the biggest fast-food chains in the world. Its name and its golden arches are instantly recognizable. We feel we’re making a point about all fast food when we talk about McDonald’s.”

Harvard Medical School, September 2010

Q. I heard somewhere that the type of earwax you have is linked to your risk of heart disease. Can that be true?

A. One part of that “connection” is correct — humans have different types of earwax, also known as cerumen (suh-ROO-men). Wet earwax, which is brownish and sticky, contains about 50% fat and 20% protein. Dry earwax, which is gray and flaky, contains 18% fat and 43% protein. The type of earwax a person has is genetically determined.

In the early 1960s, one small study demonstrated a connection between wet earwax and atherosclerosis. In 1993, Lithuanian researchers found that people with wet earwax were more likely to have higher levels of apolipoprotein B, a protein that travels with particles of LDL (bad) cholesterol, while those with dry earwax were more likely to live longer. These data aren’t nearly enough to be “a connection.”

In 2009, Japanese researchers discovered that the gene that determines earwax type also codes for a transport protein called ABCC11 that may play a role in breast cancer. Women with wet earwax were somewhat more likely to have breast cancer (and a stronger body odor) than those with dry earwax. The researchers suggest that earwax type could someday be a tip-off of breast cancer risk. Whether they are right, or whether there is an association between earwax and heart disease, remains to be seen.

— Thomas Lee, M.D.
Editor in chief, Harvard Heart Letter