Thursday, August 11, 2011

Red meat linked to increased risk of type 2 diabetes

A new study by Harvard School of Public Health (HSPH) researchers finds a strong association between the consumption of red meat—particularly when the meat is processed—and an increased risk of type 2 diabetes. The study also shows that replacing red meat with healthier proteins, such as low-fat dairy, nuts, or whole grains, can significantly lower the risk.

Based on these results, the researchers advise that consumption of processed red meat—like hot dogs, bacon, sausage, and deli meats, which generally have high levels of sodium and nitrites—should be minimized and unprocessed red meat should be reduced. If possible, they add, red meat should be replaced with healthier choices, such as nuts, whole grains, low-fat dairy products, fish, or beans.

The study, led by An Pan, research fellow in the HSPH Department of Nutrition, will be published online in the American Journal of Clinical Nutritionon August 10, 2011 and will appear in the October print edition.

Pan, senior author Frank Hu, professor of nutrition and epidemiology at HSPH, and colleagues analyzed questionnaire responses from 37,083 men followed for 20 years in the Health Professionals Follow-Up Study; 79,570 women followed for 28 years in the Nurses’ Health Study I; and 87,504 women followed for 14 years in the Nurses’ Health Study II.

They also conducted an updated meta-analysis, combining data from their new study with data from existing studies that included a total of 442,101 participants, 28,228 of whom developed type 2 diabetes during the study. After adjusting for age, body mass index (BMI), and other lifestyle and dietary risk factors, the researchers found that a daily 100-gram serving of unprocessed red meat (about the size of a deck of cards) was associated with a 19% increased risk of type 2 diabetes. They also found that one daily serving of half that quantity of processed meat—50 grams (for example, one hot dog or sausage or two slices of bacon)—was associated with a 51% increased risk.

“Clearly, the results from this study have huge public health implications given the rising type 2 diabetes epidemic and increasing consumption of red meats worldwide,” said Hu. “The good news is that such troubling risk factors can be offset by swapping red meat for a healthier protein.”

The researchers found that, for an individual who eats one daily serving of red meat, substituting one serving of nuts per day was associated with a 21% lower risk of type 2 diabetes; substituting low-fat dairy, a 17% lower risk; and substituting whole grains, a 23% lower risk.

Worldwide, diabetes has reached epidemic levels, affecting nearly 350 million adults. In the U.S. alone, more than 11% of adults over age 20—25.6 million people—have the disease, according to the Centers for Disease Control and Prevention. Most have type 2 diabetes, which is primarily linked to obesity, physical inactivity, and an unhealthy diet.

Previous studies have indicated that eating processed red meats increases the risk of developing type 2 diabetes. Risks from unprocessed meats have been less clear. For instance, in 2010, HSPH researchers found no clear evidence of an association between eating unprocessed meats and increased risk for either coronary heart disease or type 2 diabetes, but that study was based on smaller samples than the current study, and the researchers recommended further study of unprocessed meats. Another HSPH study in 2010 linked eating red meat with an increased risk of heart disease—which is strongly linked to diabetes—but did not distinguish between processed and unprocessed red meats.

This new study—the largest of its kind in terms of sample size and follow-up years—finds that both unprocessed and processed meats pose a type 2 diabetes risk, thus helping to clarify the issue. In addition, this study is among the first to estimate the risk reduction associated with substituting healthier protein choices for red meat.

“Our study clearly shows that eating both unprocessed and processed red meat—particularly processed—is associated with an increased risk of type 2 diabetes,” said Pan. He noted that the 2010 U.S. dietary guidelines continue to lump red meat together with fish, poultry, eggs, nuts, seeds, beans, and soy products in the “protein foods” group. But since red meat appears to have significant negative health effects—increased risk of diabetes, cardiovascular disease, and even total mortality, as suggested by several recent studies—Pan suggested the guidelines should distinguish red meat from healthier protein sources and promote the latter instead.

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Support for the study was provided by the National Institutes of Health’s National Institute of Diabetes and Digestive and Kidney Diseases and the National Heart, Lung, and Blood Institute.

“Red Meat Consumption and Risk of Type 2 Diabetes: 3 Cohorts of U.S. Adults and an Updated Meta-Analysis,” An Pan, Qi Sun, Adam M. Bernstein, Matthias B. Schulze, JoAnn E. Manson, Walter C. Willett, and Frank B. Hu, American Journal of Clinical Nutrition, online August 10, 2011.

Student brings home new expertise to answer question in antibiotic resistance

Posted by Biomechanism

(Biomechanism.com) — Working out the structure of a complex formed when a protein binds to DNA has proved to be key in understanding how an antibiotic-producing organism controls resistance to its own antibiotic, and may be an example of how other antibiotic producers regulate export to prevent self-toxicity.

Caption: Pictured are Tung Le and Mark Buttner of the John Innes Centre. Credit: John Innes Centre

The natural production of antibiotics by certain microorganisms is a complex and highly regulated process, not least because the organism making these compounds must protect itself from their toxic effects. Researchers at the John Innes Centre, which is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), have been studying the production of simocyclinone, produced by Streptomyces antibioticus, and in particular how the production of this potent antibiotic triggers an efficient pumping mechanism that exports the antibiotic from the cell.

Much of the work elucidating this protection mechanism has been carried out by Tung Le, a Vietnamese PhD student enrolled in the JIC’s four-year rotation PhD programme. Tung, working under the supervision of Mark Buttner and David Lawson, showed that SimR, the protein Streptomyces antibioticus uses to regulate antibiotic export, can bind either to DNA or to the antibiotic itself, but crucially cannot bind to both. This means that when the antibiotic is around, SimR releases the DNA, which allows the expression of a gene that encodes a pump responsible for removing simocyclinone from the cell.

“This provides a mechanism that couples the potentially lethal biosynthesis of the antibiotic to its export, which has wider implications for resistance to clinically important antibiotics,” commented Prof. Buttner. “However, we needed to know more detail about the interaction between SimR and DNA.”

In this latest research, published in the journal Nucleic Acids Research, they show that the SimR protein has a novel ‘arm’ and that cutting off this arm unexpectedly weakened SimR binding to DNA. To determine the function of this arm, the researchers needed to work out the crystal structure of the protein bound to DNA, something which hadn’t been achieved in Norwich before.

To overcome this skills gap, Tung won both a Korner Travelling Fellowship and an EMBO Short-Term Travel Fellowship to visit the University of Texas M.D. Anderson Cancer Center, home to one of the leading laboratories specialising in this technique. Tung spent three months working in the labs of Richard Brennan and Maria Schumacher, learning how to solve the structures of protein-DNA complexes. He was then able to apply this to his own project.

“I learned a lot and it was a great experience,” said Tung. “The knowledge I brought back was not only useful for my project but will also be beneficial for others, and I feel very proud about that.”

Usually, the SimR arm is unstructured, but in the presence of DNA they saw that it becomes ordered and binds into the minor groove of the DNA molecule. The crystal structure also shows how other parts of the SimR protein form sequence-specific interactions with a binding site in front of the export pump gene.

SimR is a member of a large family of regulatory proteins found in bacteria, and is the fifth one to have its structure solved when bound to DNA. The way these proteins recognise their target DNA sequences differs. This new example has wider implications, as a bioinformatic search of this family of regulators showed that many of them also have arms similar to the one characterised in this study.

Tung submitted his PhD thesis in early August, and his research has already produced four first-author papers. He is due to take up a post-doctoral position at the Massachusetts Institute of Technology in January.

“It can be very difficult for non-EU students to find the funding to study for a PhD in the UK, and so I was delighted to be offered a place on the JIC rotation programme. I am keen to encourage and help build relations between JIC and Vietnam. I was very happy to see the JIC is involved in joint work with Vietnam to sequence the genomes of different varieties of rice” said Tung, who left Vietnam at the age of seventeen for a bioscience career in the UK.

The researchers have also recently received a grant from the BBSRC to continue investigating the complexities of the regulation of antibiotic biosynthetic pathways, focussing on SimR and two other antibiotic-responsive transcription factors encoded in the simocyclinone biosynthetic cluster. This will establish the roles that the antibiotic plays in regulating self-resistance and its own biosynthesis. With the ever-growing problem of resistance, this kind of fundamental research is vital.

How to Build a Better Learner

Brain studies suggest new ways to improve reading, writing and arithmetic--and even social skills

By Gary Stix

Eight-month-old Lucas Kronmiller has just had the surface of his largely hairless head fitted with a cap of 128 electrodes. A research assistant in front of him is frantically blowing bubbles to entertain him. But Lucas seems calm and content. He has, after all, come here, to the Infancy Studies Laboratory at Rutgers University, repeatedly since he was just four months old, so today is nothing unusual. He—like more than 1,000 other youngsters over the past 15 years—is helping April A. Benasich and her colleagues to find out whether, even at the earliest age, it is possible to ascertain if a child will go on to experience difficulties in language that will prove a burdensome handicap when first entering elementary school.

Benasich is one of a cadre of researchers employing brain-recording techniques to understand the essential processes that underlie learning. The new science of neuroeducation seeks the answers to questions that have always perplexed cognitive psychologists and pedagogues.

Thinking cap records electrical signals from the brain of one-year-old Elise Hardwick, who is helping scientists figure out how the youngest children process sounds that make up the building blocks of language.Image: Photograph by Andrew Hetherington

In Brief

The technology and research methods of the neuroscientist have started to reveal, at the most basic level, what happens in the brain when we learn something new.
As these studies mature, it may become possible for a preschooler or even an infant to engage in simple exercises to ensure that the child is cognitively equipped for school.
If successful, such interventions could potentially have a huge effect on educational practices by dramatically reducing the incidence of various learning disabilities.
Scientists, educators and parents must also beware overstated claims for brain-training methods that purport to help youngsters but have not been proved to work.

Turning Japanese

Debt and politics in America and Europe

The absence of leadership in the West is frightening—and also rather familiar

A GOVERNMENT’S credibility is founded on its commitment to honour its debts. As a result of the dramas of the past few weeks, that crucial commodity is eroding in the West. The struggles in Europe to keep Greece in the euro zone and the brinkmanship in America over the debt ceiling have presented investors with an unattractive choice: should you buy the currency that may default, or the one that could disintegrate?

In the early days of the economic crisis the West’s leaders did a reasonable job of clearing up a mess that was only partly of their making. Now the politicians have become the problem. In both America and Europe, they are exhibiting the sort of behaviour that could turn a downturn into stagnation. The West’s leaders are not willing to make tough choices; and everybody—the markets, the leaders of the emerging world, the banks, even the voters—knows it. It is a mark of how low expectations have sunk that the euro zone’s half-rescue of Greece on July 21st was greeted with relief. As The Economistwent to press, it still was not clear on what terms America’s debt limit would be raised, and for how long. Even if the current crises abate or are averted, the real danger persists: that the West’s political system cannot take the difficult decisions needed to recover from a crisis and prosper in the years ahead.

The world has seen this before. Two decades ago, Japan’s economic bubble popped; since then its leaders have procrastinated and postured. The years of political paralysis have done Japan more harm than the economic excesses of the 1980s. Its economy has barely grown and its regional influence has withered. As a proportion of GDP, its gross public debt is the highest in the world, twice America’s and nearly twice Italy’s. If something similar were to happen to its fellow democracies in Europe and America, the consequences would be far larger. No wonder China’s autocrats, flush with cash and an (only partly deserved) reputation for getting things done, feel as if the future is on their side.

Though both about debt, the arguments in Europe and America have very different origins. The euro crisis was brought on by investors with genuine worries about the solvency of several euro-zone countries. By contrast the stand-off in Washington is a political creation, thrust upon initially incredulous investors (see article). Increasing America’s overdraft beyond $14.3 trillion should have been relatively simple. But Republican congressmen, furious about big government, have recklessly used it as a political tool to embarrass Barack Obama.

Compare world debt levels over time with our updated interactive debt guide

The similarity between the European and American dramas lies in the protagonists’ refusal to face reality. European politicians, led by Angela Merkel, have gone to absurd lengths to avoid admitting two truths: that Greece is bust; and that north Europeans (and Mrs Merkel’s thrifty Germans in particular) will end up footing a good part of the bill, either by transferring money to the south or by bailing out their own banks. They have failed to undertake a serious restructuring: the current rescue package reduces Greece’s debt, but not by enough to give it a genuine chance of recovery (see article). As a result, Greece, and maybe other peripheral European countries too, will need another bail-out sooner or later. Just as in Japan, politicians have failed to make the structural labour- and product-market reforms essential to spurring growth. If this deal spawns a fiscal union within Europe, as it may well, that will not be because Mrs Merkel and her peers took a bold, strategic and transparent decision to create one, but because they ran away from more immediate forms of pain (see article).

America’s debt debate seems still more kabuki-like. Its fiscal problem is not now—it should be spending to boost recovery—but in the medium term. Its absurdly complicated tax system raises very little, and the ageing of its baby-boomers will push its vast entitlement programmes towards bankruptcy. Mr Obama set up a commission to examine this issue and until recently completely ignored its sensible conclusions. The president also stuck too long to the fiction that the deficit can be plugged by taxing the rich more: he even wasted part of a national broadcast this week bashing the wealthy, though the Democrats had already withdrawn proposals for such rises.

Yet Mr Obama and his party seem a model of fiscal statesmanship compared with their Republican opponents. Once upon a time the American right led the world when it came to rethinking government; now it is an intellectual pygmy. The House Republicans could not even get their budget sums right, so the vote had to be delayed. A desire to curb Leviathan is admirable, but the tea-partiers live in a fantasy world in which the deficit can be reduced without any tax increases: even Mr Obama’s attempts to remove loopholes in the tax code drive the zealots into paroxysms of outrage.

In both Europe and America electorates seem to be turning inward. There is the same division between “ins” and “outs” that has plagued Japan. In Europe one set of middle-class workers is desperate to hang on to protections and privileges: millions of others are stuck in unprotected temporary jobs or are unemployed. In both Europe and America well-connected public-sector unions obstruct progress. And then there is the greatest (and also the least sustainable) division of all: between the old, clinging tightly to entitlements they claim to have earned, and the young who will somehow have to pay for all this.

Sometimes crises beget bold leadership. Not, unfortunately, now. Japan has mostly been led by a string of weak consensus-seekers. For all their talents, both Mr Obama and Mrs Merkel are better at following public opinion than leading it.

The problem lies not just in the personalities involved, but also in the political structures. Japan’s dysfunctional politics were rooted in its one-party system: petty factionalism has survived both the Liberal Democratic Party’s resounding defeat in 2009 and the recent tsunami (see article). In America’s Congress the moderate centre—conservative Democrats and liberal Republicans—has collapsed, in part because partisan redistricting has handed over power to the extremes. In Europe national politicians, answerable to their own electorates, are struggling to confront continent-wide problems.

Autocrats need not sneer at the troubles of Western democracies. The problems the latter face would tax any government; and, as the Asian financial crisis a decade ago showed, dictatorships are often worse at distributing pain. Moreover, Western politics is less broken than many allege. Since 2009 Congress has passed a huge stimulus and the health-care bill, both controversial yet also evidence that the legislature can get things done. For all their petty foolishness, the Republicans are bringing issues like tax reform and entitlements into the national debate. Outside the euro zone—in Britain, and in the Baltic republics, for instance—politicians have implemented reforms and austerity programmes with admirable speed.

Our views on what the West should do will be painfully familiar to readers. Europe’s politicians need to implement not just a serious restructuring of the peripheral countries’ debts but also a serious reform of their economies, to clean out cronyism, corruption and all the inefficiencies that hold back their growth. America’s Democrats need to accept entitlement cuts and Republicans higher taxes. Independent commissions should set electoral boundaries. And so on.

Japan’s politicians had umpteen chances to change course; and the longer they avoided doing so, the harder it became. Their peers in the West should heed that example.

Painting by numbers

Digital analysis is invading the world of the connoisseur

JUDGING artistic styles, and the similarities between them, might be thought one bastion of human skill that machines could never storm. Not so, if Lior Shamir at Lawrence Technological University in Michigan is correct. A paper he has just published in Leonardosuggests that computers may have just as good an eye for style as humans do—and, in some cases, may see connections between artists that human critics have missed.

Dr Shamir, a computer scientist, presented 57 images by each of nine painters—Salvador Dalí, Giorgio de Chirico, Max Ernst, Vasily Kandinsky, Claude Monet, Jackson Pollock, Pierre-Auguste Renoir, Mark Rothko and Vincent van Gogh—to a computer, to see what it made of them. The computer broke the images into a number of so-called numerical descriptors. These descriptors quantified textures and colours, the statistical distribution of edges across a canvas, the distributions of particular types of shape, the intensity of the colour of individual points on a painting, and also the nature of any fractal-like patterns within it (fractals are features that reproduce similar shapes at different scales; the edges of snowflakes, for example).

All told, the computer identified 4,027 different numerical descriptors. Once their values had been established for each of the 513 artworks that had been fed into it, it was ready to do the analysis.

To look for such distinguishing features, Dr Shamir programmed the computer to use a statistical method that scores the strength of the distance between the values of two or more descriptors for each pair of artists. As a result, he was able to rank each of the 4,027 descriptors by how useful it was at discriminating between artists.

Dr Shamir’s aim was to look for quantifiable ways of distinguishing between the work of different artists. If such things could be established, it might make the task of deciding who painted what a little easier. Such decisions matter because, even excluding deliberate forgeries, there are many paintings in existence that cannot conclusively be attributed to a master rather than his pupils, or that may be honestly made copies whose provenance is now lost.

Surprisingly, the values of 19 of the 20 most informative descriptors showed dramatically higher similarities between Van Gogh (left below) and Pollock (right) than between Van Gogh and painters such as Monet and Renoir, who conventional art criticism would think more closely related to Van Gogh’s oeuvre than Pollock’s is. (Dalí and Ernst, by contrast, were farther apart then expected.)

What is interesting, according to Dr Shamir, is that no single feature makes Pollock’s artistic style similar to Van Gogh’s. Instead, the connection is based on a broad set of image-content descriptors which reflect many aspects of the two artists’ styles, including a shared preference for low-level textures and shapes, and similarities in the ways they employed lines and edges.

What was intended, then, as a way of improving the ability to distinguish between different hands has also thrown up a new way of looking for stylistic similarities. Whether Pollock was actually influenced by Van Gogh, or merely happened upon a similar way of doing things through a similar artistic sensibility, is not clear. But it gives art historians a new line of investigation to pursue.