Tag Archives: luca

We’re all hosts on a viral planet: Meet Luca, the ancestor of all living things

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Some people look to the stars. Some look to themselves. I’ve always been interested in the cosmic goings on of DNA and RNA and their minuscule hosts.

dogma-jesusAccording to science writer legend Nicholas Wade of The New York Times life first emerged on Earth via a single-cell, bacterium-like organism, known as Luca, the Last Universal Common Ancestor, and is estimated to have lived some four billion years ago, when Earth was a mere 560 million years old.

The new finding sharpens the debate between those who believe life began in some extreme environment, such as in deep sea vents or the flanks of volcanoes, and others who favor more normal settings, such as the “warm little pond” proposed by Darwin.

The nature of the earliest ancestor of all living things has long been uncertain because the three great domains of life seemed to have no common point of origin. The domains are those of the bacteria, the archaea and the eukaryotes. Archaea are bacteria-like organisms but with a different metabolism, and the eukaryotes include all plants and animals.

Specialists have recently come to believe that the bacteria and archaea were the two earliest domains, with the eukaryotes emerging later. That opened the way for a group of evolutionary biologists, led by William F. Martin of Heinrich Heine University in Düsseldorf, Germany, to try to discern the nature of the organism from which the bacterial and archaeal domains emerged.

Their starting point was the known protein-coding genes of bacteria and archaea. Some six million such genes have accumulated over the last 20 years in DNA databanks as scientists with the new decoding machines have deposited gene sequences from thousands of microbes.

Genes that do the same thing in a human and a mouse are generally related by common descent from an ancestral gene in the first mammal. So by comparing their sequence of DNA letters, genes can be arranged in evolutionary family trees, a property that enabled Dr. Martin and his colleagues to assign the six million genes to a much smaller number of gene families. Of these, only 355 met their criteria for having probably originated in Luca, the joint ancestor of bacteria and archaea.

Genes are adapted to an organism’s environment. So Dr. Martin hoped that by pinpointing the genes likely to have been present in Luca, he would also get a glimpse of where and how Luca lived. “I was flabbergasted at the result, I couldn’t believe it,” he said.

The 355 genes pointed quite precisely to an organism that lived in the conditions found in deep sea vents, the gassy, metal-laden, intensely hot plumes caused by seawater interacting with magma erupting through the ocean floor.

A fresh perspective on alleged pesto outbreak in Italy

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It’s better to rely on locals who know their stuff, so I turned to our Italian food safety friend, Luca Bucchini to clarify the alleged-botulism-in-pesto story. He writes:

There was probably no botulin toxin in the Italian basil pesto that sent more than 100 people to the emergency departments across Italy. Of the 100, 10 have been initially hospitalised, but 8 were later sent home: none had symptoms which suggested botulism. While tests on products and humans are still pending, the toxin has yet to be found in any sample.

The company, Bruzzone and Ferrari, which has been producing basil for pesto for two centuries, had identified a “potentially pathogenic microorganism” in a lot of its pesto: it is widely believed that the organism was C. botulinum, the bacterium which basil.salmonellacan, under certain conditions, produce the lethal toxin. The product, which is a fresh sauce requiring refrigeration, was already on the market: when the shelf life of a product is relatively short and time required for testing is relatively long, products are shipped before the results of the testing are known. This procedure is often required by retailers. When Bruzzone and Ferrari realised that they had a positive finding for the pathogen, though not for the toxin, they decided to issue a recall; a public recall is uncommon in Italy.

Italy’s Ministry of Health, usually stingy with information, issued a Press Release (http://www.salute.gov.it/portale/news/p3_2_4_1_1.jsp?lingua=italiano&menu=salastampa&p=comunicatistampa&id=4053) on July 20, 2013, calling the incident an “alarm” and explained that the botulin toxin is potentially fatal. However, it failed to mention the retail brands under which the product was sold, and did not offer advice to consumers, for example on when to seek medical care. Only the lot, the sell-by date and the producer’s name were mentioned; it was assumed that consumers are able to scan the back of the label and identify the small print needed to identify the producer. The press release also suggested that products were mostly off the shelf and the recall was limited. Ministry of Health press releases are immediately taken up by the main press agencies, and automatically become major news.

It soon became apparent that 15,000 jars were affected, and that many consumers had eaten the product, which had been on the market for at least a week; there was no information for them in the official communication. Panic ensued. Officials communicated sparingly, with the exception of Liguria, the region where the company is based. Hospitals were slow to explain that no cases were confirmed and that people without symptoms did not need hospitalisation; the Facebook site of Bruzzone & Ferrari was the pesto.basil.cyclosporaonly formal source of information, with only a few independent media outlets providing further details. The affected lot had been sold under several brands, including those of Italy’s top supermarket chains. The supermarket chains posted alert signs in shops and frantically e-mailed and phoned customers with loyalty cards to inform them of the recall; they probably hoped to avoid going public. As consumers reported about the calls received on Facebook and on other sites, some eventually capitulated and published on their website a recall notice, while others are still silent.

At this point in time, it seems likely that there was no toxin in most or all jars, and that people sought medical attention for reasons unrelated to product content. Some suspect that other pathogens may be present; however, no specific information supports this, and reported symptoms by few patients (vomit, diarrhea) may be unrelated to the exposure.

Nevertheless, the presence of the toxin in some jars cannot be excluded. The product does not appear to be heat-treated; it is part of a broad global trend to produce raw, semi-raw fresh products which require refrigeration. The pH of the product is permissive for growth of botulin (specifications: 4.8-5.8); it is rich in oil providing anaerobic conditions; it is used on pasta as a sauce without cooking; it has a shelf life of 30 days. While the product is to be refrigerated, the cold chain, especially in summer, with ambient temperatures above 30 C, is often not reliable: retailers often don’t prioritise temperature control. Consumers may not understand the difference between shelf-stable pesto (which is more common) and the refrigerated variety, or underestimate the importance of refrigeration.

Though food safety officials praised the company for not hesitating to issue a public recall, magistrates, as it is usual in Italy, were quick to start a criminal investigation for alleged unintentional injuries. In Italy, companies fear issuing precautionary recalls as magistrates generally try and convict in criminal court those who publicly confess to the mere presence of a pathogen in their products. This has been a factor in the hesitation of businesses to embrace European food law which requires issuing immediate recalls.

Overall, it is early to draw final conclusions from this episode. Hopefully, the results of the testing will be made public and confirm that there was no outbreak (incidentally, Italy has an ongoing foodborne Hepatitis A outbreak with hundreds of cases of which were little is being said). It is perhaps time to question products which, while nicely fresh, depend on the cold chain for being safe from botulin. It is quite clear that the authorities, and particularly the Ministry of Health, need risk communication training: consumers need to reliably identify products, get quickly rid of them, and not rush to the ER if they don’t need to.