Nature News

Diskutera fysik, kemi, biologi, samt direkta tillämpningar såsom teknik och medicin.
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Re: Nature News

Inlägg av Tryggve » tis 28 okt 2014, 16:25

I senaste Nature Highlights så har man specialare om att det är tio år sedan "hobbiten" upptäcktes. D v s Homo floresiensis

Det är flera artiklar, plus länkar gamla artiklar.

http://www.nature.com/news/hobbit-1.161 ... S-20141028
The remains of the tiny hominin Homo floresiensis (nicknamed the ‘hobbit’) still raise supersize questions ten years after the publication in Nature of their discovery in a cave on the remote island of Flores in Indonesia. This collection of reporting, comment and research — new and from Nature’s archives — examines the controversy surrounding the origins and validity of this species, including whether it belongs in our genus, Homo.

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45 000 år gammalt genom sekvenserat

Inlägg av Tryggve » tis 28 okt 2014, 16:29

Man har lyckats sekvensera genomet från en ca 45 000 år gammalt mänskligt ben.
Oldest-known human genome sequenced

DNA shows a group of modern humans roamed across Asia.

A 45,000-year-old leg bone from Siberia has yielded the oldest genome sequence for Homo sapiens on record — revealing a mysterious population that may once have spanned northern Asia. The DNA sequence from a male hunter-gatherer also offers tanta­li­zing clues about modern humans’ journey from Africa to Europe, Asia and beyond, as well as their sexual encounters with Neanderthals.

His kind might have remained unknown were it not for Nikolai Peristov, a Russian artist who carves jewellery from ancient mammoth tusks. In 2008, Peristov was looking for ivory along Siberia’s Irtysh River when he noticed a bone jutting from the riverbank. He dug it out and showed it to a police forensic scientist, who identified it as probably human.

The bone turned out to be a human left femur, and eventually made it to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where researchers carbon-dated it. “It was quite fossilized, and the hope was that it might turn out old. We hit the jackpot,” says Bence Viola, a palaeo­anthropologist who co-led the study of the remains. “It was older than any other modern human yet dated.” The luck continued when Viola’s colleagues found that the bone contained well-preserved DNA, and they sequenced its genome to the same accuracy as that achieved for contemporary human genomes (Q. Fu et al.Nature 514, 445–449; 2014).

The researchers named their find Ust’-Ishim, after the district where Peristov found the remains. They dated him to between 43,000 and 47,000 years old, nearly twice the age of the next-oldest known complete modern-human genome, although older, archaic-human genomes exist.

DNA may be the only chance to connect the remains to other humans. “This guy came out of nowhere — there’s no archaeology site we could connect it to,” says Viola, suggesting that his group roamed far and wide.

The Ust’-Ishim man was probably descended from an extinct group that is closely related to humans who left Africa more than 50,000 years ago to populate the rest of the world, but later went extinct, Viola says.

http://www.nature.com/news/oldest-known ... S-20141028

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Re: Nature News

Inlägg av Tryggve » fre 28 nov 2014, 13:42

En artikel som handlar om en nyligen upptäckt skandal där några forskare granskade sina egna artiklar. Det har tidigare omnämnts på bloggen Retractionwatch, bland annat.

Det började med att en editor blev lite misstänksam över att en forskare ofta fick sina artiklar granskade så snabbt. Det var inte så att det alltid var strålande omdömen, utan just det att det gick så fort för just denna granskare att bearbeta manusen.

Sedan har det uppdagats fler (och värre!) exempel.

http://www.nature.com/news/publishing-t ... am-1.16400

Publishing: The peer-review scam

When a handful of authors were caught reviewing their own papers, it exposed weaknesses in modern publishing systems. Editors are trying to plug the holes.

Most journal editors know how much effort it takes to persuade busy researchers to review a paper. That is why the editor of The Journal of Enzyme Inhibition and Medicinal Chemistry was puzzled by the reviews for manuscripts by one author — Hyung-In Moon, a medicinal-plant researcher then at Dongguk University in Gyeongju, South Korea.

The reviews themselves were not remarkable: mostly favourable, with some suggestions about how to improve the papers. What was unusual was how quickly they were completed — often within 24 hours. The turnaround was a little too fast, and Claudiu Supuran, the journal's editor-in-chief, started to become suspicious.

In 2012, he confronted Moon, who readily admitted that the reviews had come in so quickly because he had written many of them himself. The deception had not been hard to set up. Supuran's journal and several others published by Informa Healthcare in London invite authors to suggest potential reviewers for their papers. So Moon provided names, sometimes of real scientists and sometimes pseudonyms, often with bogus e-mail addresses that would go directly to him or his colleagues. His confession led to the retraction of 28 papers by several Informa journals, and the resignation of an editor.

Moon's was not an isolated case. In the past 2 years, journals have been forced to retract more than 110 papers in at least 6 instances of peer-review rigging. What all these cases had in common was that researchers exploited vulnerabilities in the publishers' computerized systems to dupe editors into accepting manuscripts, often by doing their own reviews. The cases involved publishing behemoths Elsevier, Springer, Taylor & Francis, SAGE and Wiley, as well as Informa, and they exploited security flaws that — in at least one of the systems — could make researchers vulnerable to even more serious identity theft. “For a piece of software that's used by hundreds of thousands of academics worldwide, it really is appalling,” says Mark Dingemanse, a linguist at the Max Planck Institute for Psycholinguistics in Nijmegen, the Netherlands, who has used some of these programs to publish and review papers.

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Nytt antibiotika

Inlägg av Tryggve » ons 07 jan 2015, 19:51

Ett ämne (Teixobactin) som har hittats i jordlevande bakterier har visat sig vara ett effektivt antibakteriellt ämne. Det verkar inte heller lika lätt utvecklas resistens mot ämnet hos bakterierna som bekämpas.

http://www.nature.com/nature/journal/va ... 14098.html
Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.

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Re: Nature News

Inlägg av Hexmaster » ons 07 jan 2015, 21:09

BBC har en fin artikel om samma sak (det här måste vara den första gången jag hittat en sådan nyhet på egen hand innan jag läst den hos dig) som även går in på hur de burit sig åt med bakterieodling i jorden, m.m.

http://www.bbc.com/news/health-30657486

Att jord användes från en av forskarnas egen trädgård låter nästan för bra för att vara sant. :-)
Detta skall jag visa dig medelst ett stort papper som jag har fyllt med faktiska upplysningar! - Strindberg

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Re: Nature News

Inlägg av Tryggve » ons 07 jan 2015, 21:12

Snyggt system för att odla jordbakterier, det borde en del kollegor vara intresserade av. Seriöst, alltså. :-)

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Re: Nature News

Inlägg av devadatta » tor 08 jan 2015, 04:23

Bästa nyheten på länge, som i att det kan rädda mitt liv i framtiden!
Vetenskap - det är roligt för att det är sant!

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Re: Nature News

Inlägg av Tryggve » mån 12 jan 2015, 14:35

Jag postar detta även i denna tråd, liksom i antibiotika-tråden.

Efter att ha ögnat igenom Nature-artiklen så måste jag säga att man får en hel del vibbar till just upptäckten av penicillin. Efter att ha gjort ett antal in vitro tester så inokulerades möss med en mängd antibiotikaresistentS. aureussom i normala fall är dödligt i 90% av fallen. Alla möss som behandlades med teixobactin överlevde, och inga biverkningar observerades. Dock var antalet möss rätt lågt. Det som behövs är ju ytterligare studier, förstås. Men nog verkar teixobactin kunna vara en rätt lovande kandidat för att behandla en del infektioner av grampositiva bakterier.

Dock så är just själva systemet för att odla bakterierna också väldigt spännande. Som man säger i artikeln, ca 1% av de bakterier som lever i jord har gått att odla under labförhållanden. Detta system kan göra det möjligt att odla kanske 50% av de jordlevande bakterierna.

Detta plus de framsteg som man har gjort när det gäller genomsekvensering på senare år gör väl att det borde vara lättare att utföra denna typ av stora screeningar nu än vad det var på 1960-talet.

Man har som sagt screenat ca 10 000 olika bakterier efter denna aktivitet.

Spännande.

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Re: Nature News

Inlägg av Tryggve » lör 17 jan 2015, 12:41

Nu rör jag mig utanför mitt eget fält, men en reviewartiklel i Nature nyligen menar att världshavens tillstånd målas upp som värre än vad det faktiskt är.

http://www.nature.com/news/ocean-calami ... rs-1.16714
Ocean 'calamities' oversold, say researchers

Team calls for more scepticism in marine research.

The state of the world's seas is often painted as verging on catastrophe. But although some challenges are very real, others have been vastly overstated, researchers claim in a review paper. The team writes that scientists, journals and the media have fallen into a mode of groupthink that can damage the credibility of the ocean sciences. The controversial study exposes fault lines in the marine-science community.

Carlos Duarte, a marine biologist at the University of Western Australia in Perth, and his colleagues say that gloomy media reports about ocean issues such as invasive species and coral die-offs are not always based on actual observations. It is not just journalists who are to blame, they maintain: the marine research community “may not have remained sufficiently sceptical” on the topic.

“There are a lot of conversations around meetings about the excess doom and gloom in our reporting of ocean health, but perhaps this is the first paper to bring these concerns out of the privacy of peer conversations,” says Duarte. “This is a silent movement, as there is a lot of peer pressure against voicing those concerns openly, so my co-authors and I expect significant heat upon us to be derived from our paper.”

In their review, published on 31 December in BioScience1, Duarte and his colleagues look at purported catastrophes, including overfishing, jellyfish blooms, invasive species and the impact of ocean acidification on organisms such as corals. In some cases, they say, there is strong evidence for global-scale problems bringing severe disruption — overfishing is a prime example. But for other topics that have excited scientific and media attention, the evidence is equivocal or weak. In these categories, Duarte places global blooms of jellyfish and the problems caused by invasive species.

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TBC

Inlägg av Tryggve » tis 20 jan 2015, 15:12

En rätt intressant artikel om tuberkolosbakteriens historia.

http://www.nature.com/news/tuberculosis ... ry-1.16733
Tuberculosis genomes track human history

A pernicious family of TB strains emerged in Asia more than 6,000 years ago.

From the dawn of agriculture to the fall of the Soviet Union, major events in human history have left marks in the DNA of the bacterium that causes tuberculosis (TB). A study of nearly 5,000 samples of Mycobacterium tuberculosis from around the world shows how a lineage of the bacterium that emerged thousands of years ago in Asia has since become a global killer that is widely resistant to antibiotic drugs1.

Alhough M. tuberculosis probably first emerged some 40,000 years ago in Africa2, the disease did not take hold until humans took to farming — with the consequent settling down — Thierry Wirth, an evolutionary geneticist at the National Museum of Natural History in Paris and lead author of the study.

The grouping together of people in settlements made it easier for the respiratory pathogen to spread from person to person, says Wirth. A previous analysis by his team had shown that the common ancestor of all the M. bacterium strains circulating today began spreading around 10,000 years ago in the ancient Fertile Crescent2, a region stretching from Mesopotamia to the Nile Delta that was a cradle of agriculture — enabling lots of people to live in close proximity. “It’s basically a dream setting for a bug like TB,” says Wirth.

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möjlig tillämpning av teknik

Inlägg av Tryggve » fre 06 feb 2015, 13:28

Rätt intressant text om hur man möjligen kan utnyttja en upptäckt praktiskt. Man har letat efter proteiner som fungerar som receptorer för hormonet ABA, som signalerar till växter att stänga sina klyvöppningar. Därmed så minskar vattenavgången via klyvöppningarna.

Man har hittat ett specifikt ämne som binder starkt till ABA-receptorn. Detta ämne skulle kunna användas tillsammans med designade växter för att förbereda gröda för torka.

http://www.nature.com/news/protein-twea ... ce-1.16850
Protein tweak boosts plants' drought tolerance

Creative technique is a welcome step in the face of warming climates and water shortages.


An innovative 'on-off' switch added to a plant protein may one day allow farmers to prep crops for drought by spraying them with a commonly used agricultural compound.

The technique, reported on 4 February in Nature1, works by closing tiny pores — called stomata — in leaves that let in carbon dioxide, a key ingredient in photosynthesis, but lose water in the process.

“It’s fine to lose that water when there’s lots of water around,” says Sean Cutler, a plant biologist at the University of California, Riverside, and lead author of the study. “But when it becomes limiting, a plant needs to stop growing to conserve water.”

Breeding programmes have historically focused on achieving high yields rather than managing plants' water use, but the looming threats of water shortages and climate change are pushing researchers to think more about crops' ability to tolerate water shortages.

One way that plants respond to limited water is to boost levels of a hormone called abscisic acid (ABA). That hormone, in turn, reduces water loss by closing stomata.


Protein problem


Researchers searched for decades to find the proteins that sense ABA and trigger those responses. In 2009, Cutler’s group and others succeeded2, 3.

Cutler's team then began to explore how to put the discovery to practical use. The researchers mapped where ABA binds to one such protein receptor, and created a library containing every possible mutation at that site. They then tested their mutant receptors against a host of chemicals used in agriculture.

One, a fungicide called mandipropamid, was particularly potent at binding to the ABA receptor and causing it to change shape, as ABA itself would. Expressing the engineered receptor in a model plant, Arabidopsis thaliana, and in tomatoes yielded plants that, when sprayed with mandipropamid, were better able to survive water deprivation.

Even so, it is unclear how the approach will fare in agricultural crops in the field, says Cutler. Syngenta, a large agricultural company headquartered in Basel, Switzerland, has licensed patents on the work and is evaluating the technology, he says.

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Tarmmikrober i Amazonas

Inlägg av Tryggve » tis 21 apr 2015, 14:45

I senaste Nature News så presenterades en studie av mikrobdiversiteten hos en grupp indianer i den Venezuelanska delen av Amazonas, Yanomami. Här fanns tydligen den mest diversifierade mikrobfloran som man har hittat. Det mest överraskande är dock att man även har hittar gener för antibiotikaresistens här, vilket man anser märkligt eftersom människorna här inte har utsatts för moderna mediciner. Då är det kanske naturligt förekommande antibiotikum som har orsakat detta.
Vad det visar är väl att man fortfarande har mycket att lära sig om detta. :-)

http://www.nature.com/news/bacteria-bon ... ge-1.17348
Bacteria bonanza found in remote Amazon village

Genes for antibiotic resistance among those found in most-diverse human microbiome.

An isolated American Indian group in the Venezuelan Amazon hosts the most-diverse constellation of microbes ever discovered in humans, researchers reported on 17 April in Science Advances1. Surprisingly, the group's microbiome includes bacteria with genes that confer antibiotic resistance — even though its members, part of the Yanomami tribe, are not thought to have been exposed to the drugs.

“We knew that the microbes living on Yanomami would probably be more diverse, but we were surprised by the extent,” says Maria Gloria Dominguez-Bello, a microbial ecologist at New York University and an author of the paper.

The work adds to a growing body of research on the microbiome. Studies have suggested, for instance, that the microscopic communities that occupy the human body could be a new source of drugs2. And comparing the composition of different groups' microbiomes has given researchers clues about how humans lived and migrated long ago3.

Blast from the past


But scientists still do not understand all the factors that determine the make-up of a person's microbiome. “We do know that food, environment and chemicals play the big roles,” says Sarkis Mazmanian, a microbiologist at the California Institute of Technology in Pasadena. The wide adoption of antibiotics, rigorous hygiene and processed diets is thought to have have cut down the genetic diversity of microbiomes in the developed world.

This makes the microbiomes of individual Yanomami particularly interesting, Dominguez-Bello says. The researchers took oral, faecal and skin samples from 34 people in a small Yanomami community that was unknown to the Western world until 2008, when it was spotted by helicopter. A medical team made contact in 2009, but the group remains relatively isolated. (Mindful of this, only one of the study's authors interacted with the villagers to collect the microbe samples.)

When researchers analysed the microbial DNA in those samples, they found that the average Yanomami's microbiota had twice as many genes as that of the average US person. More surprisingly, the Yanomami microbiome was even more diverse than those reported for other indigenous groups in South America and in Africa4.

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Mikrobskepcisism, eller vad man ska säga.

Inlägg av Tryggve » tis 21 apr 2015, 14:50

Det fanns även en länk till den när artiklen från 2014 där författaren menar att det behövs en dos skepsis i hur man kopplar mikrobiomets roll till olika sjukdomar som t ex cancer och diabetes. Helt enkelt att det inte övertolkas och blåses upp.

http://www.nature.com/news/microbiology ... sm-1.15730
Microbiology: Microbiome science needs a healthy dose of scepticism

To guard against hype, those interpreting research on the body's microscopic communities should ask five questions, says William P. Hanage.

Explorations of how the microscopic communities that inhabit the human body might contribute to health or disease have moved from obscure to ubiquitous. Over the past five years, studies have linked our microbial settlers to conditions as diverse as autism, cancer and diabetes.

This excitement has infected the public imagination. 'We Are Our Bacteria', proclaimed one headline in The New York Times. Some scientists have asserted that antibiotics are causing a great 'extinction' of the microbiome, with dire consequences for human health1. Companies offer personalized analysis of the microbial content of faecal samples, promising consumers enlightening information. Separate analyses from the same person can, however, vary considerably, even from the same stool sample. Faecal transplants have been proposed — some more sensible than others — for conditions ranging from diabetes to Alzheimer's disease. With how-to instructions proliferating online, desperate patients must be warned not to attempt these risky procedures on themselves.

Microbiomics risks being drowned in a tsunami of its own hype. Jonathan Eisen, a microbiologist and blogger at the University of California, Davis, bestows awards for “overselling the microbiome”; he finds no shortage of worthy candidates.

Previous 'omics' fields have faltered after murky work slowed progress2. Technological advances that allowed researchers to catalogue proteins, metabolites, genetic variants and gene activity led to a spate of associations between molecular states and health conditions. But painstaking further work dampened early excitement. Most initial connections were found to be spurious or, at best, more complicated than originally believed.

The history of science is replete with examples of exciting new fields that promised a gold rush of medicines and health insights but required scepticism and years of slogging to deliver even partially. As such, the criteria for robust microbiome science are instructive for all researchers. As excitement over the microbiome has filtered beyond academic circles, the potential mischief wrought by misunderstanding encompasses journalists, funding bodies and the public.

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Experimentell behandling mot MS, med ett problem

Inlägg av Tryggve » ons 22 apr 2015, 13:35

Här fanns en artikel om en eperimentell behandling mot MS. En behadling som är tänkt att stimulera återväxt av det myelinsikt som skyddar neuroner, och är det som skadas vid MS.
Problemet är att man inte har en metod för att mäta återväxt av myelinskikt ännu.

Det finns också andra lovande kandidater för behandling av MS, bland annat ett par mediciner som används för att behandla hudsjukdomar.

(samtidigt så nämner artikeln också att en tidigt test inte visade att det aktuella preparatet var bättre än placebo i att förbättra synen på en grupp patienter som fått synnedsättningar p g a MS, däremot så ökade det signalhastigheten i synnerven).

http://www.nature.com/news/drug-that-bo ... is-1.17367
Drug that boosts nerve signals offers hope for multiple sclerosis

Trialled antibody treatment thought to work by renewing the protective coating of neurons.

An experimental antibody drug aimed at protecting nerves from the ravages of multiple sclerosis offers hope for a new way to combat the neurological disease — if researchers can definitively show that it works.

The antibody, anti-LINGO-1, is intended to stimulate regrowth of the myelin sheath, the fatty protective covering on nerve cells that is damaged by multiple sclerosis. Its developer, Biogen of Cambridge, Massachusetts, will present results from a small clinical trial at an American Academy of Neurology meeting this week in Washington DC. If the initial promising results from the trial are confirmed, it will be the first such myelin-regeneration therapy. Other researchers are racing to find more targets and compounds that act similarly.

Once we get a positive result, the field will move very quickly,” says Jack Antel, a neurologist at McGill University in Montreal, Canada. But that excitement is tempered by practical hurdles: there is as yet no proven way to measure remyelination of nerve cells in living humans.

Myelin sheaths insulate and support axons, the fibres that transmit signals between nerve cells. In multiple sclerosis, immune attack destroys these sheaths. Stripped of this protective coating, the axons gradually wither away, causing the numbness and muscle spasms that are characteristic of the disease. The 12 drugs approved in the United States to treat multiple sclerosis slow this immune attack — although sometimes with dangerous side effects. But none stops it, says Bruce Trapp, a neuroscientist at the Cleveland Clinic in Ohio.

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Forskare anklagade för att ha orsakat träddöd

Inlägg av Tryggve » tis 02 jun 2015, 14:09

I Italien så har man sedan en tid problem med en bakterie som infekterar bland annat olivträd. Det pågår forskning kring denna bakterie och hur den ska bekämpas. Nu har forskare vid institut i Puglia blivit anklagade för att ha orsakat dessa angrepp (genom att ha tagit dit bakterierna för en kurs), och polisen har beslagtagit datorer och dokument.

Lite grann får man intrycket att det är lokala odlade och aktivister som inte gillar de restriktioner och åtgärder som har vidtagits, vilket också diskuteras i artikeln.

Skulle forskarna ha släppt loss dessa bakterier så torde det vara rätt lätt att bevisa genom sekvensering av genomet. De menar själva att det rör sig om olika stammar, och att anklagelserna är befängda. De menar att stammen som har hittas härstammar från Costa Rica.

http://www.nature.com/news/italian-scie ... hs-1.17651
Italian scientists vilified in wake of olive-tree deaths

Police investigate researchers' role in devastating bacterial epidemic.

They did not expect to be hailed as heroes, say the scientists tasked with researching a deadly pathogen that is ravaging olive groves in Puglia, southern Italy. But they certainly did not predict that they would end up feeling like villains.

In the past year, plant scientists at various institutes in Bari, the capital of the Puglia region, have seen their work and their motivations criticized by local campaigners. Most recently, they have been subject to a police investigation about whether they are responsible for the introduction of the bacterium, Xylella fastidiosa, into Puglia, or for allowing its subsequent spread.

Police have called in several researchers involved in Xylella research for questioning and confiscated computers and documents from scientific institutes.

We’d just like to be left to do our work without this suspicion and this stress,” says Donato Boscia, head of the Bari unit of the CNR Institute for Sustainable Plant Protection (IPSP), whom police questioned in April.

“The scientists in Puglia working on the Xylella outbreak have been working non-stop for two years,” adds Rodrigo Almeida, a Xylella expert at the University of California, Berkeley. “Their reward has been to get attacked constantly — I just can’t imagine how this would feel.”

Xylella is endemic in parts of the Americas, including Costa Rica, Brazil and California, but was not previously found in Europe. That changed in October 2013, when scientists at the IPSP and the University of Bari identified1 the bacterium as the cause of an unusual disease outbreak in olive trees. The outbreak immediately became subject to European Union (EU) regulations to limit its spread, and regional scientists began a systematic effort to understand the disease and contain it: the scientists went on to show that the bacterium was being carried by the spittlebug insect2.

Ornamental plants

From the start, farmers and environmentalists in Italy objected to containment measures, which involved uprooting trees and spraying the groves with pesticides. But trouble for the Puglian scientists began in April 2014, when individuals told police that they suspected that the epidemic was caused by bacteria that scientists had brought in from California for a European training course on Xylella at the Mediterranean Agronomic Institute of Bari (IAMB) in 2010.

Scientists say that this suggestion is ludicrous because the Puglia strain is different from the strains used at the workshop; the widely accepted theory is that the infection was imported with ornamental plants from Costa Rica, where the endemic Xylella strain matches the Puglia strain.

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