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Re: Nature News

Inläggav Tryggve » tor 02 jun 2016, 16:30

manifesto skrev:
Nature skrev:CHALLENGES IN IRREPRODUCIBLE RESEARCH
Tryggve eller någon annan med access får gärna summera artikeln.

När jag klickar runt så tycker jag att det verkar gå att komma åt artiklarna även utan att sitta vid en universitetsdator.
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Re: Nature News

Inläggav manifesto » tor 02 jun 2016, 16:35

Tryggve skrev:
manifesto skrev:
Nature skrev:CHALLENGES IN IRREPRODUCIBLE RESEARCH
Tryggve eller någon annan med access får gärna summera artikeln.

När jag klickar runt så tycker jag att det verkar gå att komma åt artiklarna även utan att sitta vid en universitetsdator.
Såg det nu, bra.
War is peace.
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Re: Nature News

Inläggav Tryggve » tor 02 jun 2016, 23:43

I alla hast: detta är ett föreslaget projekt, "efterföljaren" till HUGO. Bygga ett mänskligt genom. Från grunden.

Att detta tas emot lite blandat är inte så konstigt. Frågan är som påpekas i artikeln om detta inte kommer att ske ändå till slut, men inte så centraliserat.

http://www.nature.com/news/plan-to-synt ... se-1.20028
Plan to synthesize human genome elicits mixed response

Some admire project's ambition; others say it hasn't justified its aims.

Proposals for a large public-private initiative to synthesize an entire human genome from scratch – an effort that could take a decade and require billions of dollars for technological development – were formally unveiled today, a month after they were first aired at a secretive meeting.

Proponents of the effort, named ‘Human Genome Project-write’ (HGP-write), wrote in the journal Science that $100 million from a range of funding sources would help get their vision off the ground1. The team is led by synthetic biologist Jef Boeke, at New York University, genome scientist George Church, at Harvard Medical School in Boston, and Andrew Hessel, a futurist at the commercial design studio Autodesk Research in San Rafael, California.

But the idea – which primarily aims to develop technologies that reduce the cost of DNA synthesis – was not met with universal excitement among researchers.

o some, the proposal is praiseworthy for its ambition and sheer chutzpah: at present, only tiny bacterial genomes and portions of the baker’s yeast genome have been made from scratch. But other researchers told Nature that they felt HGP-write represented a needless centralization of work that is already taking place in companies working to lower the price of synthesizing strings of DNA. Some of HGP-write’s proponents have financial stakes in those firms, which include Gen9 in Cambridge, Massachusetts.

“My first thought was ‘so what’,” says Martin Fussenegger, a synthetic biologist at the Swiss Federal Institute of Technology in Zurich.“I personally think this will happen naturally. It’s just a matter of price at the end.”
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Prosit!

Inläggav Tryggve » fre 03 jun 2016, 13:50

Den här artikeln (med vidhängande video) var rätt intressant. Matematikern Lydia Bourouiba studerar nysningar. Framför allt så verkar det vara relativt lätt att få en försöksperson att nysa.... :-)
Nose tickeling....

Lång artikel som jag rekommenderar att läsa.

http://www.nature.com/news/the-snot-spa ... ad-1.19996
The snot-spattered experiments that show how far sneezes really spread

Mathematician Lydia Bourouiba uses high-speed video to break down the anatomy of sneezes and coughs — and to understand infectious disease.

So, how do you get your research subjects to sneeze on cue?

“That's a question I get a lot,” says Lydia Bourouiba with an easy smile. The solution turns out to be surprisingly simple: just take a small, rod-shaped device, use it to tickle a subject's nostril for a few seconds, and — achoo!

For Bourouiba, a mathematician and fluid dynamicist, that sneeze is the pay-off. She and her team at the Massachusetts Institute of Technology (MIT) in Cambridge record the explosive aftermath in gross detail using one or sometimes two cameras running at thousands of frames per second. Played back in slow motion, the videos reveal a violent explosion of saliva and mucus spewing out of the mouth in sheets that break up into droplets, all suspended in a turbulent cloud.

The videos that Bourouiba has recorded in this way allow her to measure everything from the diameter of the droplets to their speed — data that help her to learn more about how these particles carry viruses and other pathogens to their next host. She has shown that sneeze and cough particles can travel the length of most rooms and can even move upwards into ventilation shafts — suggesting that microbes in the droplets could potentially spread farther and over longer periods of time than current theories suggest.

Ultimately, says Bourouiba, her goal with this work is to ground epidemiology and public health in physics and mathematics. When trying to keep diseases from running rampant, she says, “we want to be giving recommendations that are based on science that has been tested in the lab”. In practical terms, such insights could lead to maps showing the contamination risks in the vicinity of infected people, protective equipment optimized to shield hospital workers from specific kinds of germs, and better predictions of how diseases move through a population.
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fågelfjädrar i bärnsten

Inläggav Tryggve » ons 29 jun 2016, 11:49

Bärnsten som innehåller fragment av fågelvingar. Ålder: 99 miljoner år, uppskattat. Det verkar vara ett fullständigt unikt fynd. Verkar innehålla ben, fjädrar och skinn.

Fjädrarna verkar vara rätt lika de som finns på dagens fåglar. Färgmönster verkar också vara bevarat, om än fläckvis.

http://www.nature.com/news/bird-wings-t ... rs-1.20162

Bird wings trapped in amber are a fossil first from the age of dinosaurs


Preserved feathers and tissue provide a picture of hatchlings from the Cretaceous.

Two tiny wings locked in amber 99 million years ago suggest that in the middle of the Cretaceous period — when dinosaurs still walked the planet — bird feathers already looked a lot like they do today.

A team of researchers led by Lida Xing, a palaeontologist at the China University of Geosciences in Beijing, recovered a first for the time period: a few cubic centimetres of amber from northeastern Myanmar that contained the partial remains of two bird wings. The specimens include bone, feathers and skin, according to a study published on 28 June in Nature Communications1.

Prior evidence of bird plumage from the Cretaceous, which stretched from 145 million to 66 million years ago, came from 2D impressions left in sedimentary rocks and feathers that had been preserved in amber but that gave no skeletal clues to their species of origin.

“For the first time, we’re seeing the feathers associated with the skeletal materials,” says co-author Ryan McKellar, who studies fossils in amber as curator of invertebrate palaeontology at the Royal Saskatchewan Museum in Regina, Canada.
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Re: Nature News

Inläggav Tryggve » fre 01 jul 2016, 11:04

Ett Zikavaccin som testades på möss gav ett gott skydd redan efter en dos. Spännande.

http://www.nature.com/nature/journal/va ... 18952.html
Zika virus (ZIKV) is a flavivirus that is responsible for an unprecedented current epidemic in Brazil and the Americas1,2. ZIKV has been causally associated with fetal microcephaly, intrauterine growth restriction, and other birth defects in both humans3-8 and mice9-11. The rapid development of a safe and effective ZIKV vaccine is a global health priority1,2, but very little is currently known about ZIKV immunology and mechanisms of immune protection. Here we show that a single immunization of a plasmid DNA vaccine or a purified inactivated virus vaccine provides complete protection in susceptible mice against challenge with a ZIKV outbreak strain from northeast Brazil. This ZIKV strain has recently been shown to cross the placenta and to induce fetal microcephaly and other congenital malformations in mice11. We produced DNA vaccines expressing full-length ZIKV pre-membrane and envelope (prM-Env) as well as a series of deletion mutants. The full-length prM-Env DNA vaccine, but not the deletion mutants, afforded complete protection against ZIKV as measured by absence of detectable viremia following challenge, and protective efficacy correlated with Env-specific antibody titers. Adoptive transfer of purified IgG from vaccinated mice conferred passive protection, and CD4 and CD8 T lymphocyte depletion in vaccinated mice did not abrogate protective efficacy. These data demonstrate that protection against ZIKV challenge can be achieved by single-shot subunit and inactivated virus vaccines in mice and that Env-specific antibody titers represent key immunologic correlates of protection. Our findings suggest that the development of a ZIKV vaccine for humans will likely be readily achievable.
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Transformation av växter

Inläggav Tryggve » tor 03 nov 2016, 14:03

Oj, dej här tråden har legat i träda ett tag. Det måste åtgärdas. Då kanske det passar med ett inlägg om verktyg för växtförädling. Det finns gott om idéer (så brukar det vara), men problemet är att det är rent praktiskt svårt att genomföra dem. Vilket man också känner igen.... :-)

Det stora problemet idag är att det är svårt att effektivt få in dessa modifierade gener i växterna.

Plant-genome hackers seek better ways to produce customized crops

As gene editing opens doors, plant researchers are hamstrung by the need for better ways to slip their molecular tools into cells.

When crop engineers from around the world gathered in London in late October, their research goals were ambitious: to make rice that uses water more efficiently, cereals that need less fertilizer and uberproductive cassava powered by turbocharged photosynthesis.

The 150 attendees of the Crop Engineering Consortium Workshop were awash with ideas and brimming with molecular gadgets. Thanks to advances in synthetic biology and automation, several projects boasted more than 1,000 engineered genes and other molecular tools, ready to test in a researcher’s crop of choice. But that is where they often hit a wall. Outdated methods for generating plants with customized genomes — a process called transformation — are cumbersome, unreliable and time-consuming.

Asked what hurdles remain for the field, plant developmental biologist Giles Oldroyd of the John Innes Centre in Norwich, UK, had a ready answer: “The big thing would be to improve plant transformation,” he said.

“What we’re all facing is this delivery problem,” says Dan Voytas, a plant biologist at the University of Minnesota in Saint Paul. “We have powerful reagents, but how do you get them into the cells?”

At issue is the decades-old problem that it is difficult to modify plant genomes and then regenerate a whole plant from a few transformed cells. Genome-editing techniques such as CRISPR–Cas9 hold out the promise of sophisticated crop engineering that would once have been unthinkable — making it all the more frustrating when researchers run up against an old roadblock.


http://www.nature.com/news/plant-genome ... ps-1.20913
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Re: Nature News

Inläggav Tryggve » sön 06 nov 2016, 00:01

En annorlunda, men tidigare använd, metod för bekämpning av smittor som sprids av myggor används. Myggor infekterade men bakteriestammen Wolbachtia har släppts ut på några ställen i Brasilien. Bakterien förhindrar att myggorna infekteras och sprider sjukdomar som Zika och denguefeber.

I naturen så smittas inte de myggor som sprider dessa sjukdomar av denna bakterie. Det är dock inte festaställt huruvida spridning av myggor med denna infektion faktiskt leder till minskat antal sjukdomsfall hos människor, men det är det som man vill undersöka med dessa försök.

http://www.nature.com/news/rio-fights-z ... es-1.20878
Rio fights Zika with biggest release yet of bacteria-infected mosquitoes

Wolbachia-infected mosquitoes will be widely deployed in two South American cities to combat viral infections.

Two South American metropolises are enlisting bacteria-infected mosquitoes to fight Zika, in the world’s biggest test yet of an unconventional yet promising approach to quell mosquito-borne diseases.

Mosquitoes that carry Wolbachia bacteria — which hinder the insects' ability to transmit Zika, dengue and other viruses — will be widely released in Rio de Janeiro, Brazil, and Medellín, Colombia, over the next two years, scientists announced on 26 October. The deployments will reach around 2.5 million people in each city.

“This really has the potential to be a game changer in terms of vector control — the biggest thing since DDT,” says Philip McCall, a medical entomologist who studies mosquito control at the Liverpool School of Tropical Medicine, UK.
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Re: Nature News

Inläggav Tryggve » fre 11 nov 2016, 11:49

Nature har en artikel om hur forskarvärlden i USA reagerar på valresultatet. Många är rädda för att anslagen ska minskas rejält. En del utländska forskare verksamma i USA överväger att lämna landet.

http://www.nature.com/news/how-scientis ... ts-1.20965
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Glada råttor

Inläggav Tryggve » fre 11 nov 2016, 11:55

Och man har även en artikel om kittliga råttor. :-)



Playful rats reveal brain region that drives ticklishness

Experiments also reveal that rats are ticklish in similar places to humans

Like people, rats are ticklish. Now, by implanting electrodes in the brains of these laboratory workhorses, researchers have identified the brain region that seems to drive the trait — an insight that could illuminate the origins of ticklishness in people.

The work, published in the 11 November issue of Science1, also reveals that rats' susceptibility to tickling is affected by mood, rather like in people. Separate from the study, the researchers say they have found that rats are ticklish in similar places to people — on their tummies and back paws, but not on their backs or on their front paws.

In the late 1990s, neuroscientist Jaak Panksepp, who was then of the Bowling Green State University in Ohio, discovered that rats make ultrasonic ‘chirps’ when being tickled and while playing2, which may be similar to human laughter.

Several other animals are ticklish, including dogs and chimps, but rats seem particularly so, and are easy to handle in the lab. So neuroscientists Michael Brecht and Shimpei Ishiyama of the Bernstein Center for Computational Neuroscience in Berlin decided to use the animals to probe what is going on in the brain.



http://www.nature.com/news/playful-rats ... ss-1.20973
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Re: Nature News

Inläggav Tryggve » ons 28 dec 2016, 14:28

Som molekylärbiolog så tror jag väl inte att det vore realistiskt att kunna stoppa denna teknik ens om det vore önskvärt. Nu blev det nej till ett stopp på ett FN-möte angående biodiversitet. Cynikern i mig vill väl även hävda att det förmodligen finns bra mycket större hot mot biodiversitet än just denna teknik, så ska den förbjudas så borde man väl förbjuda mycket annat.

Samtidigt så är det förstås önskvärt att få fram ett regelverk för arbetet med "gene drives" så fort man kan.


Gene drive’ moratorium shot down at UN biodiversity meeting

Freeze on genetic technology would have been a disaster, say scientists, but activists plan to renew the fight.

World governments at a United Nations biodiversity meeting this week rejected calls for a global moratorium on gene drives, a technology that can rapidly spread modified genes through populations and could be used to engineer entire species. But environmental activists’ appeals for a freeze on gene-drive field trials, and on some lab research, are likely to resurface in the future.

“I’m very relieved,” says Andrea Crisanti, a molecular parasitologist at Imperial College London, who is part of an effort that seeks to use gene drives to control malaria. He and others worry that a moratorium would make research on the technology more difficult, scare away funders and prevent field tests. “It would have been a disaster for developing the technology,” he says. But the calls for a ban, discussed at the meeting of the UN Convention on Biodiversity (CBD) in Cancún, Mexico, on 4–17 December, are not going to go away, he says. “Those who are opposed to this technology will be more organized next time.”

The idea of a moratorium found support among some countries. But a final agreement released on 16 December merely urged caution in field-testing the products of synthetic biology, including gene drives, while supporting better risk-assessment of the products’ potential effects.

“It’s a way of governments saying ‘we need to know more about these technologies before making these decisions. At the same time, we are worried they may have impacts on biological diversity,’” says Calestous Juma, a former executive secretary of the CBD and an expert on science and technology policy at Harvard University in Cambridge, Massachusetts."




http://www.nature.com/news/gene-drive-m ... ng-1.21216
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Re: Nature News

Inläggav Tryggve » lör 12 aug 2017, 20:41

Denna nyhet har varit rätt spridd på en del ställen, men n jag vet inte hur mycket det har spridits.
Nå, en forskargrupp har använt Crispr-Cas9 teknik för att ta bort patogena mutationer i mänskliga embryon
Främst så har man arbetat med en mutation som betecknas MYBPC3, vilket ger hjärtfel.

http://www.nature.com/nature/journal/va ... lback=true
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Re: Nature News

Inläggav Tryggve » lör 19 aug 2017, 09:10

Dagens medicin skriver om dessa resultat.

https://www.dagensmedicin.se/artiklar/2 ... a-embryon/

Forskargruppen ville försöka korrigera en ärftlig mutation som ger hjärtsjukdomen hypertrofisk kardiomyopati. Den drabbar ungefär en av 500 personer och karaktäriseras av att hjärtats vänstra kammare är förstorad, vilket bland annat kan orsaka hjärtsvikt. Encelliga embryon producerades på laborativ väg genom att befrukta en äggcell från en frisk kvinna med en spermie från en man som bar på en enkel uppsättning av mutationen för hjärtsjukdomen.

I tidigare publikationer av crispr/cas-9 på mänskliga embryon har cas-9, som klipper i arvsmassan, injicerats någon dag efter att äggcellen befruktats. Men nu valde i stället forskarna att injicera cas-9 tillsammans med spermien. Resultatet blev att majoriteten av embryon, 42 av totalt 58 stycken, inte längre bar på någon mutation för hjärtsjukdomen. Det är ett bra resultat, menar Fredrik Lanner.

Endast ett embryo i studien hade mosaicism, rapporterar forskarna. De skriver också att få embryon drabbades av nya mutationer, vilket kan hända när crispr/cas-9 används.

– Cellen verkar reparera arvsmassan mer precist om cas-9 injiceras i äggcellen tillsammans med spermien. Och det är precis vad vi vill ska ske, säger Fredrik Lanner.
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Re: Nature News

Inläggav Tryggve » tis 14 nov 2017, 17:05

För några år sedan så startades ett projekt, The Reproducibillity Projet, där målet var att reproducera resultat från 50 artiklar (sedan reducerat till 29) kring cancerforskning som har publicerat i tidskrifter som Nature, Science mm. Bakgrunden här.

The Reproducibility Project: Cancer Biology launched in 2013 as an ambitious effort to scrutinize key findings in 50 cancer papers published in Nature, Science, Cell and other high-impact journals. It aims to determine what fraction of influential cancer biology studies are probably sound — a pressing question for the field. In 2012, researchers at the biotechnology firm Amgen in Thousand Oaks, California, announced that they had failed to replicate 47 of 53 landmark cancer papers2. That was widely reported, but Amgen has not identified the studies involved.


http://www.nature.com/news/cancer-repro ... ts-1.21304

De första resultaten kom i januari 2017, då fem artiklar publicerades. Resultaten kan väl förmodligen tolkas på olika sätt, men är ändå rätt nedslående.

But seven of the replication studies are now complete, and eLife is publishing five fully analysed efforts on 19 January.

These five paint a muddy picture (see ‘Muddy waters’). Although the attempt to replicate Ruoslahti’s results failed3, two of the other attempts4, 5 “substantially reproduced” research findings — although not all experiments met thresholds of statistical significance, says Sean Morrison, a senior editor at eLife. The remaining two6, 7 yielded “uninterpretable results”, he says: because of problems with these efforts, no clear comparison can be made with the original work.
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Re: Nature News

Inläggav Tryggve » tor 23 nov 2017, 13:53

En ledare i Nature om sexuella trakasserier inom universitetsvärlden. Tystnadskultur. Som inom så många andra områden. :x
Poängen att man som ung forskare är i en beroendeställning till sin handledare är ju också helt sann, och är också en parallell till Hollywood på ett sätt.

http://www.nature.com/news/university-s ... 1508_RHBox

In this regard, Hollywood and academia have troubling similarities. Both rely too much on mentor–protégé relationships, with few checks on individual power. In academia, there is scant protection for lab members. Graduate students and postdocs are viewed more as part of their supervisor's lab than part of the university community. By contrast, institutions have many incentives to protect their powerful, permanent and often lucrative faculty members.

Administrators can reasonably assume that, if they ignore claims for long enough, they will never be held to account. People like me graduate or leave without a degree, the statute of limitations passes, and the harassers get promoted. Sometimes universities don't interview suggested witnesses or collect other evidence; in my view, this allows them to claim that they investigated complaints but found insufficient reasons for further action. (The University of Rochester has said it took the allegations seriously and that its investigation was thorough.)


Stora namn kan ju komma undan med mycket. James Watson är ju ett exempel.
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