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Re: Nature News

Postat: tis 18 mar 2014, 19:11
av Tryggve
Hexmaster skrev:Intressant. Har inte tänkt på att fördelarna med GMO kan minska över tid men det är ju likadant som med andra motmedel.
“That’s two of the three toxins on the market now,” says Gassmann. “It’s a substantial part of the available technology.”
Jo precis. Det handlar ju om selektionstryck även här. Att organismer utvecklar resistens mot vanliga bekämpningsmedel är ju vanligt, så det är ju på det sättet inte förvånande att samma sak kan ske här.

Vete på efterkälken

Postat: tor 27 mar 2014, 14:18
av Tryggve
Förädlingen av vete har halkat på efterkälken jämfört med de resurser som läggs t ex på majs. ... E-20140327
Wheat lag

Growth in yields of the cereal must double if the Green Revolution is to be put back on track.

Wheat is widely considered to be the world’s most important crop, and Norman Borlaug knew a thing or two about how to grow it. The US agronomist developed varieties that could better resist disease and gave higher yields. In doing so, he saved an estimated one billion people from starvation.[/b]

This week marks a century since Borlaug’s birth, so what better time to consider why millions still go hungry, and to ponder how the next Green Revolution can be kick-started? At a meeting in Mexico this week, organized by the International Maize and Wheat Improvement Center (CIMMYT) in collaboration with the Association for Agricultural Research and Experimentation of the State of Sonora, researchers will look again at the prospects for wheat. Although wheat consumption is growing, the investment needed to build on Borlaug’s legacy is scarce.

Wheat provides 20% of the dietary energy for the world’s population. Yet growth in yields has stagnated at around 0.9% per year over the past decade ­— by contrast, maize (corn) yields grow by almost double that at approximately 1.6% per year. To meet future demand for food, researchers say that wheat yields must grow by 1.7% each year. That will require investment. The total global spend on wheat breeding and research, around US$500 million per year, is currently one-quarter of that spent to improve maize.

The discrepancy arises because seed companies can make higher profits from maize than from wheat. Maize is a hybrid crop that produces seeds with poor yields, so there is little incentive for farmers to keep and replant them. To get the best results, they must buy new maize seeds each year. Seed producers get no such annual income from wheat because farmers can reap and replant seeds from several successive harvests without losing much yield.

Existing solutions to this are as much economic as agronomic. One strategy is for plant breeders to collect royalties from farmers who save seeds — as is done in countries such as Australia and the United Kingdom. Although this approach is reasonable for farmers who harvest substantial profits, it is less applicable to subsistence farmers in the developing world; for them, science might provide better solutions.

An international research effort to boost wheat yields by 50% by 2035 will be officially launched at this week’s meeting. The International Wheat Yield Partnership — a consortium of research institutions including CIMMYT and the United Kingdom’s Biotechnology and Biological Sciences Research Council — is a long-term project that aims to raise US$100 million in the next five years.
Det är tydligen 100 år sedan Norman Borlaug föddes också.


Postat: tor 03 apr 2014, 21:20
av Tryggve
Denna artikel om epigenetik var rätt intressant. Lovande resultat, men också en hel del kritik och problem påpekas.
¨Epigenomics starts to make its mark

Analysis of chemical patterns on DNA shows promise for explaining disease, but few results have yet been replicated.

Obesity may be written not only in the genes, but also on top of them. One of the largest studies so far to probe the human epigenome — the collective name for the patterns of chemical groups that adorn DNA sequences and influence their activity — has found some tags that are linked to differences in body mass index (BMI).

Chemical alterations in a gene thought to be involved in metabolism were identified in the blood and fat cells of more than 2,500 people1, scientists reported last month. The work, led by Nilesh Samani at the University of Leicester, UK, is part of an emerging line of research that is probing disease through epigenome-wide association studies (EWAS). Those in the field hope that because many epigenetic changes are influenced by the environment, such studies will reveal mechanisms of disease that have remained elusive. However, many scientists remain sceptical.

EWAS take their inspiration from genome-wide association studies (GWAS), which compare genetic variations in ill and healthy people to identify variations associated with disease. EWAS do the same for the epigenome. They look at differences in the distribution of methyl groups at thousands of specific DNA nucleotides across the genome to identify arrangements that are common in a disease, or associated with variation in a trait.

Methylation — the addition of methyl groups — tends to suppress the activity of genes. It is important in development, when it helps to guide the differentiation of embryonic stem cells into specialized tissues by orchestrating the expression of genes. But it also occurs in response to environmental changes, and these gene modifications may be inherited. They may also contribute to conditions such as cancer and type 2 diabetes. ... E-20140403

Re: Nature News

Postat: fre 04 apr 2014, 07:16
av Hexmaster
Skulle en pubföreläsning om epigenetik vara något?

Re: Nature News

Postat: sön 06 apr 2014, 14:02
av Tryggve
Den här artikeln har ju nämnts i annan tråd. Det handlar om en spännande upptäckt som kan göra stor nytta vid cancerbehandling.
(kolla antalet författare... :-) )
Det som är roligt är ju att svenska forskare är med, Uppsala Universitet har en rätt bra pressrelease om det. ... a=&lang=sv ... 13181.html
(artikeln i sig ligger väl bakom en betalvägg).
MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool

Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bind in the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.

Anticancer treatments are dominated by targeting the genetic defects found in cancers, such as oncogenes (for example, imatinib for BCR-ABL mutated cancer1) or non-oncogenic genetic defects (for example, PARP inhibitors for BRCA1 and BRCA2 mutated cancer2, 3). Although a few cases show impressive results, these treatments have, in general, not replaced radiotherapy or chemotherapy. Targeting genetic defects in a personalized strategy is limited by the high degree of intra-tumour heterogeneity, adaptation of genetic networks and high somatic mutation rates in cancer4. Here, we reasoned that a de-personalized anticancer strategy, targeting the cancer phenotype using a synthetic-lethal approach, may tackle the problem of intra-tumour heterogeneity and be more widely applicable to a range of tumours.

Altered redox regulation is a general phenotype of many cancers and has a crucial role in cancer aetiology, progression and metastasis5. Dysfunctional redox regulation and an increased reactive oxygen species (ROS) tension can cause oxidative damage to DNA directly, or to free bases in the cellular and mitochondrial deoxynucleoside triphosphate (dNTP) pool6. Damage on double-stranded DNA has been the main therapeutic focus in spite of the fact that the free dNTP precursor pool is 190–13,000 times more susceptible to damage7. The MTH1 protein sanitizes the oxidized dNTP pool, for example, by converting 8-oxodGTP or 2-OH-dATP into 8-oxodGMP or 2-OH-dAMP, thus avoiding incorporation of these oxidized nucleotides into the DNA, which otherwise can result in mispairing, mutations and cell death8, 9, 10. Interestingly, overexpression of MTH1 suppresses the mutator phenotype in mismatch-repair-defective colorectal cancer cells11, indicating that the oxidized dNTP pool is a major source of damage causing mutations in cancer. Furthermore, overexpression of MTH1 reverses Ras-induced senescence by suppressing the overall level of DNA damage12, underscoring the importance of oxidized dNTPs in cancer. As altered redox status can be exploited for cancer treatments5, we reasoned that the normally non-essential MTH1 protein13 may be important for sanitizing cancer-associated damage in the dNTP pool and required for survival in cancer cells. Here, we wanted to evaluate whether MTH1 could be a general target for cancer treatment owing to non-oncogene addiction; that is, cancer phenotypic lethal.

Mer om MTH1

Postat: sön 06 apr 2014, 22:30
av Tryggve
Ytterligare en artikel har publicerats angående MTH1.

Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy ... 13194.html
Activated RAS GTPase signalling is a critical driver of oncogenic transformation and malignant disease. Cellular models of RAS-dependent cancers have been used to identify experimental small molecules, such as SCH51344, but their molecular mechanism of action remains generally unknown. Here, using a chemical proteomic approach, we identify the target of SCH51344 as the human mutT homologue MTH1 (also known as NUDT1), a nucleotide pool sanitizing enzyme. Loss-of-function of MTH1 impaired growth of KRAS tumour cells, whereas MTH1 overexpression mitigated sensitivity towards SCH51344. Searching for more drug-like inhibitors, we identified the kinase inhibitor crizotinib as a nanomolar suppressor of MTH1 activity. Surprisingly, the clinically used (R)-enantiomer of the drug was inactive, whereas the (S)-enantiomer selectively inhibited MTH1 catalytic activity. Enzymatic assays, chemical proteomic profiling, kinome-wide activity surveys and MTH1 co-crystal structures of both enantiomers provide a rationale for this remarkable stereospecificity. Disruption of nucleotide pool homeostasis via MTH1 inhibition by (S)-crizotinib induced an increase in DNA single-strand breaks, activated DNA repair in human colon carcinoma cells, and effectively suppressed tumour growth in animal models. Our results propose (S)-crizotinib as an attractive chemical entity for further pre-clinical evaluation, and small-molecule inhibitors of MTH1 in general as a promising novel class of anticancer agents.


Postat: ons 16 apr 2014, 15:21
av Tryggve
Detta kanske inte är så känt, men det har stormat en del kring ett par artiklar angående stamceller publicerat av Nature i januari.. Nu ska metoden granskas än mer ingående. ... od-1.15055

Japanese author of controversial papers denies wrongdoing and stands by results as testing of her protocol begins.

The lead author of two hotly debated stem-cell papers made a tearful plea for forgiveness last week after her employer found her guilty of misconduct. Haruko Obokata, a researcher at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan, struggled to answer questions about errors in the papers, which described how simple stressors such as acid or pressure could reprogram mature cells into an embryonic-like state. But that did not stop her from insisting that the reports were not fraudulent and that the phenomenon described in them is real.

Her comments have left observers wondering about the outcome of a controversy that has raged since the papers were published in Nature in January1, 2. Clarity on the claimed creation of STAP cells (for stimulus-triggered acquisition of pluripotency) now awaits three key events, all expected in the next few months. Stem-cell scientists hope that one of these — a replication attempt based on Obokata’s protocol, by Hitoshi Niwa, a co-author of the papers who also works at the CDB — will be conclusive.

“This looks like a rigorous protocol that hopefully will settle the question of whether pluripotent STAP cells can be generated or not,” says Rudolf Jaenisch, a stem-cell biologist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, who was shown Niwa’s protocol by Nature. (Nature’s news and comment team is editorially independent of its research editorial team.)

Problems with the papers, including accusations that Obokata had plagiarized passages of text and used duplicated images, arose soon after publication. Moreover, other groups said that they were unable to reproduce the results.

RIKEN decided to investigate, and on 1 April reported a number of uncomfortable findings (see Nature; 2014). Two problems were deemed misconduct: the re-use of an image that Obokata had included in her 2011 doctoral dissertation to describe different kinds of cells from those described in the STAP papers, and an image of an electrophoresis gel that had been spliced into another image, making it appear to be part of a different experiment.
Forskaren Haruko Obokata står på sig och menar att metoden är korrekt och att hon inte har fuskat.

Sund forskning

Postat: ons 16 apr 2014, 20:35
av Tryggve
In intressant ledare (jag antar att det är rätt beteckning) i Nature. Colin Macilwain menar att krav på "sound science" som ska användas vid relegeringar är något som låter bra, men att det finns en annan sida av myntet.

Hur mycket poäng han har vet jag inte riktigt för egen del, men jag tyckte att det var en intressant artikel. ... E-20140417
Beware of backroom deals in the name of 'science'

The term 'sound science' has become Orwellian double-speak for various forms of pro-business spin, says Colin Macilwain.

Scientific and environmental groups enjoyed a small victory in Washington DC earlier this year, when an insidious little item called the sound-science bill was removed from farm legislation signed into law by US President Barack Obama on 7 February.

The defeat of the bill was but a minor skirmish, however, in a broader, global war that rumbles on over how science should be used in regulating everything from smoking to pollution.

The term 'sound science' may sound innocuous — comforting, even. Don't be fooled. In policy circles, its use is now pretty-much confined to the determined band of brothers who make their livings trying to roll back government regulation, by fair means or foul.

Many of these people are neo-conservatives — members of the powerful right-wing cult whose founder, former Trotskyist Irving Kristol, adopted various tricks from the revolutionary politics of the far left. One of these was the casual misuse of the word 'sound' to denote colleagues or ideas as being ideologically reliable.

'Sound science' is thus science that big business knows it can trust. In its name, businesses that sell contentious products are working night-and-day to deflect rules and regulations by exploiting a schoolboy image of science to make their case.

And whatever the issue — nuclear power, pesticides, pharmaceuticals, alcohol, oil or coal — they take the basic game plan from the lessons learned by the tobacco industry over the past twenty years.

I don't think many people realize that shares in British American Tobacco (BAT), the world's second-largest tobacco company, have risen tenfold since the year 2000 — while the main UK stock index, the FTSE 100, has stood still. It has been party time for BAT shareholders, even though everyone knows that cigarette smoking kills thousands. Even as cigarettes are being pushed to the edges of social acceptability in the United States and parts of Europe, much larger and more lucrative markets keep opening up.

That is because the tobacco industry has learned to game the regulatory and trade system. Back in 1993, it hijacked the term sound science, when it set up The Advancement of Sound Science Coalition to question early evidence linking passive smoking to cancer. The coalition pioneered an effective approach that abuses science to hold back regulation for long enough for BAT and others to haul in extraordinary profits.

Glutenallergi i det antika Rom

Postat: ons 07 maj 2014, 21:57
av Tryggve
En glutenallergiker som levde för ca 2000 år sedan hade uppenbarligen mycket svårt.

Ancient bones show signs of struggle with coeliac disease

An affluent young woman with a probable gluten intolerance tried to manage it by altering her diet.

If going gluten-free seems hard now, try doing it in ancient Rome. A well-heeled young woman with coeliac disease tried to adapt her diet in an unsuccessful effort to cope with gluten sensitivity, studies of her remains suggest.

The woman’s remains were buried in a 2,000-year-old tomb at the Cosa archaeological site on the Tuscan coast in Italy. The ancient Roman city's economy depended on growing wheat and olives and was not particularly prosperous, yet archaeologists discovered gold and bronze jewellery entombed alongside the woman’s bones. They concluded that she was relatively wealthy and would have had access to plenty of food.

Yet the skeleton of the woman — who researchers estimate was 18–20 years old — bore signs of malnutrition and osteoporosis. Both can be complications of untreated coeliac disease, which is characterized by a severe allergic reaction to gluten in the intestinal lining. Many of the woman's bones were eroded at the tips, and she would have stood just 140 centimetres (4 feet, 7 inches) tall.

DNA analysis had previously shown that the woman carried two copies of an immune system gene variant that is associated with coeliac disease2. Although coeliac is a complex disease in which multiple environmental factors may play a role, the gene variant is found in nearly all patients in contemporary populations.

The combination of those genetic risk factors and malnutrition in someone likely to have good access to food make coeliac disease a reasonable diagnosis, says Gabriele Scorrano, a biological anthropologist at the University of Rome Tor Vergata, who led the latest study, published this month in American Journal of Physical Anthropology1. ... S-20140506

Smittkoppor i zombieforim?

Postat: ons 07 maj 2014, 22:04
av Tryggve
En på sätt och vis rätt skrämmande artikel om vad som kan gömma sig på inte så gamla kyrkogårdar. På en byggarbetsplats i New York fick byggjobbare fram vad de trodde var ett nyligen begravt mordoffer. Det visade sig vara ett mycket välbevarat lik från ca 1850-talet, med konstiga upphöjningar och ärr på kroppen... När man insåg att den mycket omsorgsfullt förseglade kistan kanske inte var avsedd att bevara liket, utan skydda mot smittspridning, så blev det lite mer allvar över det hela...

Även om risken för att att smittkoppor skulle kunna komma tillbaka från en grav är rätt liten så måste man ta den på allvar, menar en del forskare.
Infectious diseases: Smallpox watch

Frozen mummies and envelopes of scabs could contain remnants of one of history's most prolific killers

In 2011, while construction workers were digging a foundation at a site in Queens, New York, their equipment struck against something metal. Then a body rolled out of the rubble. Thinking that they might have unearthed the shallow grave of a murder victim, the workers immediately called the New York chief medical examiner's office, and forensic anthropologist Scott Warnasch drove over with a team to check it out.

The body, which had probably been buried in the cemetery of a nearby church, turned out to be a mid-19th-century mummy — of an African-American woman dressed in a nightshirt and socks who had been exceptionally well preserved by her ornate iron coffin. The find struck the forensics team as odd: a black woman in the mid-1800s was unlikely to have been able to afford such a luxurious resting place.

Then the examiners noticed the lesions and raised bumps that covered the corpse. The marks reminded Bradley Adams, New York City's chief of forensic anthropology, of photos he had seen of smallpox victims. The pricey coffin with its airtight seal, the scientists realized, might have been meant not to preserve the body of a wealthy individual but to quarantine an infection. “We took a step back,” says Warnasch. The site instantly changed from potential crime scene to potential biohazard, and the city's public-health department called the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia, for advice.

CDC officials reassured the New York investigators that the risk of infection was low. But the agency quickly dispatched epidemiologist Andrea McCollum and a team of scientists in protective clothing to autopsy the body and retrieve tissue samples. No one knows how long the smallpox virus can survive in a human corpse, and McCollum's team hoped to recover DNA or even viable virus particles from the woman's body. ... S-20140506

Re: Nature News

Postat: ons 07 maj 2014, 22:13
av Tryggve
Sedan skulle jag blir rätt förvånad om det inte finns smittkoppsvirus på andra ställen än Ryssland och USA. Visst, det är sagt att allt är rapporterat och destruerat, men med tanke på vad som kan gömma sig i frysar på labb, och med tanke på hur många sådana frysar och labb det finns världen över....
(eller så är anekdoterna man har hört från föreläsare bra historier och inget annat.... :-P )

Re: Sund forskning

Postat: tor 08 maj 2014, 07:21
av devadatta
Tryggve skrev:In intressant ledare (jag antar att det är rätt beteckning) i Nature. Colin Macilwain menar att krav på "sound science" som ska användas vid relegeringar är något som låter bra, men att det finns en annan sida av myntet.

Hur mycket poäng han har vet jag inte riktigt för egen del, men jag tyckte att det var en intressant artikel. ... E-20140417
När jag läste "Merchants of Doubt" om det ekonomiskt motiverade vetenskapsförnekandet så kom termen "junk science" upp ganska ofta som exempel på retorik från förnekarna, dvs att vanlig vetenskap som visade att rökning ger cancer, global uppvärmning finns osv var "junk science". Har för mig att de kontrasterade det mot "sound science". I vilket fall används "junk science" av bägge sidorna, men det är ett nyckelfras man bör se upp med.

Syntetisk biologi

Postat: tor 08 maj 2014, 17:20
av Tryggve
Artikel om utvecklingen av syntetisk biologi, ett tema nummer nu.
Synthetic biology: Beyond divisions

Since the birth of synthetic biology nearly 15 years ago, the field has splintered into diverse tribes of scientists, all attempting to bestow cells with new abilities.

Until just a short time ago, the boundaries of biology were set by nature. But those limits are receding. In the past decade, the field of synthetic biology has shattered the idea that living cells must stick to the biomolecular widgets that have evolved naturally. Synthetic biology — a more complex form of genetic engineering — allows researchers to assemble molecular gears on an entirely new scale. From such tools, biological freedom has emerged; even the rule that DNA's alphabet consists of just four letters has been thrown out of the window.

In this special issue, Nature surveys the messy landscape of synthetic biology and the various scientific tribes that are pushing it forward. Although the field is young, it is already divided into factions that foresee different futures.

A News Feature on page 152 investigates the schism between those who advocate free-for-all tools, such as open-source repositories, and the groups that seek to protect the fruits of research using legal instruments such as patents (see also Editorial, page 133). Volker ter Meulen follows that theme on page 135, highlighting the threat of excessive regulation in the field. On page 155, experts diagnose the discipline's biggest challenges and suggest solutions through building bridges across scientific and cultural divides. A News & Views Forum on page 166 debates the merits and drawbacks of engineering useful features into cells by fashioning genetic circuits directly or through successive rounds of screening and selection. And on page 168, Daniel G. Gibson and J. Craig Venter describe the research power of a synthetic yeast chromosome built to scramble genes and then probe which combinations can keep cells growing. ... E-20140508

How to best build a cell.

Postat: tor 08 maj 2014, 17:25
av Tryggve
Och här är temanumret med lite artiklar. ... l?code=552

Detta rapporterades det om i tidningarna idag såg jag. Man har fått E.coli att replikera DNA med ett par extra typer av baser. De kopieras i cellerna när de delar sig, men kodar inte för något. Än.
A semi-synthetic organism with an expanded genetic alphabet

Organisms are defined by the information encoded in their genomes, and since the origin of life this information has been encoded using a two-base-pair genetic alphabet (A–T and G–C). In vitro, the alphabet has been expanded to include several unnatural base pairs (UBPs)1, 2, 3. We have developed a class of UBPs formed between nucleotides bearing hydrophobic nucleobases, exemplified by the pair formed between d5SICS and dNaM (d5SICS–dNaM), which is efficiently PCR-amplified1 and transcribed4, 5 in vitro, and whose unique mechanism of replication has been characterized6, 7. However, expansion of an organism’s genetic alphabet presents new and unprecedented challenges: the unnatural nucleoside triphosphates must be available inside the cell; endogenous polymerases must be able to use the unnatural triphosphates to faithfully replicate DNA containing the UBP within the complex cellular milieu; and finally, the UBP must be stable in the presence of pathways that maintain the integrity of DNA. Here we show that an exogenously expressed algal nucleotide triphosphate transporter efficiently imports the triphosphates of both d5SICS and dNaM (d5SICSTP and dNaMTP) into Escherichia coli, and that the endogenous replication machinery uses them to accurately replicate a plasmid containing d5SICS–dNaM. Neither the presence of the unnatural triphosphates nor the replication of the UBP introduces a notable growth burden. Lastly, we find that the UBP is not efficiently excised by DNA repair pathways. Thus, the resulting bacterium is the first organism to propagate stably an expanded genetic alphabet.

Nature podcast

Postat: tor 08 maj 2014, 17:26
av Tryggve
Vill också påpeka att Nature har en podcast som kan vara värd att lyssna på.