Archive for October 5, 2014

Explore The World’s Most Detailed Map Of The Seafloor, Released Today

Posted in SCIENCE, GEOLOGY,HEALTH, INVIRONMENT, TECHNOLOGY,ANTHROPOLOGY, ARCHAEOLOGY, with tags , on October 5, 2014 by 2eyeswatching

Post 3809

Robbie Gonzalez

Explore The World’s Most Detailed Map Of The Seafloor, Released Today

Explore The World's Most Detailed Map Of The Seafloor, Released Today

Researchers today published the most detailed map of the ocean floor ever produced. Data collected by satellites and remote sensing instruments were used to created a model at least twice as accurate as previous maps, revealing thousands of previously uncharted seafloor features in the process. And best of all, you can explore the maps for yourself!

Above: A marine gravity map of the North Atlantic Ocean Red dots show locations of earthquakes with magnitude > 5.5 and they highlight the present-day location of the seafloor spreading ridges and transform faults. This gravity information shows the details of the plate tectonic history of the rifting of these continents including the subtle signatures of fracture zones that are currently buried by sediment. | Image & Caption Credit: David Sandwell, Scripps Institution of Oceanography

Much of what we know about the ocean floor’s topology we know from data collected by multibeam sonar systems. It is estimated that these sonar systems – which have to be lugged back and forth across the ocean’s surface by ships in order to acquire soundings of the seafloor deep beneath them – have left a staggering 90% of the deep-sea bottom uncharted.

Now, researchers led by geophysicist David Sandwell, of Scripps Institution of Oceanography in San Diego, California, have used data collected from satellite-based radar altimeters to fill in huge swaths of missing seafloor. What’s incredible is that these satellites map the ocean deep not by scanning the seafloor, but by repeatedly scanning the waters’ surface. Correcting for waves and tides creates a picture of sea-surface topography that reflects features of the seafloor far below. “A seamount, for example, exerts a gravitational pull, and warps the sea surface outward,” said Sandwell, in an interview with Science News, “so we can map the bottom of the ocean indirectly, using sea-surface topography.”

So what has the new scan turned up? Here’s Science News‘ Carolyn Gramling:

Among the new features they’re now able to detect, Sandwell says, are thousands of previously unknown seamounts between 1000 and 2000 meters tall dotting the ocean floor. They also discovered an 800-kilometer-long now-extinct (i.e., no longer actively spreading) ridge in the South Atlantic Ocean that formed after Africa and North America rifted apart. The team also reports the exact location of a now-extinct seafloor spreading ridge, a zone where two tectonic plates began pulling apart 180 million years ago to form the deep basin that became the Gulf of Mexico. “That was a surprise to me—you’d think everyone would know everything about the Gulf because it’s so well-studied,” he says. “Of course, people knew it opened from seafloor spreading, but they didn’t know exactly where the ridge and transform faults were.” Those features were so deeply buried by sediment that the gravity signals were extremely faint.

Also cool: Sandwell’s team, in addition to publishing its findings in the latest issue of Science,has put its charts online in the form of several interactive maps (overlapys can also be downloaded for navigation in Google Earth). Here’s the team’s vertical gravity gradient map:

Happy exploring!

[Science via Science News]

First Baby Is Born to Woman with Womb Transplant


Post 3808

First Baby Is Born to Woman with Womb Transplant


Neuroticism and Long-Time Stress Linked to Alzheimer’s in Women


Post 3807

Neuroticism and Long-Time Stress Linked to Alzheimer’s in Women


4 New Substances Added to List of Carcinogens


Post 3806

4 New Substances Added to List of Carcinogens


Did You Know Meth Has Its Origins In Traditional Eastern Medicine?


Post 3805

Robbie Gonzalez

Did You Know Meth Has Its Origins In Traditional Eastern Medicine?

Did You Know Meth Has Its Origins In Traditional Eastern Medicine?

Meth’s pop cultural relevance, and its prevalent use, might lead you to believe that it is a relatively modern creation. But the notoriously addictive stimulant was first synthesized in the late 1800s, from a plant commonly used in traditional Chinese and Japanese medicines.

The drug was first synthesized by Japanese researcher Nagai Nagayoshi, who, following a 12-year stint studying chemistry and pharmacology in Germany, returned to Tokyo to put his newly acquired laboratory skills to work. Sarah Laskow has the details at The Atlantic:

[Nagai] began, in his new role, applying the tools of chemistry that he had learned in Europe to the traditional Japanese and Chinese medicine his family had studied for years. One of those remedies was ma huang, a bushy, evergreen plant that grows in Central Asia and was used to treat simple complaints—colds, headaches, congestion. Nagai discovered, according to Sumitomo Dainippon Pharma, a drug company established in 1885, “some crystalline material recognizable to the naked eye coexisting in the blackish brown essence extracted from wild ma huang.” He started studying its chemical structure and soon isolated the compound ephedrine.

Nagai and his students kept tinkering with the ephedrine, and within the next decade, Nagai had used it to synthesize methamphetamine. In 1919, a student of his, Akira Ogata, figured out how to more simply manufacture the same compound in crystallized form. By the 1930s, its properties as a stimulant were well known. The Japanese chemists had not patented their work, though, and in World War II, armies on all sides of the war used methamphetamine to keep their soldiers alert.

More at The Atlantic.

Photo Credit: Radspunk via Wikimedia Commons | CC BY-SA 3.0


This Viral DNA Infects Cells by Changing From a Solid to a Liquid


Post 3804

George Dvorsky

This Viral DNA Infects Cells by Changing From a Solid to a Liquid

This Viral DNA Infects Cells by Changing From a Solid to a Liquid

Two new studies are showing that viral infections are possible owing to a remarkable biological phase transition. The research shows that viral DNA transforms from a glassy solid to a fluid-like state when the conditions for infection are just right. The new insight could result in new antiviral therapies.

Above: A fluorescence image of viral DNA complexes in the cytoplasm of a cell. Cells use different mechanisms, including special proteins, to prevent infection. But as the new studies point out, these defensive measures often fail owing to special features of viral DNA. (Credit: A. Rottach / LMU)

The DNA that’s tightly packed inside a virus’s protein shell is denser than what’s found in the nucleus of a human cell. Because of this tight packing, the genetic chain can barely budge. But as we know, infections most certainly do happen. Viruses somehow inject their DNA into the host cell at high speed. But how? How can the frozen and highly pressurized DNA suddenly become liquid enough for this to happen? Well, it’s because the DNA does become liquid enough for this to happen.

This Viral DNA Infects Cells by Changing From a Solid to a Liquid

Two new studies, one in PNAS and the other in Nature Chemical Biology, have worked out the mechanics behind this process. Carnegie Mellon University’s Alex Evilevitch has shown that certain viruses undergo a phase transition at the temperature of infection, allowing the DNA to morph from a stiff, rigid crystalline structure into a fluid-like mass that facilitates infection. (In the image at left, you can see how HSV-1 DNA undergoes a solid-to-fluid transition within the capsid. (credit: Evilevitch et al))

“The exciting part of this is that the physical properties of packaged DNA play a very important role in the spread of a viral infection, and those properties are universal,” noted Evilevitch in a Carnegie Mellonstatement. “This could lead to a therapy that isn’t linked to the virus’ gene sequence or protein structure, which would make developing resistance to the therapy highly unlikely.”

Indeed, the new insight could provide a promising new target for antiviral therapies.

Writing in Chemistry World, Michael Gross explains how viral DNA is capable of this trick:

For the bacteriophage lambda, which infects Escherichia coli bacteria in the human gut, the researchers studied the compressibility of the DNA using atomic force microscopy, and the energy released upon injection as a function of temperature. They found that the tightly-packed DNA melts and becomes sufficiently mobile for injection as the temperature approaches human body temperature, around 37°C.

‘The evidence for a structural transition is very striking,’ comments Smith, who led the earlier work on viral DNA packaging. ‘The effect on ejection is not strict because lambda phage viruses do infect bacteria grown in a Petri dish at lower temperatures. Temperature also has complex effects on the metabolism of the host cells from which viruses draw their resources. However, the present studies reveal a clear and interesting effect of temperature on the physical properties of densely packed DNA.’

In a separate study on Herpes simplex virus type 1, which can reside in human cells for long periods and injects its DNA into the nucleus when it awakens, the Evilevitch group found that the ionic conditions in the cytoplasm of the host cell, as well as temperature, are key factors that determine when the DNA is liquefied in preparation for injection.

Fascinatingly, DNA maintains its solid-like state when the conditions are not ideal for infection, thus stabilizing the virus particle and ensuring that its DNA isn’t ejected at the wrong time. It’s here where therapists are going to look when devising their antiviral therapies.

Read the studies at PNAS: “Solid-to-fluid–like DNA transition in viruses facilitates infection” and Nature Chemical Biology, “Solid-to-fluid DNA transition inside HSV-1 capsid close to the temperature of infection.” Supplementary information viaCarnegie Mellon University and Chemistry World.

Geneticists Slam Study Claiming Schizophrenia Is Eight Disorders


Post 3803

George Dvorsky

Geneticists Slam Study Claiming Schizophrenia Is Eight Disorders

Geneticists Slam Study Claiming Schizophrenia Is Eight Disorders

Last month, a study published in the American Journal of Psychiatry made international headlines by claiming that schizophrenia is not a single disease, but rather a group of eight distinct genetic disorders. Now, ten leading geneticists say this extraordinary claim isn’t justified by the data.

In the AJP paper, C. Robert Cloninger, Igor Zwir, and colleagues analyzed genetic influences on more than 4,000 people with schizophrenia. This helped them identify distinct gene clusters that appeared to contribute to eight different classes of the disorder. The researchers concluded that, “[S]chizophrenia is a group of heritable disorders caused by a moderate number of separate genotypic networks associated with several distinct clinical syndromes.” It was a stunning declaration — one with profound implications to our understanding of the disorder and how it might be treated.

Results ‘Not Relevant’

Writing in Genomes Unzipped: Public Personal Genomics, a group of geneticists led by Patrick Sullivan of Sweden’s Karolinska Institute are now claiming that the authors of the study did not provide the necessary evidence. They write:

Their claims are based upon complex (and we believe flawed) analyses that are said to reveal links between clusters of clinical data points and patterns of data generated by looking at millions of genetic data points. Instead of the complexities favored by Arnedo et al., there are far simpler alternative explanations for the patterns they observed. We believe that the authors have not excluded important alternative explanations – if we are correct, then the major conclusions of this paper are invalidated.

The geneticists identified five specific areas of concern that they feel were not adequately addressed in the study, “each of which calls into question the conclusions.”

  • Ancestry/population stratification: The geneticists are not happy with the samples used, saying they introduce too many confounders that could give false associations.
  • The x chromosome: The researchers failed to account for sex in their matrix factorization; in statistical genetics, sex chromosomes require special handling — an issue not addressed by the authors.
  • Linkage disequilibrium: The geneticists question the authors’ interpretation of SNP clusters (single nucleotide polymorphism).
  • SNP selection: The reported P-values are incorrect, say the critics, the result of a selection effect.
  • Replication: “[I]t is unclear precisely what [was] replicated, exactly how this was done, and whether the degree of ‘replication’ deviated from that expected by chance,” write the geneticists.

Sullivan and his colleagues say it’s “highly likely” that the results are not relevant for schizophrenia, and urge “great caution” in the interpretation of the results of the study.

Criticism Without Peer Review?

We contacted the study’s lead authors for a response.

“My colleagues and I will prepare a reply to the comments in PubMed Commons next Monday,” said the Washington University School of Medicine’s C. Robert Cloninger via email. He continued:

Patrick Sullivan and his colleagues organized PGC on the rationale that increasing sample size could correct the problem of weak and inconsistent results in GWAS [genome-wide association studies]. Unfortunately their rationale is questionable as shown by the facts that their subjects are clinically heterogeneous and their associations remain weak.

Cloninger said it’s unfortunate they have taken the unconventional route of publishing criticisms without peer review, which ultimately is not in the best interests of objective science.

“In contrast, our paper was thoroughly peer-reviewed,” he told io9. “Their criticisms are seriously flawed and their rush to specious fault-finding does not serve science or anyone well.”

To which his colleague Igor Zwir added:

This is not the way real science works — science is peer review and that’s the reason why we’re delaying. We have a response, but we’re going to go about it through the appropriate channels. Otherwise we’d be guilty of doing what they’ve done.

In response to these criticisms and concerns, Gerome Breen of King’s College London sent io9 this email:

Prof Cloninger is not addressing the issue, which is about the paper he and his collaborators published. Science moves quickly these days and we wanted to use modern means of communication to make the point that there are apparent serious flaws with the study. Letters to editors are essentially old technology, science blogs and PUBMED commons are the way scientists communicate now.

It would also be good if all the parties involved declared any potential conflicts of interest. We wrote our piece, not as part of the Psychiatric Genomics Consortium, but rather as a set of experts in genetics of this disorder and in the type of analyses they use, in the desire to stop false memes entering the field and to avoid giving the public false conceptions of what genetics and cannot do for this really serious disorder.

When asked to clarify what he meant by a potential conflict of interest, Breen responded:

Many previous papers like this [have] been accompanied by patenting or the launch of a company or test. We don’t know if the authors are doing that but we would prefer if they made it clear one way or the other.

So he’s got no evidence for conflict of interest. That said, the paper also does not contain a COI statement, which is pretty standard for papers like this.

We’ll keep you updated as this story develops.

Read the entire Genomes Unzipped article here.

Top image: a genotypic network in which nodes indicate SNP sets linked by shared SNPs (blue lines) and/or subjects (red lines). Arnedo et al.