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Prof. A's Science Fix- November 16 2012 Edition

This edition will be an all-biology edition. I have been unable to keep up with general science news and blog writing as I would like to do, but fortunately, the “obstacle” was actually doing science so I’m not complaining. Biology is my comfort zone and I can process information and write much faster if I stick to it. So you’re getting a Bio Fix today.  My apologies to fans of other sciences.


WHAT I’M READING: Spillover: Animal Infections and the Next Human Pandemic, by David Quammen. I’m only on the third chapter but I can already assure you that this is a fantastic book, that you cannot afford not to read this book. David Quammen is an extraordinary science writer; he never resorts to sensationalism or hyperbole, his books are very well research and in addition, they read like an adventure novel. The book is impossible to put down.  The subject is of course fascinating: zoonosis.  Zoonosis is the transmission of diseases from animals to man.  Many of these are emerging, strange new diseases, such as Ebola, HIV, SARS that seemed to have appeared out of nowhere in recent decades. What these diseases have in common are a wild animal reservoir, and an intermediate host from which it spills over to man.  These diseases all have the potential to rapidly become a pandemic because we live in an age of very fast travel, globalization, constant human migration, ecological changes, etc., all factors contributing to these emerging diseases.  David Quammen interviewed and followed the many scientists involved in studying these truly scare diseases, from the field, into specialized labs used for studying these very dangerous pathogens. He spoke to survivors and family members of the deceased in the various out breaks. The result is a gripping read, a work of non-fiction, heavily based on scientific evidence and rich with information, that is as easy and pleasurable to read as a riveting fictional story. Here are two very good reviews that I hope finish the job to convince you to buy this book and read it, right now: NYT review and The Guardian review




Ebola transmitted from pigs to monkeys. And while we are on the subject of deadly viruses, the reservoir for Ebola in the wild is still a matter of debate, though the strongest candidates so far are bats. While Ebola is deadly for many primates, including humans, it can infect pigs without making them ill. In a Canadian lab, Ebola has now been seen to spread from pigs to monkeys without any evidence for direct contact between these animals. In this experiment, pigs were infected with Zaire Ebola (a variant deadly to primates and humans) using nasal swabs, and placed in a room where cynomolgus monkeys (Macaca fascicularis, or crab-eating macaque, an Asian species). The pigs got mildly sick, as with a cold, but were basically fine. The monkeys, on the other hand, developed bloody spots on their chests and a very severe lung infection typical of a deadly Ebola infection; they had to be euthanized for humane reasons. Ebola, unlike influenza, is not an airborne disease, so the scientists speculate the transmission could have occurred through aerosol droplets.  A few years ago, a variant of Ebola not deadly to humans, known as Reston Ebola, was found in domestic pigs in the Philippines and antibodies against the virus were found in pig farmers. The team is now investigating whether Ebola is found in wild pig species in Africa, to determine if they could act as a reservoir. The fact that pigs can transmit the disease is a very scary possibility, given that there are pig farms basically everywhere in the world and they could potentially end up being a source of a massive outbreak.  The observation of non-contact transmission is also useful to adopt containment measures in case of an outbreak.


Identifying source of MRSA outbreak using whole-genome DNA sequencing. In many cases new technologies allow us to do very rapidly something that had never been done before. This is an excellent example of use of new technology. An outbreak of the very serious bacterial infection caused by a “superbug”, methicillin-resistant Staphylococcus aureus, or MRSA. This outbreak was particularly scary because it occurred in an infant ward, at a hospital in Cambridge (England).  When three babies came down with MRSA in rapid succession, doctors suspected it was the same bug, from a common source, immediately because all three cases were resistant to the same spectrum of antibiotics. Even after extensive cleaning, another baby caught the “superbug”. Because there had been a previous MRSA outbreak at the hospital, six months before the outbreak in the infant ward, scientists decided to investigate whether the two were linked, hoping this will give clues to the original source of the outbreak. The suspicion was an adult carrier who continued the spread. With the use of whole genome sequencing, using the Illumina MiSeq benchtop sequencer (I have this machine in my lab and we are extremely pleased with its performance and speed), they could identify mutations that naturally occur in the bug’s genome as it moves from one person to another, thus creating an “evolutionary tree” and following the source of the infection to its “roots.” They screened all the hospital workers in the baby ward and found one person who, although not sick, tested positive for MRSA. The evolutionary analysis of the infants’s MRSA, as well as that of some parents who came down with the disease, the infected employee was identified as the source. They think this person unknowingly picked it up from an infant in the ward at some earlier point in time. Taking this employee out of circulation effectively stopped the outbreak.  Fortunately, nobody died, and all patients and parents recovered.  This rapid sequencing is not very expensive but analyzing the data requires bioinformatics expertise. In the future, this new technology should become common practice because of the potential to rapidly eliminate hospital outbreaks of deadly pathogens in their tracks, by identifying the source.




Grass-eating hominins. Before getting to the science, here is my personal agenda: I want you all to become exclusive grass-eaters from now; if we have a hominin cow as an ancestor and this ancestor was a healthy, robust handsome pre-human, who are you to question our ancestor’s wisdom, especially his wisdom teeth?  About 3.5 million years ago, Australopithecus bahrelghazali, a hominin related to Lucy, living in the plains of what is now Chad, munched mostly on grass roots and sedges. This was a pretty big shift from the diet of other apes such as chimps, which eat mostly fruits, seeds and woodland plants. It suggests that A. bahrelghazali lived in more open grasslands, adapting their diet to this new habitat. We know what they ate from the ratio of the two nonradioactive isotopes of carbon, 13C and 12C, in the enamel of teeth, researchers can detect whether an ancient creature ate a diet rich in woodland or grassland plants. New methods have allowed researchers to study the isotopes in fossil teeth without destroying the specimen. In the past few years, we have learned that Ardipithecus ramidus, was eating mostly a woodland ape diet, 4.4 million years ago. Four million years ago, another hominin, Australopithecus anamensis, had bigger premolars and molars, with thicker enamel, suggesting a shift in diet to a more grassland-type of diet.  Oxford scientists studied the teeth of 3 individual A. bahrelghazali fossils, from 3 million to 3.5 million years old and found that they were enriched in 13C, which is the signature of a diet rich in reeds, grasses, and tuberous roots that grew around the floodplains of the ancient Lake Chad. This hominin was the ape equivalent of a grazing cow. This shift in diet occurred earlier than previously thought in human evolution. This allowed for the opportunistic broadening of the feeding range, eating a wider range in foods than, for example, chimpanzees typically eat. Scientists will now investigate whether other hominins that lived 3 to 3.5 million years ago had also switched to grass-feeding.


Evolution is letting our sense of smell down. Compared to many other mammals, our sense of smell is pitiful. Primates are visual animals, and compared to other mammals, the number of olfactory receptors is pretty small. But humans have even a much smaller number than monkeys.  A team of French scientists studying the human genome and the selective pressures that shaped it, have now focused on negative selection instead of positive selection. Negative selection is the force that weeds out certain mutations or variants that have deleterious effects. They show that in 10 human populations, the majority of gene categories are still under negative selection. The major exception is the vast gene family encoding olfactory receptors. Damaging mutations in these receptors have not been weeded out, meaning that negative selection is relaxed for this gene family. In other words, evolution does not care if our sense of smell is pretty pathetic or if it gets worse. This is likely due to the fact that our sense of smell no longer plays an important role in survival or reproduction.  Hopefully future generations will keep a certain number of olfactory receptors functional: it’s nice to stop to smell the roses, and nuzzling and smelling babies, puppies, and lovers are some of the most rewarding experiences in life.




Carnivorous sponge found in deep sea. A newly described sponge found in the deep sea off the coast of Northern California, 3300 meters (~10,000 feet) below the surface, looks like a delicate candelabra. It was named the harp sponge (Chondrocladia lyra) because it looks a bit like the musical instrument. It’s not only unusual in shape, it’s also unusual in feeding habits. Most sponges are filter-feeders; they filter the water for bacteria and other single cell organisms present in the water. But the harp sponge uses barbs on its vertical branches to snag tiny copepods swimming in its proximity. They have cells that specialized in digesting, that surround the minuscule prey and digest it. The branches do not only have a feeding purpose, they are also used in its reproduction. The tips the branches contain knobs full of packets of sperm that once released in the water, come in contact with the eggs found along the branches of another harp sponge.


Massive “gene borrowing” in rotifersBdelloid rotifers are microscopic invertebrates with very a very unusual lifestyle. They have survived for ~80 million years without sexual reproduction. They have been proposed to be candidate for one of the few survivors of extreme conditions such as those of unprotected space travel: they can survive for very long in a dried-out form and they can tolerate extremely high doses of ionizing radiation.  A few years ago, scientists discovered another oddity: the DNA adjacent to the tips of their chromosomes (telomeres) seems to have been borrowed from other organisms, by a process called horizontal gene transfer (HGT). Now scientists have actually investigated how many of these borrowed genes are actually functional, and they have found that an astonishing 10% of their transcribed genome comes from other organisms, bacteria, fungi, protists (protozoans), and algae. About 80% of these horizontally acquired genes code for enzymes, and they make a huge contribution to its metabolism; these allow these tiny invertebrates to degrade toxins or generate new metabolites. Horizontal gene transfer can thus act as a mechanism to allow asexual organisms to adapt to changing environments even if they can’t enjoy the adaptability advantages of sex.


New species of colorful tarantulas found. Nine new species of arboreal tarantulas have been recently discovered in Brazil, each more colorful than the other. Go to the link to see them all, unless you are an arachnophobe. This rare beauty is Typhochlaena costae. These tree-dwelling tarantulas are lighter in build and more agile, making them suitable for hunting arboreal prey. This particular species was discovered in the Brazilian cerrado, which is a savanna-like environment. Unfortunately, the bright colors last only until the spider reaches maturity, at which point they lose their unusual, beautiful bright hues.


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Comment by archaeopteryx on November 30, 2012 at 10:12am

Comment by archaeopteryx on November 29, 2012 at 2:59pm

From what I've read, the hexagonal pattern seems to be caused somehow by the Saturnian jetstream.

Comment by Michel on November 29, 2012 at 1:01pm

@Arch - Posted about this in the Daily Cosmos.

These pictures are incredible! Both my favorite planet and my favorite spaceship =)
This vortex of vortices is at the center of a huge hexagonal storm.

These look like storm drains at both poles of the planet where all the gases fall inward. 

Comment by archaeopteryx on November 29, 2012 at 12:01pm

And we thought Sandy was bad --

Huge Saturn Vortex Swirls in Stunning NASA Photos

Roiling storm clouds and a swirling vortex at the center of Saturn's famed north polar hexagon is seen in an image from NASA's Cassini mission taken November 27, 2012. The camera was pointing toward Saturn from approximately 224,618 miles (361,488 kilometers) away. REUTERS/NASA/JPL-Caltech/Space Science Institute/Handout (UNITED STATES - Tags: SCIENCE TECHNOLOGY) THIS IMAGE HAS BEEN SUPPLIED BY A THIRD PARTY. IT IS DISTRIBUTED, EXACTLY AS RECEIVED BY REUTERS, AS A SERVICE TO CLIENTS. FOR EDITORIAL USE ONLY. NOT FOR SALE FOR MARKETING OR ADVERTISING CAMPAIGNS

Roiling storm clouds and a swirling vortex at the center of Saturn's famed north polar hexagon is seen in an image from NASA's Cassini mission taken November 27, 2012.

Amazing new photos from NASA's Cassini probe orbiting Saturn reveal a dizzying glimpse into a monster storm raging on the ringed planet's north pole.

Cassini took the spectacular Saturn storm photos Nov. 27 and relayed them back to Earth, mission scientists said in a statement. The pictures reveal a swirling storm reminiscent of the recent Hurricane Sandy that recently plagued our own planet.

The tempest is located in a strange hexagonal cloud vortex at Saturn's north pole that was first discovered by the Voyager spacecraft in the early 1980s, and sighted more closely by Cassini since then. The strange six-sided feature is thought to be formed by the path of a jet stream flowing through the planet's atmosphere.

Comment by Doone on November 29, 2012 at 8:01am

Primary and secondary endosymbiosis is depicted in this diagram, which shows movement of DNA from the cyanobacterial progenitor of plastids to the primary host nucleus and, subsequently, to the nucleus of the secondary host. (Credit: John M. Archibald, Dalhousie University, Canada)

Tiny algae shed light on photosynthesis as a dynamic property
Comment by Doone on November 28, 2012 at 10:02pm

Submitted by: Unknown (via MinutePhysics)

Does the Universe Have a Purpose?

Comment by Doone on November 28, 2012 at 5:06pm
Comment by Adriana on November 28, 2012 at 4:55pm

My favorite is the CILIA FLOW!

Comment by Doone on November 28, 2012 at 4:54pm

Wow, great fluid and flow images, Thanks!

Comment by Michel on November 28, 2012 at 4:51pm

I love the coiling honey.
Would it coil less in oil?

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