Puddles of Goo? Brainless Slime Molds Have Memories

The yellow slime mold leaves a thick mat of translucent slime (left on the agar plate) behind it as it moves, ooze that it later avoids. Now researchers have found the goo uses the gel trail as a kind of memory to navigate. 

CREDIT: Image courtesy of Audrey Dussutour                                           

Scientists have found that just because an organism does not have a brain, does not mean that it cannot remember things. Slime molds, which were once considered fungus and later put into the protists classification, have been investigated in order  to see if they truly do have memories. Although it may not be the same definition of intelligence we think of inside of the human brain such as having the ability to create, store, and recall memories, this slime mold uses a different technique in order to remember where it has been. Slime molds do not have brains or even neurons; however, who needs either of those when you have ooze to lie down and retrace your steps.

This type of slime mold, also known as Physarum polycephalum, “leaves a thick mat of translucent slime behind it as it moves” (Choi). The slime mold can detect it’s own trail and use this as form of memory. It is almost like allowing itself “to communicate with it’s future self” (Choi). When the scientists tested this theory, slime mold that was able to detect it’s own trail reached the food placed in a maze 30% faster while slime that was blinded to their own trail took up to 10 times longer looking in places it had already visited. This was the first tested evidence that supported “a spatial memory system in a creature without a brain” (Choi).

Blog Post Author: Tyler Davis Section 124-26

Work Cited
Choi, Charles. "Puddles of Goo? Brainless Slime Molds Have Memories." LiveScience. N.p., 8 Oct. 2012. Web. 3 Mar. 2013. <http://www.livescience.com/23797- brainless-slime-mold-memories.html>.

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Discovery Of Giant Roaming Deep Sea Protist Provides New Perspective On Animal Evolution

Tracks of the Bahamian Gromia sphaerica(A) Gently sloping seafloor with numerous G. sphaerica visible. White arrowheads indicate notably curved tracks; black arrowheads indicate adjacent tracks running in opposite directions.(B) Alignment of the tracks on a steeper slope.(C–F) Details of the tracks, demonstrating the characteristic bilobed profile with the central ridge that is especially prominent near the organism. In panel (E), note that the track proceeds through a dip in the terrain, suggesting active locomotion. In panel (F), a group of three large cup corals growing on a half-buried sea urchin test indicate a remarkable sediment stability that may facilitate track persistence. Photos courtesy of sciencedirect.com.

New evidence about protists has led to the disproval of our current understanding of the evolution of the kingdom Animalia. A Biologist, Mikhail Matz, from the University of Texas at Austin was researching the ocean floor of the Bahamas when he came upon an amazing discovery. He found grooves on the deep floors of the ocean that came from protists, but showed a bi lateral pattern that is considered to be a trait of animals.

This is so incredible because it is the first time bi-lateral animal-like traces are appearing in single celled organism’s movements. The connection comes from the fact that the Precambrian era multi-cellular animals have very comparable trails left behind due to movement. “Bilateria appeared in the fossil record in the early Cambrian about 542 million years ago” (Science Daily). Mats says, “if our giant protists were alive 600 million years ago and the track was fossilized, a paleontologist unearthing it today would attribute it to a kind of large, multi-cellular, bilaterally symmetrical animal…We now have to rethink the fossil record” (Mats).  It is an amazing thing to be able to add knowledge to the pool of evolutionary theory.

External Appearance of the Bahamian G. sphaerica(A) Collected specimen demonstrating transparent membranous test, multiple evenly scattered apertures, and dark-green sediment contained in the protoplasm under the test's surface.(B) Freshly collected specimen with collapsed pseudopodia still visible (white projections).(C) Typical grape-shaped specimen in situ, fully covered with sediment. The track of this one is toward the top right corner of the picture.

Since fossils are a customary means of examining organisms, it is hard to be one hundred percent positive about this evidence because it is hard to extract a fossil from the ocean floor due to water movements. Fortunately for this protest, it’s location, with little current, made it possible to maintain the tracks. With such evidence it is now evident that the fossil record must be re examined to fit these protists in their appropriate location.

Blog Post Author: Jonathan Zirna Section 124-26

Works Cited

University of Texas at Austin (2008, November 21). Discovery Of Giant Roaming Deep Sea                     Protist Provides New Perspective On Animal Evolution. ScienceDaily. Retrieved March   3, 2013, from http:wwwsciencedaily.com/releases/2008/11/081120130531.htm

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New Insights Into Protein Synthesis and Hepatitis C Infections

From left, Jennifer Doudna, Bunpote

 Siridechadilok and Eva Nogales, used this cryo 

electron microscope to create a 3-D model of

 the protein complex eIF3 that shed new light 

on protein synthesis and Hepatitis C viral

 infections. Photo courtesy of lbl.gov

This article shows how cryo electron microscopy (cryo-EM) was used to create a 3-D model of the protein complex called eukaryotic translation initiation factor 3 (eIF3).  The cryo-EM reconstructions of Biochemist Jennifer Doudna and biophysicist Eva Nogales show that eIF3 consists of five lobes; a head and a pair of arms and legs. 

The study shows that the left “arm" of the eIF3 complex binds to the eukaryotic protein complex that recognizes the methylated guanosine cap at the 5’end of the eukaryotic mRNAs.  By drawing the mRNA’s 5’end cap through the ribosome entry site and towards the exit, eIF3 ensures the mRNA is properly positioned for its genetic code to be translated. EIF3 will also wrap its arms and legs around a structural element of RNA for the hepatitis C virus (HVC), known as the internal ribosome entry site, and pin it to the exit site of the 40S ribosome subunit. The IRES leaves through the left arm of the eIF3 complex at the same location where interaction with the human mRNA cap-binding complex takes place. 

This act might explain the ability of the HVC IRES to hijack the human ribosome and its associated translation factor. This new information gives insight into how the initiation mechanisms of protein synthesis work specifically for humans. It also provides a step towards understanding what happens when a viral infection occurs at the molecular level. By understanding these methods, scientists may be able to come up with new and improved therapies for viral infections.

Blog post Author: Jenn Gregorio Section 124-26

Work Cited:
"New Insights Into Protein Synthesis and Hepatitis C Infections." Research News:. N.p., 5 Dec. 2005. Web. 03 Mar. 2013. 

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DNA sequence may be lost in translation

Photo courtesy of  wired.com

A new mysterious, unexpected phenomenon was brought to the attention to the Annual Meeting of the American Society of Human Genetics in Washington, DC. This phenomenon is called “RNA editing.”  RNA editing is, “The process by which messenger RNA is modified (edited) after it is synthesized before it is translated into protein” (MedTerms). We all know that DNA is transcribed first to form RNA and then what codes for the amino acids depends on the triplets of RNA. The RNA sometimes “edits” for different bases, switching them, hence the name “RNA editing.” Two studies, conducted by Mingyao Li and Emmanouil Dermitzakis presented at the meeting suggested and showed many different opinions and findings. 

Li and her colleagues observed this marvel in a number of organisms such as plants, mice and even human diseases. In the plants they studied, it was linked to cell metabolism and in mice, it was linked to their brain function. This editing was also linked to ALS and epilepsy in humans. 

According to the article, Li and her colleagues also have been conducting a project known as the “1000 Genomes Project”, with a goal to reach the genomes of 1000 people. In this project, the researchers plan to compare the DNA and RNA sequences. “The results suggest that a vast amount of editing could be occurring across the genome, with the researchers identifying more than 102,000 potential editing events” (Translation). One thing the study suggested was that 97% of the gene transcripts are changed after a new template of RNA molecules has been formed from the DNA code. Li saw this rate as “surprisingly high” because normally in most cases of RNA editing, there were only 2 types of alteration, but many other differences that Li and her colleagues found are seemingly unknown. They also concluded that nobody can tell where the edited RNA is translated to. 

For Emmanouil Dermitzakis, he is more skeptical than Mingyao Li. He is also one of the researchers on the “1000 Genomes Project” and he argues DNA sequences of the mismatched pairs may simply be because of sequencing errors. He thinks that this editing varies between different cell types. The article states, “The only way to check would be to re-sequence a large number of the genes that seem to be edited.” This is being done by Li now, in hopes to be able to really prove this fascinating phenomenon. 

Blog post Author: Brooke Vasilescu Section 124-26

Work Cited:

Katsnelson, Alla. “DNA Sequence May Be Lost in Translation.” Nature.com. Nature

                       Publishing Group, 05 Nov. 2010. Web. 24 Feb. 2013.

“RNA Editing Definition-Medical Dictionary Definitions of Popular Medical Terms Easily

                       Defined on MedTerms.” Medterms. N.p., n.d. Web. 24 Feb. 2013. 

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Will This Fish Transform Medicine

Photo courtesy of popsci.com

Researchers and geneticists looking for the cause of rare diseases and illnesses are now using the translucent zebra fish in replacement of rodents. The ability to mutate zebra fish DNA is allowing researchers to manipulate human diseases into the fish as a model. 

Families of infants with suspected genetic diseases or illnesses can send a vile of blood to the Human Genome Sequencing Center at the Baylor College of Medicine. There, researchers and scientists can accurately and quickly sequence the infant’s DNA and make copies. If a mutation is found in the infant’s DNA sequence, as suspected, researchers can steadily insert the same DNA mutations into the larval zebra fish. Then, through observance, researchers can watch for any structural defects that mature. Since the fish is transparent, organ development is easy to detect. For example, researchers watched a larva zebra fish grow a heart on the right side of its body, similar to the child with the DNA sequencing for this characteristic. Scientists were able to narrow down this child’s six mutations in her sequencing to the exact one relating to the heart displacement. 

Virginia Hughes, author of the original article, reports the zebra fish have been manipulated with “DNA mutations linked to narcolepsy, muscle disorders, and the large head size associated with autism.” Not only do researchers envision the zebra fish to display DNA mutations, but also as a test for treatment. The fish, unlike rodents, absorb drugs in the water through their skin. From this, scientists can observe which drugs and molecules affect the fish. Those drugs with hopeful effects are then tested in mammals such as rodents. Leonard Zon (of Harvard Medical School) discovered with one particular drug, the animals’ blood stem-cell counts amplified. This was then used for leukemia patients who had depleted blood cells from radiation treatment. The drug was about 83% effective for his twelve “test patients.” As one can see, zebra fish are advancing the medical field. Who would have thought such an unrelated animal to humans could be a source for medical mysteries and treatments.

Blog Post Author: Nicole Boisvert, Section 124-26
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Work Cited

Hughes, Virginia. "Will This Fish Transform Medicine?" Popular Science. N.p., 21 Jan. 2013. Web. 11 Feb. 2013.

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King Richard III Found!

Photi courtesy of montrealgazette.com

An astonishing discovery has recently occurred in a parking lot located in Leicester, England. Although this parking lot may not of been where Richard III - a past king of England who has been deceased for around 500 years prior to the discovery - would have wanted to be buried, it seems that this is where he was all these years. Genealogists proved that this body was indeed Richard III by comparing his DNA taken from the bones of skeletons found from deceased family members.

            Along with DNA testing, radiocarbon dating further proves that this is Richard III – as if DNA proof isn't enough! The test proves that the bones were present in the 15^th to 16^th century, which matches up with Richard’s timeline. Furthermore, the skeleton fits with the description that Richard III was said to have: lean, slender frame with a severe case of scoliosis.

            Curious of the poor man’s death? The bones show that Richard was most likely killed by two injuries that occurred to his skull, along with ten other wounds found along the skeleton, but the skull injury being the most likely cause of his death. It seems that his hands were tied and he was also humiliated by being stabbed in the buttocks at the time of his murder by some hooligans who jumped him in the middle of a street.

            All of the factors such a skeleton positioning, carbon dating, and most importantly DNA testing proves that this skeleton found buried under a parking lot in England has been harboring a past monarch of the great English nation for over 500 years. Fascinating discovery!

Blog Post Author: Kelsey Martin, Section 124-23

Citation

            McCarthy, Eugene. "King Richard III found!." . Macroevolution.net, 7 Feb 2013. Web. 11 Feb 2013. <http://www.macroevolution.net/richard-iii-found.html>

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A Brave New World of Prenatal DNA Sequencing

Photo courtesy of bioedge.org

The leading DNA sequencing company, Illumina, is making moves to become a larger presence in the world of prenatal testing by recently acquiring the new company Verinata. The current procedures offered to mothers whose fetus's are at high risk for chromosomal abnormalities are very invasive and can cause miscarriages. Instead of withdrawing samples from the placenta and/or amniotic fluid, they wish “to search for these chromosome disorders starting from 10 weeks of gestation on, … [by] sequenc[ing] the bits of DNA floating in a sample of the mother’s blood” (Young, 6).

“Around 12% of the DNA in the mother's blood belongs to her fetus” (Young, 7). This is much less invasive and risky. Also it could be offered to all soon to be mothers instead of just those with high-risk pregnancies. They soon hope to be able to test for not just whole chromosomal errors, such as Down Syndrome or Edwards Syndrome which result from trisomy of chromosomes twenty-one and eighteen, respectively, but to be able to map the fetus's entire genome and find specific gene mutations and disorders. Right now the only thing blocking this from happening is money. “‘As sequencing gets cheaper and cheaper, if you wanted to look at a particular mutation, say, in the cystic fibrosis gene, you may be able to do that in the future,’” says Heath (Young, 16).

This of course brings up ethical issues. If parents are able to find out that their child will have a debilitating disorder some may chose to abort the pregnancy.  Many believe that this is unethical and that people should live out their lives the way their cards were dealt, even if the hand is not that good.  With these new scientific possibilities more ethical questions are being raised as well.

Blog Post Author: Dani Kaprielian, Section 124-25.

Article Citation:
Young, Susan. “A Brave New World of Prenatal DNA Sequencing.” MIT Technology Review. 30 January 2013. Web. February 2013. <http://www.technologyreview.com/news/510181/a-brave-new-world-of-prenatal-dna-sequencing/>

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