Potentially Safe Additive to Wine that Prevents Bad Taste

Apathy killed the cat

Whenever I am at my parents' house, I always partake in nightly wine tasting with them. That feeling of warmth going down my throat, that fine crisp taste when swishing it around in my mouth, it's perfect. My parents have a wine rack, and each time I visit I try a different bottle. I like to believe I am pretty indifferent to wines, as I don't usually notice big differences that could set me off of the particular brand, but sometimes wine just loses it's taste, and it's scent, making it undrinkable. This is caused by oxidation. Oxygen can enter even through a corked bottle, binding to metals such as iron to create a foul taste and/or smell. Luckily, scientists recently found a possible additive to wine that will slow the oxidation process. Two oxidation states are found in wine: iron(II)oxide and iron(III)oxide. Since both are iron, chelating agents (molecules that bind metal ions) for both states were looked at. These agents included Ferrozine, bipyridine, EDTA, and phytic acid. All chelating agents inhibited oxidation. To arrive at the conclusion that these molecules were in fact working chelators, the scientists had to measure the concentration of iron in white pinot gris wine, and then measure the oxidation that occurred when chelating agents were put in. Previous methods to get rid of the metals in the wine that caused oxidation to occur were too expensive to be the solution to the problem. However, phytic acid seems to be the best choice of chelating agent, as it is safe for consumption. My question to you is this: Why should scientists focus on this particular problem in wines? Do you think money would be better spent on human cures rather than wine cures?

For more information, click here.

Familial Alzheimer's: How Stem Cells Could Help Identify Its Origins

Alzheimer's isn't something to joke about. Never forget that!

Alzheimer's disease is a common 'forgetting' disease among older people. One type of AD, familial AD, is passed down from family members. Through the use of pluripotent stem cells, a team of scientists were able to understand more clearly the origins of familial AD by studying the protein presenilin 1 (PS1). PS1 is an enzymatic protein that regulates gamma secretase, which cleaves amyloid precursor proteins (APPs). The functions of APP are not entirely known, but it is believed that the cleaved products of APP, amyloid betas, can cause plaques to form that can kill neurons in the brain if cleaved wrong, most likely causing AD. The scientists discovered that mutant forms of PS1 caused twice the amount of APP that were cut wrong. Here is where the pluripotent stem cells came in. Neurons that were derived from Craig Ventor's own stem cells were created, each with different alleles of the PSEN1 mutant gene. This helped them figure out what effects different mutations had on the neurological level. My question to you is this: Pluripotent stem cells are stem cells that have the potential to form any other type of cell it needs to in the body, and because it has the potential, it is still in its infancy at the time and usually is taken from human embryos. However, because the stem cells used here were derived from an adult, and not from a human embryo, do you believe stem cells are now significant in scientific experimentation?

For more information, click here.

Blog 10.2 Mitotic Chromosome 3-Dimensional Structure Mapping

5-year-old's rendition of the human chromosome

Well I couldn't wait to write about this one, so I am doing another blog for this week! Finally, after approximately one and a half centuries of debate, the scientists at MIT pinpointed a universal method in all types of cells of condensed mitotic chromosome organization. Before this, scientists had no way of knowing the exact method of how DNA was condensed in the chromosome, as microscopes were not technically advanced enough to observe the process, which led to different suggested methods. It was already known that DNA had to be tightly condensed in order for successful transportation to daughter cells, but how it actually folded was debatable. The most common textbook explanation of how DNA was condensed was via multifold coiling, where coils form coils form coils (supercoils). However, there was another explanation of how DNA was condensed, stating that a series of loops were formed, attaching to a linear axial structure, ultimately becoming the chromosomal backbone. To solve this dilemma, scientists used chromosomal conformation capture to find exact contact points on different chromosomes during the metaphase part of mitosis, creating 3D models from contact point spatial arrangement. After comparing this model to the two previously suggested models, we can now throw the multifold coiling method out the window. In actuality, the chromosome was compacted in two phases: first to form loops with a circumference of approximately 100,000 base pairs, and second to tightly compress these loops like a slinky. What's strange about this is that condensed DNA is not as highly organized as we had originally thought it to be. Loops formed pretty much randomly, meaning that condensing is variable. My question to you is this: What things can scientists experiment on once the entire mitotic chromosome or
ganization process is understood?

For more information, click here.

Blog 10.1 Gastric Cancer is Lacto(ferricin) Intolerant

A cow goes, "Moooooolecular Biology"

Scientists have recently found a way to kill human stomach cancer cells using an enzyme found in cow milk called lactoferricin B25, which is a known antimicrobial and anticancer agent. Previously, like other cancers, gastric cancers have usually only been treated at an early stage via chemotherapy. Using lactoferricin B peptide fragments, the B25 fragment was the only peptide found to effectively kill human gastric adenocarcinoma cells. Scientists saw that the cells lost their ability to adhere to walls of the cell plates when lactoferricin B25 was present. A bit later, the cells started to die by, first, both apoptosis (cell suicide) and autophagy, then solely by apoptosis. It was also found that a cleaved key protein called Beclin-1 increased gradually in the presence of the lactoferricin B25. This is a good thing, as Beclin-1 is linked to tumor inhibition, which causes the anticancer effects of lactoferricin to increase. My question to you is this: How do you think scientists will/should go about experimenting with this potential cancer curing peptide (for example: testing on monkeys, testing on mice, or even straight to testing on humans)? If you can, explain why you think they will/should do this.

To read more about this, click here.

Stopping The Superbugs For Good

It's a bird, it's a plane, no... it's superbug!

Every year, new flu shots are being created to take out the new and improved influenza viruses that descended from the resistant few who survived the year before. This example of resistance increase in viruses is one of the milder cases. You could see where being resistant to everything could be a problem. Well now there is hope. Scientists recently suggested a possible solution to the problem would be to use antimicrobial peptides (AMPs) in order to poke holes in the cell membrane, holes that expand until the cell bursts. In order to observe such a small and quick action, however, the scientists had to generate and program their own AMP and get it to bind to a supported lipid bilayer (SLB) so that they could facilitate when the AMP would bind, therefore allowing the expansion of nanometer-sized pores to be seen and tested. After studying the process of pore expansion in enough detail, it was suggested that when the first AMP binds to the membrane, it triggers a response to other AMPs to start binding to the membrane, causing multiple pore expansions. My question to you is this: What makes AMP so special? Why wouldn't viral resistance come into play again and render AMP useless? This question has a specific answer, but I'd like to see some of your opinions as well.

For more information, click here.

You Are What You Eat?

Awww..... can you say, "KSR2"?

It's not uncommon to see an obese individual walking about anymore, what with all the fast food and door-to-door pizza deliveries. Well sometimes it really  isn't that person's fault. In fact, scientists recently discovered the gene (KSR2) that affects appetite and metabolism when mutations occur.  These mutations can cause metabolism to slow, and on top of that increase the desire to eat: A DOUBLE WHAMMY!!! What first led scientists to this conclusion was that when taking the KSR2 gene out of mice completely, obesity occurred. KSR2 was then studied in humans, which showed the gene worked similarly to the mice (Don't worry, I'm sure they DID NOT take the entire gene out, that would just be unethical). KSR2 was continuously observed, with mutations causing defects such as lower heart rate and severe resistance to insulin. Scientists began testing mutation-correcting (NOT gene-altering) drugs until one drug in particular, metformin, solved the problem of low fatty acid oxidation levels. My question to you is this: It seems like every week mutations in genes are being corrected for by seemingly simple methods. Could science REALLY be evolving that fast, or are there some factors being overlooked by the optimistic bloggers writing about these research stories?

For more information, click here for the research article.

Inflammatory Bowel Disease: Road to the Cure

Many of us have heard of Inflammatory Bowel Disease, right? Well, a team of scientists recently discovered a new variety of stem cells in the gut of a mouse embryo, cells not like those previously described in the gut. They knew they were able to grow the cells at just the right conditions for them to form mature intestinal tissue, and with this knowledge they transplanted these cells into adult mice with Inflammatory Bowel Disease. It took just 3 hours for the cells to repair infected areas of the gut. Scientists took human stem cells similar to the mice stem cells and are setting up another experiment to see whether the same method works for humans. Let's stay hopeful. My question to you is this: Do you think treatment could really have been this easy all along? Why hasn't this been done before now?

The Research paper can be found here.

Ancient DNA Repairs Itself

Markus Dieser

Brent Cristner

Science uses DNA as a means of identifying, learning about, and dealing with organisms. This makes DNA very important, and therefore crucial in the understanding of evolutionary development over long periods of time. But how does DNA actually stay intact for such long periods? The answer is simple: DNA repair mechanisms. Before I get in to what that means, let me talk about how this answer came to be realized. An LSU professor by the name of Brent Christner, along with his postdoctoral research associate Markus Dieser had already been working with bacteria within ice. They knew that DNA gradually decays, but that somehow they could take virtually perfect DNA from a sample of ~750,000 year old bacteria that was trapped in low layers of ice. Could the DNA be repairing itself, even within such molecule-slowing conditions? By exposing samples of specimens in Siberian permafrost to ionizing radiation (the dosage of which was felt ~250,000 years ago, about the time this permafrost layer was formed) to break up the DNA into small, unidentifiable pieces. These fragments were stored for two years in incubation. Over these two years, the DNA gradually put itself together. My question to you is this: How could this information be helpful to science in the long run?

For more information, here is a link to the research: http://aem.asm.org/content/early/2013/09/23/AEM.02845-13

Lake of Stone

Remember the fable of Medusa? Once you saw her face, your body turned to stone.

Don't look directly at her

An obvious fiction, I mean how can someone just turn into stone?

I told you not to look at her

The answer: calcification. Are you in danger of it? Most likely you're not, unless you live in Lake Natron. However, calcification does not happen overnight, as some stories say. Nick Brandt, a photographer of zoological themes, recently took grim-looking photos of calcified birds he had found washed up on the shores of Lake Natron. His photos depict birds posed perching on sticks, and floating on the sodium-salted waters. Though Brandt knows that the lake is not completely barren, and that just touching the liquid will not immediately cause your body to turn to stone, his pictures seem to suggest the worst. Why birds (and bats)  and not other forms of life you may ask. Well, Brandt suggests these flying creatures flew too close to the lake and fell into the water, unable to get back out. The cause of calcification in the lake is due to the high alkalinity of the water (around a pH of 10), and the high sodium salt content. However, flamingos are prevalent in these parts, along with two species of extremophilic bacteria. My question to you is this: What evolutionary trait could these flamingos possibly have that keeps them from calcifying?

Foldit

Have your parents ever told you when you were young that you should study hard so one day you could cure cancer and become famous? This saying is common from parents who push their kids to get off their butts and make a difference in the world. Few parents actually mean their sons or daughters must become a doctor, much less cure cancer, but what if I were to tell you there is a way that anyone, not just doctors, could contribute to a cure? Well before I do, know that there is not just one cancer that needs supervision. But, whatever the number, one common thing could help cure all or them: proteins... enzymes to be exact. Enter David Baker, a biochemist at the University of

Dr. David Baker, University of Washington

A typical Foldit protein structure

Washington. Baker figured that scientists studying the three-dimensional structure of proteins had already been educated about what to do and not to do in terms of folding a protein, but like musicians that sound good because they can't read music and therefore deviate from the normal patterns, the public might actually make more progress. Thus, he created Foldit, a downloadable computer game that allows players to mess around with the structure of proteins.... IN 3D! The game uses a score system that, unlike the standard video game, never reaches a limit. You are to fold the protein as compact as possible and yet still within the rules of natural folding. This game is MUCH more difficult than the previous three games I blogged about, but the feeling you get when your score rises is more fulfilling because you know you are actually discovering something original, and not preset. My question to you is this: I have listed the top four citizen science games (involving molecular study), but can you think of any more topics that involve molecular science that could be crowd-sourced? Leave answers in the comments below.

Eyewire

It's amazing what our own brain doesn't notice about itself. How am I typing this, and why have I decided to eat a sandwich consisting of a particular cheese on particular bread? It's questions like these that Neuroscientists are trying to find an answer for. However, many of these brain scientists are finding themselves at a wall on what to do next, as their are so many nerves in the brain that its hard to map out what controls what. But, what if the entire world were to help map it? Sebastian Seung thought about this and came up with a game in which you fill in cross sections of nerve tissue to map out a 3D image of the nerve you are looking at. It's called Eyewire, and it's available online for free. Your job is to look at a cube made up of tiny cross sections of nerve tissue in the retina, specifically the J-cell and its connections, and find the colored holes. These holes represent one line of connected nerves that the computer has colored in for you. The problem is, sometimes the computer has trouble indicating where a hole continues, and where a hole ends. That's where you come in. By sifting through the multiple layers of cross sections, you must color in the areas that the computer missed, and possibly delete the areas the computer colored wrong. Once all the holes in the cube are filled in, you can submit it and check how well you matched other players who mapped that particular cube. My question to you is this: What are some reasons that not all neuroscientists agree with this form of mapping out the brain?

Phylo

Ever wonder just how closely related humans are to chimpanzees? What about the similarities between a donkey and a horse? Questions like these are still being studied to this day, by scientists yet to find the full answer. Sure, it is easy to acknowledge outside resemblances between animals, but is there more to the picture than what meets the eye, say resemblances on the inside? There sure is. Lots more. They're called genes, and they're present in every living organism on the planet. There's only one problem: genes are too small to see with the naked eye. This makes it hard for the average Joe to picture such mind-boggling similarities between Man and Primate. Enter Phylo, a browser-based game that aims to distinguish common gene sequences of 3 or more species. The player (You) must match nucleotides from one species with as many nucleotides from another species as possible, but that's not all to the challenge: all nucleotides must stay in the order they were given to you. The point is not to match EVERY nucleotide by mixing the sequence up, but to take what is actually sequenced in each specimen and slide groups of nucleotides from one organism to similar chains in other organisms. The score you get is based on the number of matches made, and the number of spaces between groups of nucleotides (the less spaces made for matching, the less room for error). It may seem like jargon at first, but really it's simplicity allows for folks of all ages to try their hand at improving science. My question to you is this: Why do you think it is beneficial for science to get help from the public instead of relying on their own intuition and computer software? Leave comments below.

We're all familiar with RNA. There's the four nucleotides: Adenine, Guanine, Cytosine, and Uracil. Adenine always binds with Uracil and Guanine always binds with Cytosine, correct? WRONG! Actually in eteRNA, an online RNA-based puzzle game created by Rhiju Das, RNA is an ever-growing field of study, with it's complex binding sites and infinite possible sequence structures, and many of the "norms" of nucleotide bonding are thrown completely out the window. The goal of this browser-based game is to make a pre-shaped structure stable, using only certain combinations of Adenine, Guanine, Cytosine, and Uracil. Though this seems like the solutions would be limited and easy to uncover, there is much more you must be aware of. For example, say you figure that since G-C bonds are the strongest bonds, why not make all the bonds in the structure GC bonds. Well, the fact that GC bonds ARE very strong makes synthesizing the desired structure difficult, as Gs can bind to the wrong Cs and then be unable to split apart and reattach somewhere else. Obviously there are more strategies to RNA design, but I'll leave the puzzle-solving to you. This type of science game is know as Citizen Science: a REAL scientific experiment made fun and available to all people of any background. Do you think it is wise to let those who are not familiar with RNA to contribute? Leave your comments below.