Do read this. It outlines the massive scope of the problem in the first place. But it also points out the inherent problem with the “recyclability” of plastic in the first place:
But even when plastics do get recycled, in the vast majority of cases, recycling only kicks the can down the road one generation by creating a product that can’t or won’t (because of economic constraints) be recycled again. In short, the vast majority of the recycling industry isn’t doing anything to solve marine plastic pollution, and for the most part, recycling is just creating a secondary market for waste. Even if the economics of Slat’s Ocean Cleanup Array didn’t further impede its viability, more plastic would still be entering the ocean than his device would pull out. Placing fees on producers of virgin plastics, and giving breaks to those who use 100% recycled content or are actively working towards it, would help to balance this equation out and would be great news for the ocean.
What is a phage? A phage or more accurately a bacteriophage, is a virus that infects bacteria. You can read more about phages in Rajini’s post. Phage display libraries use phages to screen for peptides for diagnosis or treatment.
❈ What is a peptide?
Peptides are short chains (polymers) of amino acids. Think of peptides as the building blocks for proteins. So DNA gets translated into amino acids via mRNA, which make up peptides, which combine to make proteins. That’s an oversimplification but it’s easy to get the picture.
George P. Smith at the University of Missouri developed phage display in 1985. He figured out that bacteriophages could be modified to incorporate “foreign” DNA and translate that to a peptide on their surface, hence the “display” aspect. After incorporating a DNA sequence into a phage, it can display the corresponding peptide on its surface. Why is that important and how can we take advantage of that? You can create a whole library of phages and see which phage has the best targeting for your particular model/system.
❈ Antibodies
You probably know that antibodies are part of the immune system and that they are specific for an antigen, e.g. bacterium. The thinking is that if you can make an antibody for say a particular tumor or protein involved with Alzheimer’s Disease, you could attach a therapeutic or diagnostic agent. Say you have such an antibody. You add a fluorescent component or radioactive element to make it diagnostic. Where ever the antibody binds, you will be able to image. Alternatively, say you take the antibody and add a drug so that the drug is now targeted. You can lower the dose because you don’t need to flood the whole body. So why doesn’t that really work? It has been tried. Antibodies are specific but have poor clearance and are bulky. When you have to add something to them, either a diagnostic or therapeutic component, it only gets more bulky, maybe too bulky to cross the blood brain barrier or too bulky to be cleared from the body in a reasonable time, so you end up with more side effects.
If you search Google Scholar for RGD (Arginine-Glycine-Aspartic acid) you’ll find over 50,000 hits. RGD is a peptide that’s associated with integrins. Integrins are cell surface receptors that are involved with cell signaling, for example in wound healing and cancer. Since a phage is smaller than an antibody, you can imagine that a phage display should be more effective than an antibody in terms of clearance, especially after adding a diagnostic or therapeutic agent as compared to an antibody.
❈ Radio labeled phage
Say you create a phage that presents a peptide that’s specific for a certain integrin. You add a radioisotope and test it against a tumor that has a lot of those integrins. That’s what’s shown in the picture below. A phage that was designed to bind with an alpha V beta 6 integrin with indium-111, which is a gamma radiation emitting isotope, was used in a mouse model with two tumor types. The tumor on the left side is negative for the alpha V beta 6 integrin and the right side is positive. You can see that the indium-111 labeled phage is accumulating on the right but not the left. The histogram shows the accumulation of radioactivity, i.e., labeled phage, for the positive vs. negative alpha V beta 6 tumors.
Sources:
Structural guided scaffold phage display libraries as a source of bio-therapeutics.
You don’t love science, you’re looking at its butt when it walks by. That sums up my feelings on a lot of the IFLS type shares. I have a passion for science and science outreach. Nic Hammond jokingly asked on his share of the Cyanide and Happiness cartoon, Do you even science, Bro?
Don’t get me wrong, I’m pleased that people are interested in science. What I’m annoyed with is the flashy, hyped, hipster style science related posts. In this Twitter/SMS-speak world, where people’s attention span is about 1 minute, not many people take the time to fully read any science posts. They plus the flashy image or hyped up title and that’s it. A while ago I found an image that looked photoshopped so I started thinking about the physics of it and wrote a post about it. How many of the IFLS people shared the original image/post versus my version that discussed why it was probably photoshopped? If you really F@^king love science, did you try the experiment yourself? You only need a glass and water. I’m sorry if this comes across as jealousy or sour grapes. That’s not my intention.
It takes a lot of work to do science and take the time to share it in layman’s terms. It’s also very rewarding when we get positive discussions. A lot of us, like Buddhini, Rajini Rao Allison Sekuler , Carissa Braun , Brian Koberlein etc work hard doing science and work equally hard sharing it on social media (that’s not meant to be an exhaustive list by any stretch).
We are working on breaking out of the stereotype that scientist are boring, white lab coat wearing, nerds. There is nothing wrong with nerds. I’m just not a fan of the trying to be nerdy to be ironic and hip. Nerd Nite (http://nerdnite.com/) is actually a really cool idea. I’d love to expand Nerd Nite to Google Hangouts. If you are passionate about something, share it with all the gory details but let’s skip some of the jargon.
Here’s an old post about the scientist stereotype.
There is still work to do to get people really excited and involved with science. As a scientist, I have to look at my own evidence, and my science posts are dwarfed by my posts of drivel.
So if you really F@^king Love Science, try doing some science. Try engaging with some scientists here. Better yet, tell your legislative representative to support science with more research funding.
Brazil – Dozens of bioluminescent mushrooms sprout on a dead log, green stems glowing in the light of a full moon. This species – Mycena lucentipes – grows on the wood of flowering trees in the rain forests of Brazil and Puerto Rico. Its edibility is unknown.
I couldn’t agree more with Hannah Grimm. I’ve had people link to the Harvard study as “proof” that neonicotinoids are the cause of colony collapse disorder in my previous post, where it is discussed in more detail:
*Bad Science: pushing your agenda instead of looking for real causes*
There’s been a lot of talk recently about Colony Collapse Disorder, the mysterious disappearances of bees from their hives, a serious problem that threatens American food production. There’s a number of suspects: Varroa mites, which spread disease; monocultures, which lead to a lack of food when your lone crop isn’t in bloom; and pesticides, which (obviously) kill insects. A particular type of insecticide, the neonicotinoids, have recently fallen under suspicion after a Harvard researcher published a study in which bees fed syrup laced with the pesticide died.
Just one problem: he fed the bees a concentration of poison hundreds of times what they’d experience in the real world. The study is the equivalent of injecting people with pure mercury and then claiming that tuna fish sandwiches, with their trace amounts of the toxin, are killing us. It’s like lacing your test subject’s food with Arsenic and then claiming that apples are bad for you because you might swallow the occasional seed!
This kind of bad science isn’t harmless. It takes attention away from actual solutions. At the end of the day, it’s a lot easier to feel smug and buy your organic, pesticide-free produce than it is to ask whether that organic farmer is monoculturing or not. What happens when your heirloom tomatoes aren’t in bloom? What will the bees eat then? Odds are, CCD is just caused by starvation caused by all of the nearby plants blooming simultaneously. Preserving habitat, planting wildflowers or having different crops are hard solutions, but they’re the ones that might actual save the bees.
It’s time we stop feeling smug about our pesticide usage and ask what’s really killing the bees.
I’m vaguely familiar with the myth that your pee is essentially sterile. However, it turns out to be false. Dr. Linda Brubaker and colleagues examined the urine of 41 overactive bladder female patients and 24 control female patients. 48 of 65 of samples were negative, i.e., so-called sterile using standard urine culture procedures. However, using an expanded procedure, 80% of the samples were found to contain bacteria. I’m not a molecular biologist so I won’t try to explain the difference between the standard and expanded culture procedures. The interesting thing is that overactive bladder might be linked to changes in your microbiome. Again, we are learning more and more about the importance of our microbiome.
I don’t know if I would go diving in the “black hole” but the video is pretty cool.
#ScienceSunday
Originally shared by ScienceSunday
Let’s get this strait
Bones of a teenage girl from about 13,000 years ago, suggest that there was only one migration across the Bering Strait. Differences in facial features are thought to be due to evolution and not due to two distinctly different groups migrating to North America. Watch the video below of the discovery of the skeleton in the “black hole”. The news article is here:
Kelly Rothe decided to get a bilateral prophylactic mastectomy, i.e. preventative removal of both breasts. She’s a big Red Wings fan (who isn’t) and in particular, a big fan of goaltender Jimmy Howard. Because the Red Wings organization is so classy, the video below shows what they did for this young lady.
The rest of this post focuses on the science. You may recall that kerfuffle when Angelina Jolie decided to get a bilateral prophylactic mastectomy. So here is some info and links to hopefully inform you a bit more.
I’m not sure where Kelly get the 85% risk from. However, the risk is certainly higher for some women with specific genetic profiles.
In two studies, the estimated risks of developing breast cancer by age 70 years were 55 to 65 percent for women who carry a deleterious mutation in the BRCA1 gene and 45 to 47 percent for women who carry a deleterious mutation in the BRCA2 gene (6,7). Estimates of the lifetime risk of breast cancer for women with Cowden syndrome, which is caused by certain mutations in the PTEN gene, range from 25 to 50 percent (8,9) or higher (10), and for women with Li-Fraumeni syndrome, which is caused by certain mutations in the TP53 gene, from 49 to 60 percent (11). (By contrast, the lifetime risk of breast cancer for the average American woman is about 12 percent.)
At a seminar about BRCA1 and BRCA2, Dr. Olopade shared a story about finding women in South America that had unknown Jewish ancestors from Spain. The South American women were carriers of BRCA mutations and did not know that their Jewish ancestors fled from Spain to South America.
Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers.
Today in the modern world we take freezers, and the frozen results of freezers for granted. But in ancient times, cold drinks, frozen desserts, and chilled tropical cocktails were a luxury unknown to most people. However the idea of artificially freezing goods is nothing new. As far back as 400 BC, the ancient Persians built special freezers called yakhchals. Yakhchals were large buildings used for storage of ice and foodstuffs during the hot Persian summers. Typically they were around 60 feet tall, and had a large subterranean storage space dug out from under it. The Yakhchal itself was made from a special type of mud clay called sarooj which was composed of clay, sand, lime, goat hair, egg whites, and ash mixed in a special proportion which made it extremely resistant to heat transfer. In other words the inside stayed cool, while heat from the outside was prevented from entering the building because of the thick insulated walls. This combined with the subterranean storage ensured that whatever goods were stored in the pit stayed cool, as temperatures below ground level are usually around the 60 to 65 degree Fahrenheit range. However, these designs were not what made a yakhchal a freezer. There was one other brilliant design feature which ensured that the yakhchal would stay frosty all year long.
At the top of the dome was a small hole, or series of small holes called windcatchers. Typically windcatchers were pointed in the direction of the prevailing winds. Due to its conical shape there was always a negative pressure gradient inside the yakhchal. According to Bernoulli’s principle air flow at a high pressure will always move toward areas of low pressure. Thus air from the outside was constantly flowing through the yakhchal. In addition, according to the Venturi effect, whenever air flows through a small hole, the smaller the hole, the greater the speed of the flow. The small hole, or series of holes of the yakhchal ensured that air passed into it at great speed. While the air itself wasn’t cool, the speed of the flow at which it was being moved into and through the yakhchal created temperatures that were below freezing. Typically the windcatchers were cut in such a way that the incoming jet of air would be directed onto the storage pit.
The ancient Persians primarily used their yakhchals for storing ice and foodstuffs. During the summer, Persian nobles often enjoyed a frozen treat called faloodeh (below), which is made from thin noodles with syrup made from sugar and rose water, then flavored with lemon, lime, fruits, almond, pistachio, and other flavorings. Due to the Persian’s freezing technology, faloodeh (which is still popular today) goes down in history as one of the first frozen desserts. The practice of building and using yakhchals continued up to the 20th century, when they were eventually replaced with modern freezers and refrigerators.
h/t Letha McGarity for triggering this lazy #ScienceSunday post about Alzheimer’s Disease (AD). Many of you may have heard of amyloid plaques and how patients with AD have brains riddled with amyloid plaques. In fact, Auguste Deter pictured below, was the first AD patient and her brain was riddled with what we now know are amyloid plaques.
However, I’m going to do a lazy post and direct you to a series of videos here:
Full disclosure, I collaborate with Dr. Klein. However, he really is a great scientist and a great guy. In the videos he’ll explain how the hippocampus plays a role and how oligomers are the real story.
