In chat, e-mails, and some forum posts, I hear about new advances in DNA origami, novels involving chromosomes, and jokes on paper-writing. How about collecting these links into one thread -- this one?
I'll try to get this thread to be 'sticky' so that its one of the first posts you see when you enter getsat.
Earlier this week jandersonlee shared the happy news on the Nobel Price in chemistry given for High-Resolution Microscopy with me.
I have earlier posted material on awesome microscope breakthroughs, but this one is special. When watching cells, electron microscopes can give great detail. However if the preparation process for watching the cell doesn't kill it, surely the beam of electrons will.
What makes this new microscope something special, is that it makes it possible to observe cells on a nano scale - while they are alive. So now it is possible to watch living cells in living organisms to a far greater detail than ever before. (Poor mouse...)
Easy introduction by Periodic Table of videos
Here is the video jandersonlee sent me, which goes into great detail on why and how the microscope technique works.
Its an educational video from iBiology. They have many other great ones on different kind of microscopes and a huge range of science topics.
Time for some science stories in the Halloween department.
Mat and Machinelves have been sharing this story with me on an algae virus thought to be capable of making the brain of the human it infect process visual information 10% slower.
A Virus Found In Lakes May Be Literally Changing The Way People Think
This reminds me of the cat parasite Toxo which Jaroslav Flegr has long been studying and writing about. He has been making the case for that this parasite being in the mind bending department, with control over the brain of its human host to a degree where it induces behavioral changes.
How Your Cat Is Making You Crazy
He by the way won the Ig Nobel prize this year for his fine work.
Iroppy shared a great article on viruses among them Ebola, which is a fascinating read.
Ebola and the Vast Viral Universe
Here are two small excerpts:
“Viruses are not just these threatening or annoying parasitic agents,” he added. “They’re the creative front of biology, where things get figured out, and they always have been.”
"Viruses have managed to infiltrate the cells of every life form known to science. They infect animals, plants, bacteria, slime mold, even larger viruses."
Last some Halloween fun - the science way:
Fly larvae with fluorescence
I wanted to know a bit more about this green florescent protein, that is one of our play mates in the MS2 labs. It basically make our RNA glow if it folds as it should. How well, gets read out from how intensive it glows.
For odd reasons, I jumped the first WIKI link, and went to the next. This landed me on a special page with an awesome description.
The story about the Green Fluorescent Protein
I read the whole thing. And I couldn't shake the feeling that it kind of reminded me of something. So I decided to check the author. And there he was, David Goodsell, who made the most beautiful hand drawn images of the cell and its machinery. I earlier made an introduction to his book:
The Machinery of life
But the story gets even better. This Green Glowing Protein is the protein of the month. This means that there has basically been written an article on a protein each month, for the protein data base. So now there is a treasure trove of fine small protein stories, which is practically the natural extension of Goodsell's book about the workings of the cell.
This site holds the rest of the stories:
Molecules of the month
Hereby the tip is passed on. Enjoy!
For the further interested
I also found an article which describes both the glow in the dark protein and the MS2 hairpin we use. And how they were discovered and made to work together.
Live and in color
It has long been costume among scientists to make knock out mice. Where one gene gets deleted to see what effect it has on the mouse. One reason for this is to learn about human disease. For obvious ethical reasons one can not carry out gene knock out in humans.
For many species genes are so similar, that they are virtually interchangeable. Man and mouse shares most their genes.
"About 99 percent of genes in humans have counterparts in the mouse," said Eric Lander... (Mice, men share 99 percent of genes)
So big was my surprise when I just read about the news from the ongoing Iceland genome project deCODE. They have found many humans with naturally occurring gene knockouts, where a gene was missing from both the mothers and fathers side. Nature already did the experiment - although no surprise there. But before knockouts genes had been harder locating in humans. Also not all deleted genes, seemed to cause problems when they go missing. As one of the article headlines states:
1000 genes you can live without
You can read more background on the project:
Why Iceland Is the World’s Greatest Genetic Laboratory
Here is the original science paper on the human gene knockouts - caused by nature.
Identification of a large set of rare complete human knockouts
This find is going to help speed up ability to gain knowledge useful for creating medicine, where the lack of a gene causes problems, plus open up for earlier diagnosis.
Should be good news for some of the mice too.
Elf sent me an viral Easter egg. Virus responsible for coloring hen eggs blue. Even better, should be benevolent.
Here are a few easier read articles:
Find A Blue Chicken Egg? Congrats, Your Chicken Has A Virus
Surprise virus caused blue chicken eggs
Plus the article Elf shared, that holds more details:
Let a Virus Paint Your Eggs in Blue
Thumbs for viral Easter egg coloration!
Ok, that introduction takes some explanation. :)
Messenger RNA (mRNA) have been thought to be messy and disordered and not worth using as drug targets. But that may be about to change.
One cool scientist has figured that a protein called elF3 has been found to target specific mRNA's that are also involved in cancer.
New target for anticancer drugs: RNA
Thx to jandersonlee for sending me the article. And as he later commented back:
"It's EIF3 (or rather eIF3) not ELF3 (eukaryotic initiation factor 3). I thought you might like the visual pun of it though."
He was absolutely right about that. :)
I recently read another very interesting article about that some types of mRNA's used for particular functions, indeed have a particular structure. It is also about relationship between mRNA count and amount of proteins made and on the half life of mRNA. This paper is so awesome, that its a born classic.
I have earlier been wondering about just how mRNA behaved, when it came to forming structure.
This is going to open a lot of legal doors for medical application of our gizmos.
A detail from the National Cancer Institute seems especially pertinent:
"Identifying or developing an array of treatments that can be matched to the molecular features of a tumor to successfully control the disease."
Might Eterna players one day be solving their own meds?
Mat sent me some real promising news about microRNA being used against mesothelioma, a very dangerous form of lung cancer that is caused by work with asbestos.
Researchers have successfully shrunk mesothelioma tumours in a patient
For anyone who wish to help with figuring out the workings of microRNA, here is an open eterna microRNA lab:
miRNA Switch Lab - Round 3
Also check out these interesting videos about MicroRNA:
Around two years back, Zanna shared a wonderful story in the chat about a little girl who was dead ill of leukemia but got cured by having a weakened HIV virus reprogram her immune system to go fight of the cancer.
And I thought, What?!!! - They just didn't do that... I had my doubts until I had read more.
Recently a friend of mine made me aware there was made a documentary now about these pioneer doctors, who made this possible. The kid is the documentary and healthy now. :)
Get an intro to the documentary, learn more about the background of it or read more about the future perspective of this kind of treatment here:
Vice - Killing Cancer
Tuberculosis On Target
Machinelves shared a cool article on quick diagnostics method with potential for a broad range of detection of both bacterial and viral diseases, just using antibodies, DNA and electricity.
Last summer the podcast This Week In Microbiology interviewed a scientist who works on making a fluorescence detecting method accurate enough for detecting tuberculosis. They still had some problems then, the episode is somewhat technical, but it is cosy listening.
Also I have collected some resources, if you wish to learn more about Tuberculosis, how it has affected our world in the past and how it is still one of the real big killers.
We are working alongside a lot of scientists and taking aim at Tuberculosis to help make the world a better place.
Machinelves recently shared a couple of interesting New York Times articles on medicine and prizing. It sounded like a rude case of overpricing.
Now I have heard that developing of a drug can cost in the range of billions. For every successful drug, there are a big number of failed attempts - that still carries a very high price tag. So drug makers do need to take in a lot of money as they need to be able to pay for their failures also.
But the story in the New York times was still different. It reminded me of a disturbing pattern revealed in a documentary called The Super Rich And Us by Jacques Peretti, that I saw recently.
I basically see the same tactics in use in this latest medicine story. Buy something that everybody needs, use it as an investment object and skim as much profit as possible on something that people are dependent on. Except here it was done to something that a smaller group needs - but here they need it desperately.
Larry Wilmore over at The Nightly show, did a not so diplomatic, but hilarious covering on the medicine overpricing case. Google it, if you want to check it out. :)
Pope Francis in NYC & Deadly Selfies, The Nightly Show 24 sep 2015
To make a check on what was up and down in this story, I decided to turn to my favorite chemist blogger. (Thx to Quasispecies for the introduction).
I have been following Derek Lowe on and off during my Eterna years. First because he makes me laugh and second because he makes me think. Yeah, an Ig Nobel paraphrasing. ;)
He is involved in medicine making and is sharing his thoughts on the industry and his work in a understandable manner.
He wrote a post that I think put what happened well in perspective.
I on the other hand is writing this post to put in perspective that we are soon to join forces with scientists in a company to work on making diagnostics. First and foremost, it’s cool that they want to play with us. :)
However for the future, whatever it may bring Eterna, I wish to have EternaBot and what work we and I do, available to all who wishes to make medicine and be of help to humankind. After all that is why I became a citizen scientist in the first place.
I wish our work to be of most help possible. With no one being able to later put a big price tag on our stuff or medicine developed based on our stuff and preventing others from using it for good.
Here are a few things you can do in the meantime till eterna get started for real.
World Community Grid - AKA the coolest BOINC citizen science computing project yet, has just put up tuberculosis as one of the illnesses targeted, beside cancer and AIDS.
Help stop TB
For eterna things to do to prepare for the coming tuberculosis labs, you can give Nando's tuberculosis training puzzles a go. The TB related puzzles carrying an A, B and or C in their title.
Also the currently open lab is helping us getting prepared for what to do for catching RNA sequences - which is what we will be doing when we get the tuberculosis labs. It will just be some different sequences.
I have been complaining about paywalled papers with regular intervals. Often accompanied with a video like Open Access Explained! from PHD Comics.
Or stating things like: If it isn't accessible, it isn't relevant. ;)
Omei recently shared a nice trick on how to raise ones chance of getting access to whatever paper one is currently interested in. Here it comes:
"What I did to find this was to search by the paper's name in Google Scholar, and then click on the *All 11 versions* link. I find I can often get full text of a paper (which may not be identical to the revision published in the journal) by looking for alternate sources."
Also I have taken note that certain publishers are in the habit of sharing a free version, which means I go for those links first.
I have been complaining less about inaccessible papers lately - since my subjective observation says that more papers seems to be available - with no questions asked. :)
As a big thank you and celebration, here is a word cloud of the last 5 years of fun posts, with our names and filler words removed so we can see all the cool science topics together.
You can click on it for a full resolution image, since it will probably be fuzzy in this post:
Inhibiting LucA gene disables production of key Tuberculosis protein
“... the protein encoded by the gene, LucA, is an integral membrane protein, and is required for fatty acid and cholesterol uptake in Mtb.
... LucA stabilizes the transporters ... if removed, causes Mce1 and Mce4 to fall apart.
... LucA is required for full virulence of Mtb in vivo
... The next step for VanderVen and his team will be to investigate drugs that inhibit LucA. “This is ideal, because LucA is a bottleneck and inhibiting this protein with a chemical could disable two pathways at a time,” said VanderVen. As it happens, “we already have discovered chemicals that do just that, so the next step will be to begin refining these as potential therapeutics.”
Thx to Eternacac for volontering some serious source about CRISPR in relation to our coming lab. I will share the best I have stumbled across on the topic so far.
The new about CRISPR in comparison to earlier techniques are the radical changes one could achieve. Here it could be real healing, not just trying to take care of the worst symptoms of a disease. Which is often what is done today, for lack of better tools and medicine.
Using CRISPR to Treat Blindness by Columbia Medicine
There are already positive results with existing genetherepy
What is CRISPR? by Bozeman Science
What is CRISPR & How Could It Edit Your DNA? by DNEWS
CRISPR and the Future of Human Evolution by It's okay to be smart
Still I think the best introduction to CRISPR I have ever read, is the one I shared in a past blog. In his article "The virus that learns" Carl Zimmer gives a beautiful backstory of where CRISPR originally were found - in the bacterial and viral world - and what it does. This is the most through description I have seen that is still very understandable from a lay perspective.
CRISPR is a bacterial immune defence system, but viruses can have a immune system too, and that was what caught my interest. Basically humans have just achieved what powers bacteria and viruses have held for a long time. Viruses swap in genes, bacteria try swap them out again. The human manipulated version of CRISPR can do both.
Sciency podcasts that touch on CRISPR
Just like viruses has been used to figure out the workings of the cell, flourescence has been used to see where what goes when, CRISPR is a new strong tool for scientists to investigate and answering questions. Also it has potential to cure countless diseases and give people better lives.
TWiV 365: Blood, feuds, and a foodborne disease
BacterioFiles 195 - CRISPR/Cas Cuts Cancer Causers
TWiP 118: Crispr capers with Toxoplasma
CRISPR and the future
Will CRISPR be misused? With my knowledge of humans, yes, unfortunately. But probably the good done, will outrank the bad, on a large scale. Just like with all other medicine - medicine can be use to kill with - but most of the time it is put to its proper use for helping fellow human beings.
Neil deGrasse Tyson On CRISPR Gene Editing | NBC News
On a curious last note
Eterna plans on combining CRISPR with switches. One thing I find really funny is that CRISPR has palindromic sequences inside it and I have noticed about switches, that they harbour repeat sequence with a tendency towards palindromic sequences too. I wonder if we can use these two palindromic facts for something. :)
The 90/10 gap was a term made to highlight an observed fundamental injustice in how medical funding were distributed. That 90% of the funding in medical research, goes to 10% of the medical problems. Plus the problems that tended to get most attention were the ones that affected rich people more.
In other words, there are done more research in baldness, than in tuberculosis. Hair is a nice thing to have, but life is too. :)
There are medical problems receiving even less attention than the big killers, like tuberculosis and malaria. Diseases that only a few people around the world have.
I read an article about a girl with a really rare disease, and her fight for getting attention to the disease.
The Girl Who Turned to Bone by Carl Zimmer
This is also a story about how uncovering the workings of a rare disease, may end up providing the key to solve more common medical problems.
An enzyme will, sometimes, change an A to an I ( which is recognized as a G) when DNA is transcribed (not sure if this is the correct term) to RNA.
An A is fairly stable (only pairs with U). A G can pair with a U or a C.
I'm wondering if this might set up a switch when Adenosine is replaced with Inosine.
Now I'm curious what switches the enzyme. Curiosity, it never ends:)
I sometimes gets asked about what difference our work at eterna has made. Some of you thinking that what you have contributed may not have mattered at all.
So why does it taking so much time before we see results of our work?
There are a bunch of different reasons.
- There is waiting from lab design to lab results.
- We are trying things that hasn't always been tried before. That goes for the scientists and their equipment too.
- It also has to do with what we have been toying with up till we got the TB labs, are mainly in the basic research department.
I have found a fine video that explains basic research and why it is important.
The super power we hold through the Eterna game, is the power to find out stuff. Either if it is by accident or on purpose. It really doesn't matter.
Put your ideas in play in the lab. Use your lab slots!
I saw some wonderful news the other day. About a doctor who saw a big problem, kept thinking about it and eventually came up with an alternative solution.
This doctor didn't wait around for others to solve the problem for him. He did something.
How a shampoo bottle is saving young lives
Here in EteRNA we are players coming from all walks of life. We are not doctors. (At least most of us are not) We are not the normally approved and vetted option for solving medical problems. Yet we have got a real shot at solving some serious problems.
We are working right now to put better tools in the hands of researchers, doctors and healthcare personal in the future. It won't happen tomorrow, and that is what can sometimes be really frustrating from a player perspective. We want things happening preferably here and now. But as I have tried show with some of the posts above, things in relation to medicine takes time. A lot of time.
Some of the results of what we are doing now, it make take 2, 5 or 10 years down the road for us to see the results of. However what I am in no doubt about is that one day what we are doing in EteRNA is going to save lives. We are the alternative solution.
So hang in there! :)