Fun RNA and DNA science

General Science Discussion
102

Plants communicating via mRNA

Nascarnut shared an amazing article with me today.

Plants may use newly discovered language to communicate

Here is my favorite quote from the article, though it is all pretty mindblowing:

“His new work expands this scope of this exchange and examines the mRNA, or messenger RNA, which sends messages within cells telling them which actions to take, such as which proteins to code. It was thought that mRNA was very fragile and short-lived, so transferring it between species was unimaginable.”

And the plant internet just got even weirder.

Plants talk

I have earlier read fascinating stories about plants ability to communicate with each other.

Fungal threads are the internet of the plant world

Secret languages of plants

And a last one of the more creepy ones.

Plants can hear themselves being eaten

103

Beautiful Chemistry

Machinelves shared an amazing site with me today. Its chemistry visualized in all its beauty - caught in the act of reaction.

Here is a small taste.

[Beautiful Reactions: Precipitation](https://vimeo.com/106810691) from [L2 Molecule](https://vimeo.com/l2molecule) on [Vimeo](https://vimeo.com).

She added:

This one is cool for EteRNA especially, the description included, talking about Harvard’s lego bricks approach to DNA nano assembly:

DNA Nanostructures

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104

Monster Microscope

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.

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106

This story got an even more fascinating continuation. Machinelves sent me an article about a new and groundbreaking further development of this microscopy technique.

Now videos of cells moving can be shown to a whole new level of detail. I just saw a T-cell in action and it is halloween in the science world - I saw a cancer cell moving around. Creepy…!

Weeks after winning a Nobel Prize for his microscope, Eric Betzig just revolutionized microscopy again

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107

Happy Halloween!

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:

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108

How to glow in the dark

Fly larvae with fluorescence

Image Source

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

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109

Human genes - switched of


Image Source

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.

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110

Of Easter, viruses and blue eggs

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!

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111

Targeting cancer genes with elfs…

Ok, that introduction takes some explanation. :slight_smile:

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. :slight_smile:

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.

http://sdcsb.ucsd.edu/wp-content/uplo…

I have earlier been wondering about just how mRNA behaved, when it came to forming structure.

https://getsatisfaction.com/eternagam…

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112

A couple clicks into Eli’s knockout link yields a program I hadn’t heard of, the Precision Medicine Initiative.

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?

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MicroRNA as a weapon against cancer

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:

Have fun!

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114

Curing cancer with viruses

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. :slight_smile:

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

 

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115

DNA origami - at a whole new level

Good old DNA pulled a new trick from its hat. :slight_smile:

Meet the nano-sized rabbit made of DNA

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Here is a cool article on the effect of multiple A’s  in a mRNA on translation of the message:  http://www.the-scientist.com//?articles.view/articleNo/43600/title/AAAAA-is-for-Arrested-Translation…

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117

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.

Montreal scientists score possible breakthrough for rapid diagnostic medical tests

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.

TWiM #83: Illuminating tuberculosis and cryptococcosis

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.

Tuberculosis education and history

We are working alongside a lot of scientists and taking aim at Tuberculosis to help make the world a better place.

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119

Thanks Eli. I saved that link and will look it up on bus ride in the morning.

120

The true cost of medicine

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. :slight_smile:

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. :wink:

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. :slight_smile:

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.

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122

Total Poetic Justice

The story with the horrific medicine overpricing and raising cost per pill from 13.50$ to 750$ of a core anti parasitic medicine, just got a whole lot better.

A drug company has decided to make the drug and even in an improved version, for just around 1$ per pill. Guess who is going to make the sales. :slight_smile:

http://arstechnica.com/science/2015/10/drug-with-rage-inducing-5000-price-hike-now-has-1pill-competi…

Even better, this heroic company has plans on doing the same to a lot of other drugs. They really couldn’t have bought themselves any better advertisement.

I’m sending my respect to Imprimis Pharmaceuticals, Inc. :slight_smile:

Big thx to Machinelves for sending me this happy ending.

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123

I seen a few ask for ways to take a hit at tuberculosis - and now!

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.

http://nando.eternadev.org/web/playerpuzzles/?search=nando&switch=checked&sort=date

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.

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124

Science papers and how to get access to them

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. :wink:

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. :slight_smile:

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