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Aaron Abraham

• Biology  - 
 
Extraction of DNA


Here's a good article about extracting DNA from green split peas:
http://gslc.genetics.utah.edu/units/activities/extraction/

Check this for more on the purification of plant DNA (onion):

http://www.ncbe.reading.ac.uk/NCBE/PROTOCOLS/PDF/PlantSG.pdf

It essentially uses the same method as above, but is better explained and maybe a little bit more professional. 
In additition, it details the purification of DNA from cress and peas! 

I was thinking which organisms should contain large amounts of DNA - and what came to my mind first were BANANAS - I think they have over a dozen identical sets of full genomes per cell! Plenty of DNA! 
Probably Banana peels (soft and old ones) are best, or the actual leaves. 

One of the big disadvantages of the above methods is that the DNA gets sheared, i.e. broken into 100-500 kilobasepair pieces. Still pretty large, but for serious applications not so good. 

I do have professional protocols on how to purify mammalian DNA (or even RNA) , without much shearing. 
THey require more hard to get reagents though, such as phenol/chloroform, and proteases (although I think the soluble part of washing powders would do - as the biological washing powders of course contain proteases and lipases). In case you dont know, proteases break down proteins (proteins such as DNase, which breaks down DNA- a breakdown we WANT), and lipases break down lipids (fats). 
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Last week in Current Biology, researchers showed that male bats produce specific social calls that drive away competitors subsequently increasing their foraging success. Bats use echolocation to navigate their social and physical landscapes. Echolocation entails emitting high frequency calls and listening for the echo of those calls in order to build a sonic map of their environment. They utilize a plethora of social calls that are methodologically challenging to study in a natural environment. These scientists were able to study specific calls by triangulating the locations of the bats with microphones, reconstructing their flight paths with infrared cameras, and identifying vocalizations specific to individuals all within a laboratory. They observed that following the production of a 'frequency-modulated bout', the distance between two bats increased. If one bat was near prey when the other emitted this call, it moved away from the prey appearing to give up on its mission, allowing the caller to swoop in and steal the meal. 

#nature  

Sources
Article:http://www.sciencedirect.com/science/article/pii/S0960982214002590

Photo: Tom Whetten
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brilliant post and equally interesting are the ways of nature...which we can potentially explore to apply in the human world.
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Nick L

• Biology  - 
 
Looking at the possibility of Gene Doping already existing in professional cycling (and sport); includes summary of clinical applications of gene therapy 
“We were contacted by numerous athletes, even coaches. They didn’t understand that we were still at an early stage in terms of gene therapy moving to humans” -          Prof Lee Sweeney,Wada expert...
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Nick L
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Let me know if there is any areas that will be worth looking into! Thanks
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#Easter science: 3 ways we may use eggs in the future!

Eggs are for #science, not just for Easter. There are many uses for eggs other than eating; such as making plastics or even saving cows.

Read the blog (complete with illustrated eggs) for more: http://blogs.biomedcentral.com/bmcblog/2014/04/17/eggs-are-for-science-not-just-for-easter/
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This week in Science, researchers show that myelin distribution is diversified, and signature myelin profiles appear in different neocortical layers. Myelin encapsulates the axons of neurons and is crucial to normal function in the mammalian nervous system. It allows electrical impulses to travel quickly and efficiently by reducing sodium leakage and utilizing saltatory conduction. Action potentials hop along Nodes of Ranvier, where myelin is missing from the axon and voltage-gated ion channels are present, in order to regenerate the action potential at the next node. The degradation of myelin sheath is a trademark of many neurodegenerative disorders such as multiple sclerosis. Current research is focused on understanding the structure of myelin, and big projects focus on the regeneration of myelin (it does not regenerate, hence numerous myelin-based disorders). 

Article: http://www.sciencemag.org/content/344/6181/319.full.pdf

#neuroscience #axon  
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Regenerate one then.
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KQED SCIENCE

• Biology  - 
 
In weird Brazilian cave insects, male-female sex organs reversed

"This may be the role reversal to end all role reversals.

Scientists on Thursday described four insect species that dwell in extremely dry caves in Brazil, feed on bat guano and possess what the researchers called an "evolutionary novelty." .

The females have an elaborate, penis-like organ while the males have a vagina-like opening into which females insert their organ during mating sessions that last 40 to 70 hours, the scientists reported in the journal Current Biology."
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Why are people surprised? In seahorses the male accepts the eggs and does the carrying. Nature will do whatever it likes.
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Scientists implant lab-grown esophagi into rats.

An international team of scientists working at the Kuban State Medical University in Russia have built a working esophagus from cultured stem cells and successfully implanted the organ into rats, according to the April issue of Nature Communications journal.  

The link to the abstract is: http://www.nature.com/ncomms/2014/140415/ncomms4562/full/ncomms4562.html

The source of the photo is from the Scientific American article:
http://www.scientificamerican.com/article/lab-grown-esophagi-implanted-in-rats/

Considering this transplant in the context of the recent findings reported by Japanese researcher Dr. Haruko Obokata of the Reiken Institute, which indicate that it is possible to transform normal tissue cells of rats into STAP stem cells, the potential for a new era of medicine is emerging (particularly if the STAP stem cell discovery is verified by other researchers that can duplicate the results).

The findings of Dr Obokata in the journal Nature are here: http://www.nature.com/nature/journal/v505/n7485/full/nature12968.html

Coverage of the STAP Stem Cell discovery by BBC is here:
http://www.bbc.com/news/health-25917270
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OPTOGENETICS, A FASCINATING TOOL TO STUDY THE BRAIN
If you want to learn more about this method, watch this very informative lecture given by Karl Deisseroth who published the first demonstration of the use of microbial opsin genes to achieve optogenetic control of neuronsn and who coined the term optogenetics...

from the descriptions:
Optogenetics is a combination of genetics and optics to achieve a gain or loss of function of biochemical events such as action potentials in a particular neuron or tissue. Opsin genes encode proteins that receive light and give rise to ion flow. This talk gives an introduction to optogenetics followed by examples of how optogenetics is being used to study the brain.


#science #neuroscience #scienceeveryday #sciencesunday #optogenetics   #opsin  
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The researchers performed follow-up visits on the first four implant recipients, young women who were aged 13–18 years at the time the engineered organs were surgically implanted.
 
The women who received the implants were born with a rare form of vaginal aplasia, Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome. The vaginas they received the vaginas were engineered from their own cells.

The young women provided annual data for the researchers, agreed to physical examinations, vaginoscopies, serial tissue biopsies, and MRIs; and filled out Female Sexual Function questionnaires.
 
All this information, the researchers concluded, showed that “the engineered vaginal organs had a function within the normal range long term, with up to an eight-year follow-up to date.” The researchers added that the success of the implants provided “one more example of how regenerative medicine strategies can be applied to a variety of tissues and organs.”
 
Vaginal organs engineered in the laboratory can be used successfully in human beings, say researchers. http://ow.ly/vGl4y
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+Gary Ray R
 There is much argument around the compatability of male-female cells in the genitals. From what I have read in the past much of the argument comes from scientists comparing male and female cell function (eg. cell A in female is similar to cell B in male) and gets sexual criticism. It causes many scienctists to avoid comparitive analysis from fear of repercussions.
I only learned this a few years ago when some of my students asked me some weird questions about female genitalia and I had to go research it.
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"From Inside Cancer ( http://www.insidecancer.org )
A signaling pathway begins with the arrival of a chemical signal -- such as a hormone or growth factor -- at the cell surface. The gray structures sticking out of the cell membrane are receptors for these incoming signals. The signal, in this case a platelet-derived growth factor (here in purple and blue), encounters and binds to its matching receptor. A second receptor protein joins in, making the growth factor fit like a key in a lock. The binding of the growth factor causes the receptors to change shape. This change in the protein will be conducted through the membrane and into the cell's interior -- the cytoplasm.
The signal is conducted through the cell membrane, into the cytoplasm. The binding of the growth factor outside the cell has caused the ends of the receptor (in gray) to intertwine and activate each other (shown as yellow flashes of light). Once active, the modified receptor ends interact with messenger proteins that will carry the signal through the cytoplasm.
From our position in the cell's cytoplasm, we can see the ends of the receptor (in gray) being drawn together as the growth factor outside the cell binds. The receptor ends activate each other before binding an adaptor molecule (shown in pink) and an exchange factor (shown in light purple). An important protein in this pathway, known as Ras (shown in red) then swings around to be activated. Ras, in turn, activates three white "Raf" proteins, before another protein (shown in blue) moves in to deactivate it. Ras is a key "switch" in this pathway -- mutations in the ras gene and protein are common in cancer cells.
Many signaling pathways ultimately pass messages to the nucleus of a cell. The Raf protein (shown in white) activates another messenger protein (in brown) as it passes through fibers that make up the cell's cytoskeleton. The signal is passed to yet another messenger (in purple). These messenger proteins are known as kinases, enzymes with the ability to activate other proteins through the addition of phosphate groups. This protein travels to the nucleus past cellular organelles such as the mitochondria (in glowing orange) and the network of membranes known as the endoplasmic reticulum (shown in light brown).
The activated protein (in pink) is transported into the nucleus through a pore in the nuclear membrane. The nucleus contains tightly wound coils of DNA (shown in green). The signal is passed to two other molecules, Fos and Jun (in yellow and pink) that team up to locate a specific gene along the DNA. Fos and jun bind the DNA, starting the process of transcription. Other proteins are then called into play that unwind and open the DNA molecule so that RNA polymerase (shown in brown) can make a copy of the genetic information. The "copy," called messenger RNA (here in light green), is packaged with a set of carrier proteins and leaves the nucleus. The cell will use this copy to make a new protein.
In the cytoplasm, the messenger RNA is released from its carrier proteins and binds to a protein assembly complex called a ribosome (the multicolored structure). This begins a process called translation, where the ribosome reads the information encoded in the RNA and assembles a protein from amino acids found in the cell. Many ribosomes can operate at the same time to make multiple copies of the protein. The ribosomes are anchored on the outer membrane of the endoplasmic reticulum. If you look carefully, you can see the ghostly shapes of the newly made proteins accumulating on the inner side of the membrane. Once the job is done, the ribosomes and RNA part company.
The newly made proteins leave the endoplasmic reticulum wrapped in a layer of membrane called a vesicle. They travel toward the Golgi apparatus (on the right) where the proteins are modified and sorted for transport. The Golgi is busy with protein traffic moving in and out. The vesicle fuses with the membrane at one end of the Golgi and a new vesicle containing the modified proteins is pinched off the other side. The proteins are transported through the cytoplasm and delivered to where they are needed. Some proteins are used inside the cell. Others, like these growth factors, must be exported to function. The vesicle fuses with the cell membrane, dumping the proteins outside the cell. The released proteins will signal surrounding cells, or, in some pathways to cancer, will coax this cell into further action."
-Description from About section of the video in Youtube
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Great video. Lot of thought went into visualizing molecular processes, then the difficult art-work to display the process in an understandable way. 
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Great look at a recent popular science story on marijuana by Lior Pachter, a computational biologist. She doesn't pull any punches in calling it “quite possibly the worst paper I've read all year ”. #debunking   #marijuana  
Last week, a study was published that claimed to establish a link between casual marijuana use and abnormalities in the brains of recreational users. Intrigued by a claim made by one of the paper's authors in the wave of ensuing press coverage, UC Berkeley computational biologist Lior Pachtor decided to take a closer look.
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hahahah
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This is Glaucus atlanticus, A Sea Slug!!!

This is Glaucus atlanticus, a sea slug found in tropical and temperate waters throughout the world. These photographs make the rounds on Google+ every few months simply because they're so strangely beautiful.

However, no one ever mentions that this sea slug (like other sea slugs) is a total badass. Why, you ask? It eats incredibly venomous animals like the Portuguese Man o' War. The sting is agonizingly painful to a human and to most animals, but poses no problem to Glaucus atlanticus, which is immune. After the sea slug has consumed the Portuguese Man o' War it "selects" the most venomous cells for its own use. The slug then incorporates these cells into its own tissues, and uses them as a defense mechanism. It also concentrates the venom, making it far more venomous than the animal it "stole" the cells from.

#seaslug #slugs #animals #glaucusatlanticus #science
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I have never seen these creatures before, but they are simply beautiful!
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Keol Kruz

• Biology  - 
 
Can someone please help me with this...........
What exactly is the reason we smell different things differently???
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Please read our guideline for asking questions.

A good start for this would be to search Google for your question [how does the human nose work]  
That will bring up a bunch of articles from lots of different sources.

Also check Wiki, they have a myriad of articles that explain questions like this.  
http://en.wikipedia.org/wiki/Human_nose
http://en.wikipedia.org/wiki/Anatomy_of_the_human_nose
http://en.wikipedia.org/wiki/Taste

One good aspect of Wiki is that they have the references at the end of the article that can help for learning more.

Finally here is an article from the US National Laboratory of Medicine
How does our sense of taste work? 
http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0033701/
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Surprising Strength Discovered in the Nuclei of Embryonic Stem Cells

Scientists find unusual, surprising and unexpected characteristics of Embryonic Stem Cell's nuclei; namely they exhibit a property called Auxeticity that allows high energy absorption and fracture resistance

This could have important implications in a variety of industrial applications

http://en.wikipedia.org/wiki/Auxetics

#ScienceSunday  

"Stem cells – the body's master cells – demonstrate a bizarre property never before seen at a cellular level, according to a study published today from scientists at the University of Cambridge. The property – known as auxeticity – is one which may have application as wide-ranging as soundproofing, super-absorbent sponges and bulletproof vests.

Most materials when stretched will contract. For example, if one pulls on an elastic band, the elastic itself will get thinner. The opposite is also true: squeeze a material and it will expand – for example, if one squeezes a tennis ball between both hands, the circumference around the ball gets larger. However, material scientists have begun to explore auxeticity, an unusual property which has the opposite effect – squeeze it and it will contract, stretch it and it will expand. This means that auxetic materials act as excellent shock absorbers or sponges, a fact that is being explored for various uses.

Until now, auxeticity has only been demonstrated in manmade materials and very rarely in nature, such as some species of sponge. But today, in a paper published in the journal Nature Materials, a team of University of Cambridge researchers including biologists, engineers and physicists, report having observed auxeticity in the nuclei of embryonic stem cells, master cells within the body which can turn into any other type of cell."

Read more at: http://phys.org/news/2014-04-bulletproof-nuclei-stem-cells-unusual.html#jCp

The study: Pagliara, S. et al. Auxetic nuclei in embryonic stem cells exiting pluripotency. Nature Materials; e-pub 20 Apr 2014. http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat3943.html

Image: Mesenchymal stem cell displaying typical ultrastructural characteristics. Credit: Robert M. Hunt/Wikipedia
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KQED SCIENCE

• Biology  - 
 
Biology Paradox: Killing and Collecting Rare Creatures to Prove They’re Not Extinct

A group of biologists asks their peers to start documenting newly discovered and "rediscovered" species by non-destructive techniques instead of killing a specimen to bring home.

Learn more from Andrew Alden at KQED Science. 
Link to study summary: http://goo.gl/lNKu2h
A group of biologists asks their peers to start documenting newly discovered and "rediscovered" species by non-destructive techniques instead of killing a specimen to bring home.
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+Olin McGill
 pictures have never been evidence enough. if we were to just accept pictures then you can prove everything from frogs to ghosts.

If I take a photo of the Sahara desert and tell you it is a picture of what is occuring in the Amazon Basin then would you believe me?
Sure the devastation is bad, but is it enough to make large sand dunes? You would of course have no reason not to believe me unless you physically went there. And how many would have to physically witness it before it was proven? Wouldnt the constant trek of scientists and witnesses destroy the habitat even more?
Unfortunately we have to take specimens to prove a species so that we do not trample the existing species into the dust.
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Intellects

• Biology  - 
 
The life sustaining Red Beads - Red Blood Cells

Recently scientist have shown differentiation of iPS cells to blood cells. Can they be generated on comerical scale? 
If answer is Yes, then it will be huge for patients who need regular transfusion. But caution is advised as iPS cells has been associated with tumorogenesis.


First Red Blood Cells Made From Adult Cells Ready For Human Transfusions
In the future, man-made cells could supplement or even replace donated blood.
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?

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Tze Wen Leow

• Biology  - 
 
Manufactured red blood cells finally a possibility. Apparently it's been done!

When you consider what kind of resources have to go into collecting, managing and then certifying as safe blood samples from live donors this is a potentially huge and immensely practical breakthrough.

For example, I lived in the UK during the 80s and 90s and can't donate blood in Singapore due to possibility that my blood might contain prions which might lead to the human version of "Mad Cow" disease ( Bovine Spongiform Encephalopathy)

www.cdc.gov/ncidod/dvrd/bse/
 
Artificial red blood cells good enough to be transfused into patients have been developed for the first time: http://onforb.es/1eF05yc
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Since I have only checked over here maybe its just a Singapore thing. Not sure about elsewhere. They state that if you have lived in the UK from xx to yy you are not able to donate blood. 
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A new study explains the evolution of duplicate genes.
 
Living cells, from time to time, will accidentally make a copy of a gene during the normal replication process. These copies have made an impact on evolution. Throughout history, evolution has molded some of these seemingly meaningless genes into a genetic novelty, genetic mutations and diversity. This new study shows one way that some duplicate genes could have escaped elimination from the genome long ago, leading to genetic innovation we see today.
 
Read more about the study here: http://goo.gl/yA2L3z
 
Journal article here: http://goo.gl/wtl5Qu
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Also that's an excellent presentation.
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Evidence has been presented that coffee cuts cancer risk.
 
A daily routine of coffee may reduce an individual’s risk of developing the most common form of liver cancer, hepatocellular carcinoma (HCC). The higher the intake, the lower the risk according to the researcher. V. Wendy Setiawan from the University of Southern California presented this unpublished research at the American Association for Cancer Research (AACR) annual meeting in San Diego on April 9, 2014.
 
Setiawan and her colleagues have involved nearly 180,000 participants from a variety of ethnic backgrounds in the long-term study. The participants have been followed for up to 18 years. Overall, the participants who rank one to three cups a day had a 29 percent drop in occurrence of HCC risk. Participants who drank four or more cups saw the risk decrease by 42 percent.
 
“Now we can add HCC to the list of medical ailments, such as Parkinson’s disease, type 2 diabetes, and stroke, that may be prevented by coffee intake,” Setiawan said
 
The association between coffee consumption and lowered risk of cancer held constant even after controls for ethnicity, gender, obesity, smoking, alcohol use and diabetes.
 
“The roles of specific coffee components that are actually protective against HCC remain open to discussion,” Setiawan said. The researchers next plan to study whether the apparently protective effects of coffee hold up for other liver diseases.
 
This study provides insight, but is not meant to be taken as absolute truth, because we are still looking at an association. This is not meant to be taken as advice to increase coffee intake, only to give insight into ongoing research.
 
Source article: http://goo.gl/qr1sNS
 
Image: Roasted Coffee Beans, Photographer Robert Knapp www.modernartphotograph.com
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Good morning
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Alex P

• Biology  - 
 
amazing sea creatures :) that live up to 4000 years :)
 
This is a coral, a sea animal able to live up to 4000 years.  Google Director of Engineering Ray Kurzweil talked about how he sees the future when we will also live thousands of years and what we will do then ► Ray Kurzweil — Immortality by 2045.  For more futuristic stuff, see goo.gl/kkW80r. :)
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