99 Facts about DNA. How many do you know?

Facts About DNA

1. DNA stands for deoxyribonucleic acid.
2. DNA is part of our definition of a living organism.
3. DNA is found in all living things.
4. DNA was first isolated in 1869 by Friedrich Miescher.
5. James Watson and Francis Crick figured out the structure of DNA.
6. DNA is a double helix.
7. The structure of DNA can be likened to a twisted ladder.
8. The rungs of the ladder are made up of “bases”
9. Adenine (A) is a base.
10. Thymine (T) is a base.
11. Cytosine (C) is a base
12. Guanine (G) is a base.
13. A always pairs with T in DNA.
14. C also pairs with G in DNA.
15. The amount of A is equal to the amoun tof T, same for C and G.
16. A+C = T+G
17. Hydrogen bonds hold the bases together.
18. The sides of the DNA ladder is made of sugars and phosphate atoms.
19. Bases attached to a sugar; this complex is called a nucleoside.
20. Sugar + phosphate + base = nucleotide.
21. The DNA ladder usually twists to the right.
22. There are many conformations of DNA: A-DNA, B-DNA, and Z-DNA are the only ones found in nature.
23. Almost all the cells in our body have DNA with the exception of red blood cells.
24. DNA is the “blueprint” of life.
25. Chromosomal or nuclear DNA is DNA found in the nucleus of cells.
26. Humans have 46 chromosomes.
27. Autosomal DNA is part of chromosomal DNA but does not include the two sex chromsomes – X and Y.
28. One chromosome can have as little as 50 million base pairs or as much as 250 million base pairs.
29. Mitochondrial DNA (mtDNA) is found in the mitochondria.
30. mtDNA is only passed from the mother to the child because only eggs have mitochondria, not sperm.
31. There’s a copy of our entire DNA sequence in every cell of our body with one exception.
32. Our entire DNA sequence is called a genome.
33. There’s an estimated 3 billion DNA bases in our genome.
34. One million bases (called a megabase and abbreviated Mb) of DNA sequence data is roughly equivalent to 1 megabyte of computer data storage space.
35. Our entire DNA sequence would fill 200 1,000-page New York City telephone directories.
36. A complete 3 billion base genome would take 3 gigabytes of storage space.
37. If unwound and tied together, the strands of DNA in one cell would stretch almost six feet but would be only 50 trillionths of an inch wide.
38. In humans, the DNA molecule in a non-sex cell would have a total length of 1.7 metres.
39. If you unwrap all the DNA you have in all your cells, you could reach the moon 6000 times!
40. Our sex cells–eggs and sperm–have only half of our total DNA.
41. Over 99% of our DNA sequence is the same as other humans’.
42. DNA can self-replicate using cellular machinery made of proteins.
43. Genes are made of DNA.
44. Genes are pieces of DNA passed from parent to offspring that contain hereditary information.
45. The average gene is 10,000 to 15,000 bases long.
46. The segment of DNA designated a gene is made up of exons and introns.
47. Exons have the code for making proteins.
48. Introns are intervening sequences sometimes called “junk DNA.”
49. Junk DNA’s function or lack thereof is a source of debate.
50. Part of “junk DNA” help to regulate the genomic activity.
51. There are an estimated 20,000 to 25,000 genes in our genome.
52. In 2000, a rough draft of the human genome (complete DNA sequence) was completed.
53. In 2003, the final draft of the human genome was completed.
54. The human genome sequence generated by the private genomics company Celera was based on DNA samples collected from five donors who identified themselves only by race and sex.
55. If all the DNA in your body was put end to end, it would reach to the sun and back over 600 times (100 trillion times six feet divided by 92 million miles).
56. It would take a person typing 60 words per minute, eight hours a day, around 50 years to type the human genome.
57. If all three billion letters in the human genome were stacked one millimeter apart, they would reach a height 7,000 times the height of the Empire State Building.
58. DNA is translated via cellular mechanisms into proteins.
59. DNA in sets of 3 bases, called a codon, code for amino acids, the building blocks of protein.
60. Changes in the DNA sequence are called mutations.
61. Many thing can cause mutations, including UV irradiation from the sun, chemicals like drugs, etc.
62. Mutations can be changes in just one DNA base.
63. Mutations can involve more than one DNA base.
64. Mutations can involve entire segments of chromosomes.
65. Single nucleotide polymorpshisms (SNPs) are single base changes in DNA.
66. Short tandem repeats (STRs) are short sequences of DNA repeated consecutively.
67. Some parts of the DNA sequence do not make proteins.
68. Genes make up only about 2-3% of our genome.
69. DNA is affected by the environment; environmental factors can turn genes on and off.
70. There are many ways you can analyze your DNA using commercially available tests.
71. Paternity tests compare segments of DNA between the potential father and child.
72. There are other types of relationship testing that compares DNA between siblings, grandparents and grandchild, etc.
73. DNA tests can help you understand your risk of disease.
74. A DNA mutation or variation may be associated with a higher risk of a number of diseases, including breast cancer.
75. DNA tests can help you understand your family history aka genetic genealogy.
76. DNA tests can help you understand your ethnic make-up.
77. DNA can be extracted from many different types of samples: blood, cheek cells, urine.
78. DNA can be stored either as cells on a cotton swab, buccal brush, or frozen blood or in extracted form.
79. In forensics, DNA analysis usually looks at 13 specific DNA markers (segments of DNA).
80. The odds that two individuals will have the same 13-loci DNA profile is about one in one billion.
81. A DNA fingerprint is a set of DNA markers that is unique for each individual except identical twins.
82. Identical twins share 100% of their genes.
83. Siblings share 50% of their genes.
84. A parent and child share 50% of their genes.
85. You can extract DNA at home from fruit and even your own cheek cells.
86. DNA is used to determine the pedigree for livestock or pets.
87. DNA is used in wildlife forensics to identify endangered species and people who hunt them (poachers).
88. DNA is used in identify victims of accidents or crime.
89. DNA is used to exonerate innocent people who’ve been wrongly convicted.
90. Many countries, including the US and UK, maintain a DNA database of convicted criminals.
91. The CODIS databank (COmbined DNA Index System) is maintained by the BI and has DNA profiles of convicted criminals.
92. Polymerase chain reaction (PCR) is used to amplify a sample of DNA so that there are more copies to analyze.
93. We eat DNA every day.
94. DNA testing is used to authenticate food like caviar and fine wine.
95. DNA is used to determine the purity of crops.
96. Genetically modified crops have DNA from another organism inserted to give the crops properties like pest resistance.
97. Dolly the cloned sheep had the same nuclear DNA as its donor mom but its mitochondrial DNA came from from the egg mom. (Does that make any sense?)
98. People like to talk about DNA even if it bears no relation to science or reality.
99. A group of bloggers who write regularly about DNA and genetics have banded to gether to form The DNA Network.

Phage Therapy - The Future of "Precision Treatment"

Published on: SCIENCE,19 June, 2015

Bacteriophage WINS !!!!

#Bacteriophage_Therapy     #Phage_Therapy    #E.coli_VS_Bacteriophage

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Extra DNA Base Discovered

By Jef Akst | June 23, 2015

An epigenetic variant of cytosine is stable in the genomes of living mice, suggesting a possible expansion of the DNA alphabet.

An epigenetic mark known as 5-formylcytosine (5fC) may be more than a transitory state that helps regulate gene expression. According to a study published yesterday (June 22) in Nature Chemical Biology, 5fC is stable in the mouse genome and may represent a fifth nucleotide in the DNA alphabet.

“It had been thought this modification was solely a short-lived intermediate, but the fact that we’ve demonstrated it can be stable in living tissue shows that it could regulate gene expression and potentially signal other events in cells,” coauthor Shankar Balasubramanian of the Cancer Research UK Cambridge Institute said in a press release.

While the function of the modified base—essentially a methylated cytosine with added oxygen—remains unclear, its position within the genome points to a role in gene expression. “This modification to DNA is found in very specific positions in the genome—the places which regulate genes,” lead author Martin Bachman, who conducted the research while at the University of Cambridge, said in the release. “In addition, it’s been found in every tissue in the body—albeit in very low levels.” High-resolution mass spectrometry revealed 5fC to be most common in the mouse brain, but even there it was present at only 10 parts per million or less.

But when the researchers enriched cultures of mouse cells or mice’s diets with stable isotopes of carbon and hydrogen, they found no uptake into 5fC bases, suggesting the modification is stable.

“If 5fC is present in the DNA of all tissues, it is probably there for a reason,” added Balasubramanian. “This will alter the thinking of people in the study of development and the role that these modifications may play in the development of certain diseases.”

Source: http://www.the-scientist.com/?articles.view/articleNo/43358/title/Extra-DNA-Base-Discovered/

Earth’s sixth mass extinction has begun, new study confirms !!!

Contributor

James Dyke

Lecturer in Complex Systems Simulation at University of Southampton

We are currently witnessing the start of a mass extinction event the likes of which have not been seen on Earth for at least 65 million years. This is the alarming finding of a new study published in the journal Science Advances.

The research was designed to determine how human actions over the past 500 years have affected the extinction rates of vertebrates: mammals, fish, birds, reptiles and amphibians. It found a clear signal of elevated species loss which has markedly accelerated over the past couple of hundred years, such that life on Earth is embarking on its sixth greatest extinction event in its 3.5 billion year history.

This latest research was conducted by an international team lead by Gerardo Ceballos of the National Autonomous University of Mexico. Measuring extinction rates is notoriously hard. Recently I reported on some of the fiendishly clever ways such rates have been estimated. These studies are producing profoundly worrying results.

However, there is always the risk that such work overestimates modern extinction rates because they need to make a number of assumptions given the very limited data available. Ceballos and his team wanted to put a floor on these numbers, to establish extinction rates for species that were very conservative, with the understanding that whatever the rate of species lost has actually been, it could not be any lower.

This makes their findings even more significant because even with such conservative estimates they find extinction rates are much, much higher than the background rate of extinction – the rate of species loss in the absence of any human impacts.

Here again, they err on the side of caution. A number of studies have attempted to estimate the background rate of extinction. These have produced upper values of about one out of every million species being lost each year. Using recent work by co-author Anthony Barnosky, they effectively double this background rate and so assume that two out of every million species will disappear through natural causes each year. This should mean that differences between the background and human driven extinction rates will be smaller. But they find that the magnitude of more recent extinctions is so great as to effectively swamp any natural processes.

Cumulative vertebrate species recorded as extinct or extinct in the wild by the IUCN (2012). Dashed black line represents background rate. This is the ‘highly conservative estimate’.

Click to enla

The “very conservative estimate” of species loss uses International Union of Conservation of Nature data. This contains documented examples of species becoming extinct. They use the same data source to produce the “conservative estimate” which includes known extinct species and those species believed to be extinct or extinct in the wild.

Farewell, broad-faced potoroo, we hardly knew yew....

The paper has been published in an open access journal and I would recommend reading it and the accompanying Supplementary Materials. This includes the list of vertebrate species known to have disappeared since the year 1500. The Latin names for these species would be familiar only to specialists, but even the common names are exotic and strange: the Cuban coney, red-bellied gracile, broad-faced potoroo and southern gastric brooding frog.

These particular outer branches of the great tree of life now stop. Some of their remains will be preserved, either as fossils in layers of rocks or glass eyed exhibits in museum cabinets. But the Earth will no longer see them scurry or soar, hear them croak or chirp.

You may wonder to what extent does this matter? Why should we worry if the natural process of extinction is amplified by humans and our expanding industrialised civilisation?

One response to this question essentially points out what the natural world does for us. Whether it’s pollinating our crops, purifying our water, providing fish to eat or fibres to weave, we are dependent on biodiveristy. Ecosystems can only continue to provide things for us if they continue to function in approximately the same way.

The relationship between species diversity and ecosystem function is very complex and not well understood. There may be gradual and reversible decreases in function with decreased biodiversity. There may be effectively no change until a tipping point occurs. The analogy here is popping out rivets from a plane’s wing. The aircraft will fly unimpaired if a few rivets are removed here or there, but to continue to remove rivets is to move the system closer to catastrophic failure.

This latest research tells us what we already knew. Humans have in the space of a few centuries swung a wrecking ball through the Earth’s biosphere. Liquidating biodiversity to produce products and services has an end point. Science is starting to sketch out what that end point could look like but it cannot tell us why to stop before we reach it.

If we regard the Earth as nothing more than a source of resources and a sink for our pollution, if we value other species only in terms of what they can provide to us, then we we will continue to unpick the fabric of life. Remove further rivets from spaceship earth. This not only increases the risk that it will cease to function in the ways that we and future generations will depend on, but can only reduce the complexity and beauty of our home in the cosmos.

Source: https://theconversation.com/earths-sixth-mass-extinction-has-begun-new-study-confirms-43432

Dutch Harvest Electricity From Living Plants To Power Streetlights, Wi-Fi & Cell Phones

Plant-e, a company based out of the Netherlands, has found a way to harness electricity from living plants, using them to power Wi-Fi hotspots, cell phone chargers, and even streetlights. The company debuted their project, called “Starry Sky,” in November of 2014 near Amsterdam, where they lit up more than 300 LED streetlights at two different sites. Their plant power technology is also being used to power the company’s headquarters in Wageningen.

The company was founded in 2009, and was a spin-off from the department of Environmental Technology of Wageningen University. Again, they develop products in which living plants generate electricity. Their technology allows them to produce electricity from practically every site where plants can grow.

“Via photosynthesis a plant produces organic matter. Part of this organic matter is used for plant-growth, but a large part can’t be used by the plant and is excreted into the soil via the roots. Around the roots naturally occurring micro-organisms break down the organic compounds to gain energy from. In this process, electrons are released as a waste product. By providing an electrode for the micro-organisms to donate their electrons to, the electrons can be harvested as electricity. Research has shown that plant-growth isn’t compromised by harvesting electricity, so plants keep on growing while electricity is concurrently produced.” (source)

Just imagine, a house with a roof full of plant/tree life powering your home. On the company’s website, they feature animated pictures of mini-forests growing on building rooftops supplying power to the entire building. It’s pretty cool to imagine, isn’t it?

It’s important to mention that at the moment, the main problem is the quantity of energy that can be generated. There is still a long way to go with regards to making enough energy to have a completely reliable commercial product, but things are looking promising, as the company is already selling products that enable you to harvest energy from plants. Again, they are also using the technology to power their headquarters…

For more information on the technology or to read some of their recent publications, see: www.plantpower.eu – or visit their website listed in the sources.

Sources: http://plant-e.com/

Superbugs to Watch Out For

Contributor: Linda Thrasybule

INTRODUCTION

Superbugs, also known as drug-resistant bacterial infections, can cause infections that are hard to treat. These clever germs have found ways to survive in the face of treatments with antibiotics, the drugs that usually kill bacteria.

In fact, according to the Centers for Disease Control and Prevention (CDC), all bacterial infections in the world are slowly becoming resistant to antibiotic treatments. That's because disease-causing bacteria are living organisms that constantly evolve, enabling them to adapt to new environments. Antibiotic resistance develops over time — it can start from even a very small number of microbes within a population that have genes that allow them to continue to grow, despite the use of drugs that would normally kill them.

Researchers suggest that some microbes are able to survive antibiotic treatments because they swap genes with each other, making them drug-resistant. 

In any case, the bacteria that survive an antibiotic treatment eventually outnumber the population of bacteria that are susceptible to the drug.

Here are 6 superbugs that can be challenging to treat.

1. Shiga toxin-producing Escherichia coli

Escherichia coli are a large group of bacteria, and some normally live in the intestines of people and animals. 

Although some strains of the bacteria are harmless, others can make you sick. They can cause diarrhea, urinary tract infections, respiratory illness and pneumonia.

One harmful strain is the Shiga toxin-producing E. coli, also known as STEC, which live in the guts of animals such as cattle, goats, sheep, deer and elk. Humans can become infected by eating contaminated food, drinking raw milk or contaminated water, coming in contact with cattle or with the feces of infected people.

STEC are resistant to a number of classes of antibiotics. In fact, antibiotic treatment is generally discouraged because it may increase the risk of developing hemolytic uremic syndrome, a disorder that can destroy red blood cells, causing damage to the kidneys.

An estimated 265,000 STEC infections occur yearly in the U.S., reports the CDC.

Earlier this year, an outbreak of a particular strain of STEC, called E. coliO145, was identified in nine states. A total of 18 people were infected, four were hospitalized and one person in Louisiana died.

To prevent STEC infections, the CDC recommends washing hands thoroughly after using the bathroom or preparing food, cooking meats thoroughly and avoiding drinking raw milk.

2. Drug-resistant Gonorrhea

Gonorrhea is a sexually transmitted disease that is caused by the bacteria Neisseria gonorrhoeae.

Over time, gonorrhea bacteria have developed a resistance to antibiotics such as sulfonilamides, penicillin, tetracycline and ciprofloxacin, which are commonly prescribed to treat gonorrhea infections.

Recently, the CDC stopped recommending the use of an antibiotic called cefixime to treat gonorrhea, because the drug was losing its effectiveness. Now, they recommend treating infections with a drug called ceftriaxone, along with either azithromycin or doxycycline, as the best way to reduce the risk of the bacteria becoming even more drug-resistant.

In 2010, a total of 309,341 cases of gonorrhea were reported in the U.S. — a rate of about one case per 1,000 people, according to the CDC.

3. Tuberculosis 

Extensively drug-resistant tuberculosis (XDR TB) is rare type of tuberculosis that is resistant to a number of antibiotic drugs. This resistance leaves fewer treatment options available, which can increase the risk of death.

Tuberculosis is a contagious bacterial infection that involves the lungs, but can spread to other organs. A person with TB releases the bacteria into the air when they cough or sneeze, and the germs can float for several hours. People who breathe in the air containing the bacteria can become infected.

A total of 10,528 TB cases were reported in the U.S. in 2011, according to the CDC. 

People who don’t take their TB medications regularly are at greater risk of getting drug-resistant TB.

4. Clostridium difficile 

Clostridium difficile bacteria are found in the intestines. Healthy people who have enough "good" bacteria in their intestines may not get sick from a C. diff infection. But for people with weak immune systems, the germ can cause a number of symptoms, such as diarrhea or life-threatening inflammation of the colon.

People who take antibiotics are at greater risk of C. diff infection, because antibiotics can kill the good germs in the intestines, leaving an imbalance.

C. difficile can cause severe diarrhea, and the germ is linked to 14,000 American deaths each year, according to the CDC.

Those most at risk are the elderly who take antibiotics, and also those who get regular hospital care.

In about one in four patients, the infection may go away within two to three days after stopping antibiotic use, according to the CDC. Once the infection is gone, doctors generally prescribe another antibiotic for 10 days to make sure the infection doesn't return

5. MRSA

MRSA, which stands for methicillin-resistant Staphylococcus aureus, is a strain of bacteria that's resistant to the antibiotics used to treat typical staph infections. The bacteria can spread by touching, as often occurs in hospitals.

Once the bacteria enters the body, they can spread to bones, joints or major organs such as the lungs, heart or brain.

The rate of MRSA infections in hospital patients has increased in recent years, according to a recent study published in the August issue of the journal Infection Control and Hospital Epidemiology. Results showed that in 2003, an average of 21 out of every 1,000 hospital patients developed an infection. The number jumped up to 42 out of 1,000 patients in 2008.

The best way to prevent the spread of MRSA is for health care workers and hospital visitors to keep their hands clean, according to the CDC.

6. Klebsiella pneumoniae

Klebsiella pneumoniae bacteria can infect the lungs and lead to pneumonia. The bacteria can also infect wounds or surgical sites, or spread through the body via blood infections.

Normally, Klebsiella bacteria can be found in humans' mouths, intestines and skin, and they cause no harm to people with healthy immune systems. But certain strains, like Klebsiella pneumoniae, can be dangerous for some people with weakened immune systems, particularly those in hospitals.

One strain of the bacteria is also resistant to a number of antibiotics, making the infection hard to treat. This type of Klebsiella pneumoniaeproduces an enzyme known as carbapenemase, which prevents antibiotics called carbapenems from killing the bacteria and treating the infection.

To prevent spread of infection, the CDC recommends patients and hospital personnel follow strict hygiene procedures, such as hand-washing and wearing hospital gowns and gloves.

Source: http://www.livescience.com/36674-superbugs-drug-resistant-bacteria-infections.html

Ten Simple Rules to Win a Nobel Prize

By: Richard J. Roberts

Introduction

It is remarkable how many students, young faculty, and even senior faculty hanker after a Nobel Prize. Somehow, they think that it is possible to structure their scientific careers so that the culmination will bring this much sought-after honor. Some even think that as a Nobel laureate myself, I may have the key to success—some secrets that I can share and so greatly improve their odds of success. Unfortunately, I must begin by disappointing everyone. There is only one path that should be followed. It is summed up in Rule 1, but some of the other Rules may prove helpful—or if not helpful, then at least amusing.

1. Never Start Your Career by Aiming for a Nobel Prize

Don’t even hope for it or think about it. Just focus on doing the very best science that you can. Ask good questions, use innovative methods to answer them, and look for those unexpected results that may reveal some unexpected aspect of nature. If you are successful in your research career, then you will make lots of discoveries and have a very happy life. If you are lucky, you will make a big discovery that may even bag you a prize or two. But only if you are extraordinarily lucky will you stand any chance of winning a Nobel Prize. They are very elusive.

2. Hope That Your Experiments Fail Occasionally

There are usually two main reasons why experiments fail. Very often, it is because you screwed up in the design by not thinking hard enough about it ahead of time. Perhaps more often, it is because you were not careful enough in mixing the reagents (I always ask students if they spat in the tube or, more recently, were texting when they were labeling their tubes). Sometimes, you are not careful enough in performing the analytics (did you put the thermometer in upside down, as I once witnessed from a medical student whose name now appears on my list of doctors who I won’t allow to treat me even if I’m dying?). These problems are the easiest to deal with by always taking great care in designing and executing experiments. If they still fail, then do them over again! But the more interesting reason that experiments fail is because nature is trying to tell you that the axioms on which you based the experiment are wrong. This means the dogma in the field is wrong (often the case with dogma). If you are lucky, as I was, then the dogma will be seriously wrong, and you can design more experiments to find out why. If you are really lucky, then you will stumble onto something big enough to be prizeworthy.

3. Collaborate with Other Scientists, but Never with More Than Two Other People

Collaboration embodies much of what is good about science and makes it fun. By bringing different sets of expertise to bear on a problem, it is often the key to making discoveries. However, if you think you are getting close to a big discovery, always keep in the back of your mind that there can only be three winners on the ticket for a Nobel Prize. Pick your collaborators carefully! But seriously, don’t do as some have done and try to make a competitor of someone who would otherwise be an extremely valuable collaborator.

4. To Increase Your Odds of Winning, Be Sure to Pick Your Family Carefully

Seven children of Nobel Prize winners have gone on to win the Prize themselves, and four married couples have jointly won the Prize. Marie Curie and her husband, Pierre, won in Physics in 1903, while their daughter Irene with her husband, Frederic Joliot, won the Chemistry Prize in 1935. Carl and Gerty Cori won the Medicine Prize in 1947, and Alva Myrdal and Alfonso Robles won the Peace Prize in 1942. Lawrence Bragg shared the Physics Prize in 1935 with his father, William. Roger Kornberg (Chemistry, 2006) and his father, Arthur, (Medicine, 1959) both won. Aage Bohr (1975) and his father, Niels, (1922) both won the Physics Prize. Other father-son laureates are the Swedes Hans von Euler-Chelpin (Chemistry, 1929) and Ulf von Euler (Medicine, 1970) and Manne Siegbahn (1924) and Kai Siegbahn (1981), both in Physics. Briton Joseph John Thomson (1906) and his son George (1937) both won the Physics Prize. The only siblings to bask in Nobel glory were Jan and Nikolaas Tinbergen (Medicine, 1973) of the Netherlands. Jan won the first Prize awarded in Economics in 1969.

With a total of 586 Nobel Prize recipients in science during the 113 years since it was first awarded, these are impressive numbers, given a world population numbering at least 10,000,000,000 over the same period of time. This rule is vividly illustrated last year (2014) by another married couple sharing the Nobel Prize in Physiology or Medicine.

5. Work in the Laboratory of a Previous Nobel Prize Winner

Many Prize recipients have benefitted greatly from the inspiration that this approach can bring. Sometimes just working at an institution with a previous Prize winner can be helpful. One prime example is the Medical Research Council (MRC) Laboratory in Cambridge, United Kingdom, where no less than nine staff members have won Nobel Prizes in either Chemistry or Physiology and Medicine, including my own personal hero Fred Sanger, who won the Chemistry Prize twice (1958, 1980), once for inventing protein sequencing and once for pioneering DNA sequencing. In between, he also invented RNA sequencing, but perhaps three Prizes was more than the Nobel Committee could stomach.

6. Even Better Than Rule 5, Try to Work in the Laboratory of a Future Nobel Prize Winner

This can be very beneficial, especially if you can be a part of the Prize-winning discovery. That has proven to be a very good strategy, but it is not always easy to spot the right mentor, one who will bring you that sort of success and then share the glory with you. The corollary of this strategy is not to work in the laboratory of someone who has already won but whom you think will win again with you on the ticket. This has yet to prove successful based on the previous double recipients named in Rule 5! It is much better to make sure that any big discoveries come from you after you leave the lab and are out on your own.

7. Always Design and Execute Your Best Experiments at a Time When Your Luck Is Running High

A casual survey of Nobel Prize winners will soon confirm that most credit luck as being the biggest component in their discovery. This is partly because many discoveries arise when what we think we know turns out to be wrong and we base our further research on incorrect assumptions. However, only rarely are we lucky enough to have to make such dramatic changes in our assumptions that a really major breakthrough becomes possible—the sort that may one day be considered appropriate for a Nobel Prize.

8. Never Plan Your Life around Winning a Nobel Prize

This has proven disastrous for many people. I know several scientists who became convinced that they were going to win and had all sorts of plans for less-than-modest speeches acknowledging the award of the Prize, preparing comments for journalists and planning subsequent trips to exotic places to talk about their discovery. It is far better not to know you have been nominated so that it comes as a real surprise when you get the early morning call from Stockholm. In fact, why not just forget about the Nobel Prize altogether and focus on doing the very best science you can? If you decide to ignore this rule, under no circumstances should you bug current Nobel laureates to nominate you. This has been an all-too-common strategy employed by many who feel they should be laureates, some even going so far as to send their last year’s publications along every year with a reminder of what they consider their “big” discovery. This will almost guarantee that the laureate won’t nominate you and is likely to lead to them advising their friends similarly. Can you imagine how that conversation would go after a few late-night drinks in the bar?

9. Always Be Nice to Swedish Scientists

Several laureates had their prize severely delayed by picking a fight with the wrong person, someone who was either already a Nobel Committee member or became one subsequent to the fight. Some individuals may even have lost out altogether, although one would need to search the archives (only available 50 years after the award) to find them. This is usually an easy rule to follow as in my experience the Swedes are very nice people, good scientists, easy to collaborate with, and extremely amiable drinking partners.

It is never too early to get started on this. Then, should your name magically appear on the candidates’ list and you have to wait for it to reach the top, you may still be around to cash in. Peyton Rous had to wait from 1911 until 1966 for the Medicine Prize, just four years before his death.

10. Study Biology

There are many reasons for this. First, biology is fascinating, never boring, and directly affects our everyday lives, yet we still know relatively little about it. Thus, the odds of making a big discovery are greatly increased compared to other disciplines. Second, biology is all around us, is vastly complicated, and encompasses disciplines such as medicine, agriculture, conservation, and computer science, as well as many others, thus lending itself to the kind of interdisciplinary approaches that make science such fun and can easily lead into new territory. Third, unlike physics and chemistry, biology is ever changing, thanks to evolution. What seems to be the rule today may have changed by the time you are doing your experiments. Finally, there are two Prize categories in which biological discoveries are currently being awarded. One is Physiology or Medicine, and the other is Chemistry, in which about half the Prizes go to biologists. Already you have increased your odds by 50%.

Conclusions

In summary, Rule 1 is the best advice I can offer. There is no substitute for pursuing the very best science that you can. Even Marie Curie, John Bardeen, and Fred Sanger needed this to win their second Prize. In contrast, Linus Pauling, one of the cleverest chemists of his generation, only received his second Prize (in Peace) by working in a totally different field. Nevertheless, the odds of winning a second Prize, if you already have one, do seem rather better than average!

Full length paper:
https://dl.dropboxusercontent.com/u/80911982/FB%20Group/Ten%20Simple%20Rules%20to%20Win%20a%20Nobel%20Prize.pdf

Know every virus infection [past and present] from a drop of blood. UNBELIEVABLE

By Amanda B. Keener | June 4, 2015

Scientists devise an antibody-based test that can generate a person’s complete “viral history” with just one drop of blood.

Last summer, infectious disease specialist Gregory Poland saw a patient at the Mayo Clinic in Rochester, Minnesota, who had a fever, a rash, kidney failure, and—despite seeing several doctors—no diagnosis. Only after talking with the patient for hours and digging into her medical and travel history could Poland generate a potential diagnosis. To test his theory, he had to send a serum sample to researchers at the US Centers for Disease Control and Prevention in Atlanta, who confirmed that his patient had chikungunya.

Situations like this, explained Poland, are not uncommon. “I can’t tell you how many times we don’t know what’s going on,” he said. When tests for all of the usual suspects come back negative, it’s difficult to know what to try next. On top of that, he added, some disease-causing agents are rare. “There are viruses that I know the name of, but I’ve never seen the disease.”

Thanks to a method described today (June 4) in Science, it may be soon be possible to test patients for previous exposures to all human-tropic viruses at once. Virologist Stephen Elledge of Harvard Medical School and the Brigham and Women’s Hospital in Boston and his colleagues have built such a test, called “VirScan,” from a bacteriophage-based display system they developed in 2011. The scientists programmed each phage to expresses a unique viral peptide, collectively producing about 100 peptides from each of the 206 known human-tropic viral species.

The team combined the phage with serum collected from 569 donors in the U.S., Thailand, Peru, and South Africa, allowing antibodies in each sample to bind their target peptides. The researchers then isolated the antibody-peptide-phage complexes, and harvested and sequenced the DNA inside each. The sequences, which can be read millions at a time, represent peptides recognized by the antibodies, revealing which viruses a given donor’s immune system had previously seen.

“This is far beyond anything we’ve had before regarding the human antibody response to viruses,” said Kristine Wylie, a microbiologist at Washington University in St. Louis who was not involved in the work.

Scientists like Wylie have been cataloging viruses living in and on humans for years, typically by searching for viral DNA and RNA sequences in blood and tissues. “Healthy people carry a lot of viruses, asymptomatically,” she said. Knowledge of prior viral exposures can improve health care. For example, it’s good to know whether a patient about to start chemotherapy carries a latent virus that could resurge during treatment.

Detecting a virus by the presence of its genes, however, depends on the virus being present at high enough levels and in easily accessed fluids or tissues. Measuring antibodies produced in response to viruses makes it possible to detect an infection weeks or decades later using only blood serum. But this approach is typically limited to testing for antibodies against one virus at a time. According to Poland, testing for many viruses at once is currently too expensive and requires too much blood to be routinely feasible.

VirScan requires just one drop of blood and, for about $25, screens for antibodies against 206 viruses, covering 1,000 strains. Using the technique, Elledge’s team identified high rates of exposure to common viruses like Epstein–Barr virus (found in 87 percent of adult donors screened) and rhinovirus (found in around 70 percent), many of which Wylie said are consistent with the rates she and others have seen in asymptomatic adults.

Some viruses showed up at lower frequencies than expected. Influenza, for example, appeared to affect only 53 percent of the donors, and chickenpox, just 24 percent. Elledge noted that these apparently low rates may be the result of a potential limitation of the test: the 56 amino acid peptides used for VirScan may have been too short to attract antibodies that only bind longer spans of folded-up peptides called conformational epitopes. Despite this, the team detected antibody responses against 4,406 unique epitopes, most of which had not been recorded in the Immune Epitope Database.

Unexpectedly, each person sampled showed a strong response to just three or fewer peptides per virus, making those peptides immunodominant. Although immunodominant peptides don’t always make the best vaccines, Elledge noted they might still be useful for vaccine design. “You might be able to piggyback on pre-existing immune responses and use that to your advantage,” he said.

Improvements to VirScan—such as the inclusion of conformational epitopes and a reduction in cross-reactivity between viruses with similar proteins—are in the works, said Elledge. Going forward, the team would like to extend its approach to screen for other pathogens, like bacteria, and to use VirScan to look for correlations between viral infections and chronic conditions, such as autoimmune diseases.

Down the line, Poland sees a place for VirScan in the clinic. “They’ve made real progress in what could have been seen as a pipe dream,” he said. “If they can perfect this and move this forward, this changes everything.”

G.J. Xu, et al. “Comprehensive serological profiling of human populations using a synthetic human virome,” Science, 348:1106-1114, 2015.

Source: "A Lifetime of Virus"
http://www.the-scientist.com//?articles.view/articleNo/43156/title/A-Lifetime-of-Viruses/

New device can extract human DNA with full genetic data in minutes

Engineers have created a device that can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods.

Take a swab of saliva from your mouth and within minutes your DNA could be ready for analysis and genome sequencing with the help of a new device.

University of Washington engineers and NanoFacture (http://nano-facture.com/), a Bellevue, Wash., company, have created a device that can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods.

The device will give hospitals and research labs a much easier way to separate DNA from human fluid samples, which will help with genome sequencing, disease diagnosis and forensic investigations.

"It's very complex to extract DNA," said Jae-Hyun Chung, a UW associate professor of mechanical engineering who led the research. "When you think of the current procedure, the equivalent is like collecting human hairs using a construction crane."

This technology aims to clear those hurdles. The small, box-shaped kit now is ready for manufacturing, then eventual distribution to hospitals and clinics. NanoFacture, a UW spinout company, signed a contract with Korean manufacturer KNR Systems last month at a ceremony in Olympia, Wash.

The UW, led by Chung, spearheaded the research and invention of the technology, and still manages the intellectual property.

Separating DNA from bodily fluids is a cumbersome process that's become a bottleneck as scientists make advances in genome sequencing, particularly for disease prevention and treatment. The market for DNA preparation alone is about $3 billion each year.

Conventional methods use a centrifuge to spin and separate DNA molecules or strain them from a fluid sample with a micro-filter, but these processes take 20 to 30 minutes to complete and can require excessive toxic chemicals.

UW engineers designed microscopic probes that dip into a fluid sample -- saliva, sputum or blood -- and apply an electric field within the liquid. That draws particles to concentrate around the surface of the tiny probe. Larger particles hit the tip and swerve away, but DNA-sized molecules stick to the probe and are trapped on the surface. It takes two or three minutes to separate and purify DNA using this technology.

"This simple process removes all the steps of conventional methods," Chung said.

The hand-held device can clean four separate human fluid samples at once, but the technology can be scaled up to prepare 96 samples at a time, which is standard for large-scale handling.

The tiny probes, called microtips and nanotips, were designed and built at the UW in a micro-fabrication facility where a technician can make up to 1 million tips in a year, which is key in proving that large-scale production is feasible, Chung said.

Engineers in Chung's lab also have designed a pencil-sized device using the same probe technology that could be sent home with patients or distributed to those serving in the military overseas. Patients could swab their cheeks, collect a saliva sample, then process their DNA on the spot to send back to hospitals and labs for analysis. This could be useful as efforts ramp up toward sequencing each person's genome for disease prevention and treatment, Chung said.

The market for this device isn't developed yet, but Chung's team will be ready when it is. Meanwhile, the larger device is ready for commercialization, and its creators have started working with distributors.

A UW Center for Commercialization grant of $50,000 seeded initial research in 2008, and since then researchers have received about $2 million in funding from the National Science Foundation and the National Institutes of Health. Sang-gyeun Ahn, a UW assistant professor of industrial design, crafted the prototype.

University of Washington. (2013, May 6). New device can extract human DNA with full genetic data in minutes. ScienceDaily. Retrieved June 5, 2015 from www.sciencedaily.com/releases/2013/05/130506132100.htm

Antibiotic alternatives rev up bacterial arms race

Sara Reardon - 27 May 2015

From predatory microbes to toxic metals, nature is inspiring new ways to treat infections.

More than eight decades have passed since Alexander Fleming’s discovery of a fungus that produced penicillin — a breakthrough that ultimately spawned today’s multibillion-dollar antibiotics industry. Researchers are now looking to nature with renewed vigour for other ways of fighting infection.

Few new antibiotics are in development, and overuse of existing ones has created resistant strains of deadly bacteria. “We need a change from what we have,” says Stephen Baker, head of medicinal chemistry for antibacterials at Glaxo­SmithKline in College­ville, Pennsylvania.

Baker will talk about some of the alternatives to antibiotics on 2 June at the American Society for Microbiology’s annual meeting in New Orleans, Louisiana. Here are a few of the therapies that scientists are exploring.

Predatory bacteria

Bacteria cause infection, but some can also fight it by preying on fellow microbes. Several researchers are beginning to test these predatory bacteria in animal models and cell cultures.

The best-known species, Bdellovibrio bacteriovorus, is found in soil. It attacks prey bacteria by embedding itself between the host’s inner and outer cell membranes, and begins to grow filaments and replicate. “It’s like going into a restaurant, locking the door and starting to munch away,” says Daniel Kadouri, a bacteriologist at Rutgers University in Newark, New Jersey. The host bacterium eventually explodes and releases more B. bacteriovorus into the environment.

Kadouri and others are also studying the therapeutic potential of the predatory bacterium Micavibrio aeruginosavorus. And a team has engineered the gut bacterium Escherichia coli to produce peptides that kill Pseudomonas aeruginosa, a microbe that causes pneumonia.

This preliminary research is attracting attention. The Pathogen Predators programme of the US Defense Advanced Research Projects Agency, which aims to treat soldiers who contract infections on the battlefield, announced nearly US$16 million in research grants this week to groups studying predatory bacteria.

Antimicrobial peptides

Plants, animals and fungi have vastly different immune systems, but all make peptides — small proteins — that destroy bacteria. Peptides from creatures such as amphibians and reptiles, which are unusually resistant to infection, could yield new therapeutics.

Peptides with antibacterial activity have been isolated from frogs, alligators and cobras, among others, and some seem to be effective in epithelial cell cultures and at healing wounds in mice. These peptides can be modified to increase their potency, and several are in clinical trials. One, called pexiganan, based on a peptide from frog skin, is now in phase III clinical trials to treat diabetic foot ulcers.

But synthesizing such molecules can be expensive, a hurdle that scientists must overcome to bring new peptide drugs to market.

Phages

Of all the alternatives to antibiotics, phages — viruses that attack bacteria — have been used the longest in the clinic. Scientists in the Soviet Union began developing phage therapies in the 1920s, and former Soviet countries continue the tradition.

Phages have several advantages over antibiotics. Each type attacks only one type of bacterium, so treatments leave harmless (or beneficial) bacteria unscathed. And because phages are abundant in nature, researchers have ready replacements for any therapeutic strain that bacteria evolve to resist.

Mzia Kutateladze, who heads the scientific council at the Eliava Institute in Tblisi, Georgia, says that antibiotic resistance is driving more Western patients to phage-therapy clinics in Eastern Europe. The US National Institute of Allergy and Infectious Diseases in Bethesda, Maryland, now lists phages as a research priority for addressing the antibiotic crisis. A clinical trial of a phage treatment for infections associated with burns is planned by a consortium of European centres to start this summer.

Gene-editing enzymes

CRISPR, a gene-editing technique that has taken the scientific world by storm, is based on a strategy that many bacteria use to protect themselves against phages. Researchers are turning that system back on itself to make bacteria kill themselves.

Normally, the bacteria detect and destroy invaders such as phages by generating a short RNA sequence that matches a specific genetic sequence in the foreign body. This RNA snippet guides an enzyme called Cas9 to kill the invader by cutting its DNA.

Scientists are now designing CRISPR sequences that target genomes of specific bacteria, and some are aiming their CRISPR kill switches at the bacterial genes that confer antibiotic resistance.

Metals

Metals such as copper and silver are the oldest antimicrobials. They were favoured by Hippocrates in the fourth-century bc as a treatment for wounds, and were used even earlier by ancient Persian kings to disinfect food and water. Only now are researchers beginning to understand how metals kill bacteria.

Some groups are exploring the use of metal nanoparticles as antimicrobial treatments, although little research has been done in people. Because metals accumulate in the body and can be highly toxic, their use may be restricted mostly to topical ointments for skin infections.

An exception is gallium, which is toxic to bacteria that mistake it for iron, but is safe enough in people to be tested as an intravenous treatment for lung infections. This summer, researchers at the University of Washington in Seattle will begin a phase II clinical trial of gallium in 120 patients with cystic fibrosis. Pilot studies found that the metal was moderately successful at breaking down microbial biofilms in the lungs and improving patients’ breathing.

Nature 521, 402–403 (28 May 2015) doi:10.1038/521402a