7 Free Tools for Statistical Analysis

Which is the most important part of a research? Yes, it is ‘designing your experiments correctly’. Next comes ‘interpreting’ your results. Research in Biotechnology and other life sciences can produce a lot of quantitative data which needs to be analyzed for statistical significance. Many graduates know to use Word, Powerpoint and Excel to a certain level. However, many new emerging job opportunities in modern biology requires skill to deal with quantitative data.

Below, I’ve mentioned 7 free online tools to take care of statistical needs ranging from T-tests, multiple regressions to Cluster Analysis, Bootstrapping etc.

1. SISA (Simple Interactive Statistical Analysis)

Conduct your statistical analysis directly online, no need to download anything. Click SISA for more details. You can also study the given guides to determine the appropriate procedure for your research problem.

2. Open Epi

Open Epi is a free software program designed to cater for statistical needs in epidemiology. It can run from a web server or can also be downloaded and run without a web connection. You can also operate this program from your android or iphone.

3. Scistat Calc

This is actually a blog ( running on blogspot). It has online calculators for common probability functions and significance tests and also explanation of concepts and formulas behind each test. Please go through Scistat Calc, it’s a really useful blog.

4. Rice Virtual Lab in Statistics

It contains online statistics book, simulations, case studies and other resources for statistical analysis. You can access it here.

5. WINPEPI

This is a free software available only for Windows users. WINPEPI has many programs ranging from comparing any 2 independent samples to multiple poisson regression, for more details visit WINPEPI

6. Online Graph generators

Popular free online graph tools for producing neat scatter plots are Meta-calculator and Online Curve fitting. These are worth a try.

7. R ( Open Source Statistical software)

Most of the bachelors and masters students use MS Excel for their statistical needs. Excel can be used to calculate t-tests and other co-relations decently. But, when you are handling a lot of data and need to do something more, then Excel may not be the right choice.

R is more than a software. It is a language for statistical computing and graphics. It caters for a very wide variety of statistical analysis and the speciality of R language is that it produces quality graphs fit for publication (including mathematical symbols and formulae). It runs on Windows, Linux and also Mac. Moreover, it is free !!

Like any language it takes time to learn, but it has TONS of benefits. R language is widely used by statisticians and many commercial firms for data mining and analysis. To put it in very simple terms, it is comparable to MATLAB, but it is free. Download R language at https://www.r-project.org/

Details regarding Documentation can be found at R – documentation. Free online courses about how to use R can be found at Datacamp and Coursera (At coursera, the next session is from August 3 to August 30; 2015). R is actually one computer language which will always be useful for researchers and it is being constantly updated. Hence, it won’t be outdated soon. So why not invest your spare time to learn this useful language?

Flu Vaccine Becomes Universal

While many of us are spending the last half of the summer deciding where the nicest beaches are and who makes the best island cocktails, infectious disease scientists are looking ahead toward the next inevitable outbreak of the flu. Influenza hunters travel to hot zones that have long been the traditional breeding grounds and launching points for global seasonal pandemics. This is an important part of creating seasonal flu vaccines, which protect against only a few specific strains that researchers predict will be the most common for the upcoming year.

Anatomy of influenza virus. An array of subtypes for the surface coat protein hemagglutinin (blue) is what NIAID scientists used to create their universal vaccine. [CDC/Dan Higgins]

What if we could create a vaccine that could protect against most or all influenza strains? This has been the “grail quest” that numerous infectious disease researchers have strived toward for decades. Now, investigators from the National Institute of Allergy and Infectious Diseases (NIAID), a division of the National Institutes of Health, have developed a universal vaccine that may provide broad protection against numerous influenza strains, including ones that could cause future pandemics. 

"The reason researchers change the vaccine every year is that they want to specifically match the vaccine to the particular viruses that are circulating, such as H1N1. If the vaccine is just a little bit different to the target virus, it is not expected to offer much protection," explained senior author Jeffery Taubenberger, M.D., Ph.D., chief of the Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases at NIAID. "What we have done is design a strategy where you don't have to think about matching the vaccine antigen to the virus at all."

The findings from this study were published recently in mBio through an article entitled “An Intranasal Virus-Like Particle Vaccine Broadly Protects Mice from Multiple Subtypes of Influenza A Virus.”

Previous research into universal flu vaccines has focused on finding invariable regions of viral coat proteins that could be exploited to generate an immune response that provides significant protection. However, in this study the scientists took a different approach and engineered a virus-like particle (VLP) that expressed an array of hemagglutinin subtypes from the surface of the influenza virus, including H1, H3, H5, and H7.

"There are 16 different hemagglutinin subtypes that circulate in birds and are thought to be the basis for current and future influenza pandemics," stated Dr. Taubenberger. "The hypothesis was that the presentation of these different viral proteins would stimulate the development of cross-protective immunity that would provide broader protection against multiple subtypes."

The H1 and H3 subtypes were chosen as they have been linked to major influenza outbreaks since the 1918 Spanish flu pandemic, which has been estimated to have killed close to 100 million people. The investigators chose H5 and H7 subtypes, as they have been the cause of recent bird flu outbreaks and have a high potential to spread into humans.

The results from the study showed that 95% of mice vaccinated with the novel cocktail were protected against a lethal challenge from eight different influenza strains, while only 5% of unvaccinated mice survived. 

"Almost all of the animals that were vaccinated survived, including mice that were challenged with viruses that expressed hemagglutinin subtypes that were not in the vaccine at all, viruses that expressed H2, H6, H10, and H11," noted Dr. Taubenberger. "What that suggests is that this approach really gives us broad spectrum protection, and could serve as a basis for an effective pre-pandemic vaccine."

The NIAID team was also able to show that vaccine’s efficacy lasted for at least 6 months and that it worked well in older mice—an important point since current vaccines are less effective in the elderly.

"These initial findings are very positive and suggest a promising and practical strategy for developing a vaccine with amazing, broad protection," concluded Dr. Taubenberger.

Source: http://www.genengnews.com/gen-news-highlights/flu-vaccine-becomes-universal/81251534/

NASA finds ‘another Earth’ in Milky Way and it's called Earth 2.0

Earth 2.0 or Kepler 452b is so like Earth that Nasa believes it is possible that life once inhabited the planet. 

Nasa has found a twin Earth orbiting a star like the Sun in the Milky Way which scientists say ‘would feel a lot like home.’

Kepler 452b - which has been dubbed Earth 2.0 - is six billion years old, has a 385 day year and orbits its star at the same distance as us. It is 1,400 light-years away in the constellation Cygnus.


It is believed to be rocky, with active volcanoes and is so like Earth that Nasa believes it is possible that life once inhabited the planet.


Scientists said that the sunshine is so similar that plants could survive if taken to Kepler 452b.

But because it is 1.5 billion years older, scientists say it gives a ‘peek into a crystal ball showing a possible future for Earth’ as it reaches a point where it is no longer habitable.

“If Kepler 452b is indeed a rocky planet, its location could mean that it is just entering a runaway greenhouse phase of its climate history,” said Doug Caldwell, a SETI Institute scientist working on the Kepler mission.

“The increasing energy from its aging sun might be heating the surface and evaporating any oceans. The water vapour would be lost from the planet forever.

“Kepler 452b could be experiencing now what the Earth will undergo more than a billion years from now, as the Sun ages and grows brighter.”

The Kepler spacecraft has been looking for signs of new worlds outside the Solar System since May 2009, and has so far found more than 4,000 planets in the so-called ‘Goldilocks Zone’ – neither too hot, nor too cold to sustain life.

On Thursday Nasa announced they had found 500 new possible planets to add to the 4,175 already found by the telescope, and 12 were ‘Earth-like.’ But Kepler 452b is the first of the 12 to be confirmed as a planet and Nasa said it was the 'closest' to Earth that has ever been seen.

It is 60 percent larger in diameter than Earth and is considered a super-Earth-size planet.

“Today the Earth is a little less lonely because there is a new kid on the block,” said Jon Jenkins, Kepler data analysis lead at NASA's Ames Research Center in Moffett Field, California.

"If you travelled to this star with an arkful of plants...the plants would photosynthesise just perfectly fine. It would feel a lot like home from the standpoint of the sunshine.

“It is six billion years old. That is considerable opportunity for life to arise on its surface and its oceans should all the necessary conditions for life have appeared on this planet.

“This is the closest thing that we have to another planet like the Earth. And the Earth follows nearly in the footsteps of its older cousin and will be there in 1.5 billion years time.”



The area of the Milky Way in which Kepler is looking Credit: NASA

The discovery gives new hope that alien civilisations may exist beyond the Solar System. Earlier this week Professor Stephen Hawking and the Astronomer Royal Lord Martin Rees announced they were joining a $100 million project to seek out signs of extra-terrestrial intelligence in the Milky Way.

"We won't be going to this planet but our children's children's children might be," said Jeff Coughlin, Kepler research scientist at SETI Institute in Mountain View, California "It's a very long term goal but a very exciting one."

Kepler’s task is to look for rocky planets between half and twice the size of Earth where water could still exist on the surface.

Since liquid water is critical to life on Earth, many scientists believe the search for extra-terrestrial life should focus on planets where liquid water occurs.

The size of the planet also means it has enough gravity to pull in gases like hydrogen and helium to form an atmosphere.

The space observatory detects planets as their orbits cross in front of their star and cause a very tiny but periodic dimming of the star’s brightness.

Nasa is also trying to determine the fraction of the hundreds of billions of stars in our galaxy that might have such planets.

“We’re trying to answer fundamental questions, Where do we come from, where are we going? What’s the future of our Solar System,” John Grunsfeld, associate administrator for NASA's Science Mission Directorate .

“We’re going to take one small step in answering that question today.”

MicrobeWorld's After Hours - Antibiotic Resistant Bacteria

#Event

Titled: MicrobeWorld's After Hours - Antibiotic Resistant Bacteria

Difference between CV and Resume...........

With renovation in world, people become educated and smart but still there are few things people are unaware. Therefore today will talk about an important issue facing by beginners especially. You might be thinking that what it is. Yes there is an issue people are unaware that is difference between resume and CV. Now day’s even adults and working people do not know the exact difference. However, for understanding the difference, first of all everyone should know the definition of resume and CV.

CV Vs Resume

These two terms are entirely different from each other. People should know the difference between CV and resume.

What is CV? 

CV is basically called Curriculum Vitae.

• CV basically provides a complete summary of your educational background and extra achievements.
• It also contains your different experiences, researches, awards, honors, presentations and speeches.
• There is no word limit in CV.

CV used for what?

Normally fresh graduates and job seeker use CV. Moreover, purpose of CV is to apply for any internship, scholarship and job. It can also be called an application by a person who is applying for something.

What Resume means?

• Resume basically means complete information about your professional experiences.
• There is word or page limit in resume. Like you cannot extend from two pages.
• Precisely, resume is a way to show your capabilities in a proficient manner.

Resume used for what? 

It is used to apply for any industry, company, organization and governmental job. Through using resume anybody can show inner talent by offering good impression of personality. Main reason of resume is to get a reliable and good job.

Difference between CV and Resume: 

The major difference between CV and Resume is that person has to alter details for different position in Resume but in CV, it remains the similar. Moreover, in CV everything listed in a chain or we can say sequence but in Resume, you have to add your professional achievements and information in different manner without following any chronological order. Furthermore, CV has entire record of your educational career and your information. On the other hand, in Resume only target information is existed. No format is followed in Resume but in CV you have to follow certain format. CV can be prolonged but resume cannot be. In addition, Canada, America UK, South Africa, New Zealand, Ireland, is the countries where it is preferable to for CV instead of Resume. However, in India and Australia these two terms are transposable. People can also get differentiation information by taking help from internet as now people getting informed day by day.

So are you ready for a better life?

If you really want to achieve few goals in your life then make sure to know the dissimilarity between these two terms. Otherwise, you are unacquainted from a major distinction and for having a first-class job, cleverness and brain power both matter. So live a life with self-reliance and information by attaining your goals of life.

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

#Phage_Therapy_in_Nepal

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/