real time dna analysis

real time dna analysis

Biomeme, a new company out of Philadelphia, PA, is planning on launching an easy to use system that can perform real-time qPCR and provide results through any smartphone without using expensive lab equipment nor requiring an experienced hand to operate. The goal is to offer medical professionals, regardless of their location, the ability to do advanced diagnostics and perform disease surveillance.

Biomeme’s platform transforms a smartphone into a mobile lab for advanced DNA diagnostics and real-time disease surveillance. The system includes:

a docking station for performing real-time quantitative polymerase chain reaction (qPCR)
a mobile app to wirelessly control the system, analyze results in real-time and send them to the cloud
targeted test kits for preparing samples and identifying pathogens or diseases by their specific DNA or RNA signatures.
The low-cost system requires no special laboratory equipment and could enable mobile testing at the point-of-need for health care, agriculture, vector surveillance, veterinary medicine, environmental monitoring, and even education and citizen science.

We’re intrigued by the battery-powered system’s game changing potential and hope to interview the team in an upcoming article.


Baby born using new IVF screening technique By James Gallagher Health and science reporter, BBC News

Baby born using new IVF screening technique  By James Gallagher Health and science reporter, BBC News

Connor Levy’s parents had been trying to conceive naturally for four years.

A baby has been born in the US using a new method for screening embryos during IVF which could dramatically reduce costs, researchers report.

Connor Levy was born in May after the test, devised at Oxford University, helped doctors pick an embryo with the best chance of success.

Only one in three attempts at IVF results in a baby as abnormalities in an embryo’s DNA are common.

Large trials are now needed to see how effective the method is, experts say.

If there are abnormalities with the packages of DNA, called chromosomes, in the embryo then it will not implant in the womb or if it does the foetus will not reach term.
It is a problem which increases rapidly with age. One quarter of embryos are abnormal in a woman’s early 30s, but this soars to three quarters by the time a woman reaches her late 30s and early 40s.

Some clinics already offer a form of chromosome screening, but it can add between £2,000 and £3,000 to the cost of IVF in the UK. Connor’s mother, Marybeth Scheidts, said it would have cost her $6,000 (£4,100) for the test in Pennsylvania.

The new test takes advantage of the dramatic advances in sequencing the human genome. Within 24 hours it can ensure the correct number of chromosomes are present.

Dr Dagan Wells from Oxford University told the BBC: “Current tests are adding a significant amount of money on to an already expensive procedure and that is limiting access; most patients are having to pay for this out of pocket themselves.

“What our technique does is it gives you the number of chromosomes and other biological information about the embryo at a low cost – probably about two thirds of the price of existing methods of screening.”

How to pick the right embryo to implant is a major issue in fertility clinics
He says trials are now needed to see if it could improve IVF success rates.

Tears of joy
The baby and a further pregnancy resulting from the screening method will be announced at the European Society of Human Reproduction and Embryology conference.

Marybeth Scheidts, 36, and her husband David Levy, 41, had been trying to conceive naturally for four years and also tried artificial insemination.

In the screening three of the 13 embryos produced were healthy. Without chromosome screening, picking the right embryo would have been down to luck. Instead they were successful on their first attempt.

Marybeth told BBC News Online that the years of trying were tough: “It takes its toll, there were some days I would break down and cry, I wanted to hide in my bedroom and say stop.
“Then to see him… all this hard work and we have finally got our little tiny human being named Connor.”

Dr Michael Glassner, the fertility doctor at Main Line Health System where the IVF took place, said such techniques would become more common.

“If you have ever sat across the desk from a patient that has failed or is in that crossroads of thinking of another cycle and you look in their eyes where they are barely able to hold on to their hopes and dreams – anything that is so significantly going to impact pregnancy rates is going to become standard.

“So I think five years from now you fast forward – yes I think it will be standard.”

Commenting on the study, Stuart Lavery, a consultant gynaecologist and director of IVF at Hammersmith Hospital, said: “This is amazing science.

“They done the work in humans, they’ve pregnancies – so it’s a pretty powerful proof of concept study using an exciting technique.”

He also praised the researchers for saying proper trials needed to be conducted before it was used widely.

Scientists Discover 23 Million-Year-Old Lizard Fossil in Mexico

Scientists Discover 23 Million-Year-Old Lizard Fossil in Mexico

A team of Mexican scientists have discovered an oldest lizard fossil that was trapped in amber and are studying in the detail the complete fossil. (Photo : Wikimedia Commons )

A team of Mexican scientists has discovered a lizard fossil that lived around 23 million years ago, trapped in amber, reports IANS.
Several months ago the scientists found a small piece of fossil resin in the shape of a trapezoid in which the lizard remains were found. The fossil was retrieved from Simojovel amber deposits that are located in the northern part of the southeastern state of Chiapas.

The complete fossil of the lizard that was preserved in the amber is currently on display at the Amber Museum in San Cristobal de las Casas.
Amber is a tree resin and most often contains remains of animal and plant remains. But to find the complete remains of a specimen is very rare, as in the case of this lizard fossil. Initially, the scientists had identified the lizard as a new species belonging to the genus Anolis.
With almost 400 species, Anolis is a genus of lizards belonging to the family Dactyloidae. The Anolis lizards are best known for their adaptive radiation as well as convergent evolution, reports Wikipedia.
Francisco Riquelme of the National Autonomous University of Mexico’s Physics Institute to EFE said that the newly discovered fossil lizards measured almost 4.5 cm by 1.3 cm. What was even more interesting about this 23-million-old lizard fossil was that it had well preserved remains of not just the soft tissues but also the skin.
Gerardo Carbot, director of Chiapas’s Paleontology Museum said, “The fossil specimens found in the state date back a minimum of 23 million years because that is the age of the amber that is extracted from deposits in the municipalities of Simojovel, Huitihupan, El Bosque, Pueblo Nuevo, Palenque, Totolapa and Malpaso.”

Prehistoric DNA sequencing: Jurassic Park was not so wide of the mark

Prehistoric DNA sequencing: Jurassic Park was not so wide of the mark

Strong genes: scientists have sequenced the DNA of a horse that lived 700,000 years ago – far beyond what was thought possible. Photograph: Tierfotoagentur/ Alamy

Mapping the genome of a horse from 700,000 years ago goes far beyond what was thought possible with DNA sequencing

It remains one of the most intriguing premises for a science fiction film. Near the beginning of Steven Spielberg’s classic Jurassic Park, scientists reveal how they have collected the DNA of dinosaurs from mosquitoes trapped in amber more than 65m years ago. These insects had previously fed on dinosaurs’ blood and by extracting these blood cells, and removing their DNA, entrepreneur John Hammond (Richard Attenborough) recreates genomes of velociraptors, triceratops, and other dinosaurs. From these genomes, he clones the terrifying creatures that go on to terrorise the film’s characters.

At the time, the idea – originally outlined by Michael Crichton in his book Jurassic Park – sounded plausible until researchers pointed out that DNA simply cannot exist intact for such lengths of time. In fact, you would be lucky if you could go back more than a few thousand years before DNA becomes hopelessly fragmented, it was argued. Defences that repair DNA in living cells disappear after death. As a result, DNA strands quickly break up. Hence researchers’ limit of a few thousand years for the feasibility of creating an extinct creature’s genome.

But reality has a way of catching up on science fiction. Technical developments in DNA recovery have slowly transformed the business of recovering ancient genetic material. As a result, in 2010, a team led by Svante Pääbo, at the Max Planck Institute for Evolutionary Anthropology in Germany, revealed it had sequenced the entire genome of a Neanderthal based on three specimens at least 38,000 years old from Vindija Cave, Croatia. The work has since provided critical insights into modern humans’ genetic relationships with this ancient hominin species.

Since then Pääbo’s researchers have pushed their genome sequencing power even further into the past and last year announced they had sequenced the genome of a girl belonging to a species of humans called the Denisovans – a close relation to the Neanderthals – who lived about 80,000 years ago. The study showed she had brown eyes, hair and skin.

But now scientists have taken that sequencing age limit even further – and by a considerable margin. In Nature this week, a team led by Ludovic Orlando of Copenhagen University published a paper in which they reveal the entire genetic sequence of a species of horse that lived around 700,000 years ago – almost 10 times the current limit. It is an extraordinary achievement, one that immediately raises the prospect that scientists might soon create the genomes of creatures that died more than a million years ago, possibly several million years. By that reckoning, Crichton and Spielberg would not seem to be so far out.

Of course, Orlando and his colleagues were fortunate in one respect. Their horse genome was recreated from a bone fragment that was found in the Arctic permafrost at Thistle Creek, Canada. Its DNA had, in effect, been kept in cold storage for all that time. Nevertheless, unravelling it involved the use of advanced computing techniques, infomatics, and the ability to study the structures of proteins found in the sample. As Orlando stated: “We were amazed about the quality of the sample. We not only beat the record for [oldest] genome characterisation by almost an order of magnitude… we also discovered that a whole bunch of approaches can be used to characterise the deep evolutionary past.”

The work will certainly help scientists understand the evolution of the horse but it is the wider implications of Orlando’s work that really excites, a point stressed by molecular biologists Craig Millar and David Lambert in an accompanying editorial in Nature. The new research raises “the tantalising proposition that complete genomes several millions of years old may recoverable given the right environmental conditions”, they state. Ancient human forebears such as Homo erectus which first appeared in the fossil record around 1.8m years ago and more recent ancestors, such Homo heidelbergensis, may soon come within range of the genome sequencers, offering all sorts of insights into the evolution of Homo sapiens.

Of course, recreating ancient genomes does not mean we could actually clone such creatures. A host of ethical and practical difficulties would have to be surmounted before that became possible, issues that were ignored by Spielberg and Crichton. Nevertheless, science does indicate they were not quite as far from the mark as was previously supposed.

Avoid dementia by keeping brain ‘active’

Avoid dementia by keeping brain 'active'

Performing mental challenges leads to slower cognitive decline. It adds weight to the idea that dementia onset can be delayed by lifestyle factors.

Staying mentally active by reading books or writing letters helps protect the brain in old age, says a new American study.

The study, published in Neurology, says performing mental challenges leads to slower cognitive decline. It adds weight to the idea that dementia onset can be delayed by lifestyle factors, BBC reported.

In the study by the Rush University Medical Center in Chicago, 294 people over the age of 55 were given tests that measured memory and thinking, every year for about six years until their deaths.

They also answered a questionnaire about whether they read books, wrote letters and took part in other activities linked to mental stimulation during childhood, adolescence, middle age, and in later life.

After death, their brains were examined for evidence of the physical signs of dementia, such as brain lesions and plaques.

The study found that after factoring out the impact of those signs, those who had a record of keeping the brain busy had a rate of cognitive decline estimated at 15 percent slower than those who did not.

Robert Wilson, of the Rush University Medical Center, who led the study, said the research suggested exercising the brain across a lifetime was important for brain health in old age.

“The brain that we have in old age depends in part on what we habitually ask it to do in life. What you do during your lifetime has a great impact on the likelihood these age-related diseases are going to be expressed,” Wilson told BBC.

Commenting on the study, Simon Ridley, head of research at Alzheimer’s Research UK, said there was increasing evidence that mental activity may help protect against cognitive decline. But the underlying reasons for this remained unclear.

“By examining donated brain tissue, this study has shed more light on this complex question, and the results lend weight to the theory that mental activity may provide a level of ‘cognitive reserve’, helping the brain resist some of the damage from diseases such as Alzheimer’s,” he told BBC.

Introduction to Microbiology Culture Techniques

Nicole Gentile, PhD Candidate, provides an overview of basic microbiology and the concepts involved, including the bacterial growth curve and classifying organisms based on morphologies. This lecture describes blood, urine and skin/soft tissue cultures, focusing on the types of media, sample collection processes, culture procedures, as well as speciation and susceptibility testing. Basic staining procedures, such as the simple stain, gram stain, spore stain, negative stain, and acid fast stain are briefly discussed. Included in the staining procedure descriptions are explanations of the organisms that the stains identify. In addition to staining procedures, biochemical tests used for differentiating bacteria are covered. Concluding the lecture are some facts about fungi and viruses, focusing on the current 2009 novel H1N1 influenza pandemic.