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I Contain Multitudes | Quanta Magazine

I Contain Multitudes |  Quanta Magazine | Complex Insight  - Understanding our world | Scoop.it
Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing?
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With new methods of single cell DNA sequencing becoming available - biologists are beginning to look a the degrees of variations that exist across cells and the extent of cell to cell diversity and what this implies for biological adaptation.

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Laser spotlight reveals machine 'climbing' DNA

Laser spotlight reveals machine 'climbing' DNA | Complex Insight  - Understanding our world | Scoop.it

New imaging technology has revealed how the molecular machines that remodel genetic material inside cells 'grab onto' DNA like a rock climber looking for a handhold.

 

The experiments, reported in this week's Science, use laser light to generate very bright patches close to single cells. When coupled with fluorescent tags this 'spotlight' makes it possible to image the inner workings of cells fast enough to see how the molecular machines inside change size, shape, and composition in the presence of DNA.

 

The Oxford team built their own light microscopy technology for the study, which is a collaboration between the research groups of Mark Leake in Oxford University's Department of Physics and David Sherratt in Oxford University's Department of Biochemistry.

 

The molecular machines in question are called Structural Maintenance of Chromosome (SMC) complexes: they remodel the genetic material inside every living cell and work along similar principles to a large family of molecules that act as very small motors performing functions as diverse as trafficking vital material inside cells to allowing muscles to contract.

 

The researchers studied a particular SMC, MukBEF (which is made from several different protein molecules), inside the bacterium E.coli. David Sheratt and his team found a way to fuse 'fluorescent proteins' directly to the DNA coding for MukBEF, effectively creating a single dye tag for each component of these machines.

 

Up until now conventional techniques of biological physics or biochemistry have not been sufficiently fast or precise to monitor such tiny machines inside living cells at the level of single molecules.

 

'Each machine functions in much the same way as rock-climber clinging to a cliff face,' says Mark Leake of Oxford University’s Department of Physics, 'it has one end anchored to a portion of cellular DNA while the other end opens and closes randomly by using chemical energy stored in a ubiquitous bio-molecule called adenosine triphosphate, or 'ATP': the universal molecular fuel for all living cells.

 

'This opening and closing action of the machine is essentially a process of mechanical 'grabbing', in which it attempts to seize more free DNA, like the rock-climber searching for a new handhold.'

 

It is hoped that pioneering biophysics experiments such as this will give fresh insights into the complex processes which are vital to life, and pave the way for a whole new approach to biomedical research at the very tiny length scale for understanding the causes of many diseases in humans, and how to devise new strategies to combat them. 


Via Dr. Stefan Gruenwald
ComplexInsight's insight:

its turtles all the way down... as we obtain more and more data and insight into cellular molecular mechanisms  their organisation, interactions, spatial and temporal dynamics become increasingly mechanistic with multiscale emergent propertiesarising from local interactions. This pioneering biophysics approach will likely generate a lot more insights into molecular mechanisms as it gets increasingly adopted for other experiments.

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Interview with Brian Mathews, Group CTO @ Autodesk

Great insight into types of developments being done at Autodesk as Robert Scoble interviews Brian Mathews, group CTO at Autodesk. Conversation covers 3D printing, cloud computing, nano technology, biomimetics, applied genetic algorithms to design etc. Great interview Click image or title to learn more..

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Reviewing the anti-cancer efficacy of curcumin « Integrative Biology Blog

Reviewing the anti-cancer efficacy of curcumin « Integrative Biology Blog | Complex Insight  - Understanding our world | Scoop.it

Tumeric is long held in to have healing effects in ayurvedic medicine. Curcumin, a bioactive ingredient in the fragrant orange spice tumeric, is thought to be effective in suppressing tumor growth and promoting chemoprevention of certain cancers.

In this review article Bassel El-Rayes et al. summarise the recent studies which describe preventive and therapeutic effects of curcumin and its analogues. In particular they concentrate on the breast cancer model, as curcumin has shown responses in reversing the human breast cancer cell resistance against paclitaxel and may be responsible for the lower incidence of breast cancer in Asian countries. Click on image or title to learn more.

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Scientists reveal mechanism for cellular remodeling

Knowing precisely how a cell is built will enable scientists to reconfigure and repurpose them for various biomedical applications,” says Bruce Goode, professor of biology whose lab studies the cytoskeleton. Until recently, scientists believed that there were different nucleators, or cell- igniters, responsible for making different types of actin structures or networks. But over the last few years, genetic research has suggested that nucleators might actually collaborate more often than they act alone. Click on title to learn more...

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Scientists discover cell surface 'docking stations' play important function in membrane protein trafficking

Scientists discover cell surface 'docking stations' play important function in membrane protein trafficking | Complex Insight  - Understanding our world | Scoop.it

(Phys.org) -- Ion channel proteins – teeny batteries in cells that are the basis for all thought and muscle contraction, among other things – also serve as important docking stations for other proteins that need help figuring out where to go according to groundbreaking new research by a team of Colorado State University scientists. The research by Diego Krapf, an assistant professor in the Department of Electrical and Computer Engineering, Mike Tamkun, a professor in the Department of Biomedical Sciences and Emily Deutsch  appears this month in the peer-reviewed journal, Molecular Biology of the Cell.  Click image or title to learn more.

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Whole Cell Biosensors in the Era of Synthetic Biology - July 3 London

Whole Cell Biosensors in the Era of Synthetic Biology - July 3 London | Complex Insight  - Understanding our world | Scoop.it

If you can make it the Whole Cell Biosensors in the Era of Synthetic Biology on July 3rd in London (at the BIS conference Centre) looks very worth attending. The purpose of this meeting is to facilitate knowledge exchange between the two closely related disciplines of Whole Cell Biosensors and Synthetic Biology and stimulate further ideas for successful future developments. Learn more...

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Human Microbiome Project DACC - HMPDACC Data Browser

Human Microbiome Project DACC - HMPDACC Data Browser | Complex Insight  - Understanding our world | Scoop.it
via +Humberto González-Díaz

*NIH Human Microbiome Project*

Data Portal
http://bit.ly/LhsWi2


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Informatics, Biology Team Demonstrates Role of Foreign DNA Strands in Life-Supporting Bacteria

From - Lab Manager Magazine® : An Indiana University team of researchers has conducted the most in-depth and diverse genetic analysis of the defense systems that trillions of micro-organisms in the human body use to fend off viruses. Led by IU Bloomington assistant professor of informatics and computing Yuzhen Ye, the team of bioinformaticists and biologists reconstructed arrays of clusters of regularly interspaced short palindromic repeats -- CRISPRs -- which function as immune systems to the bacteria that play a vital role in human health. Between genomic repeats, CRISPR locations carry short strands of foreign DNA called spacers, which provide a history of past exposures to outside invaders like plasmids and bacteriophages (viruses that infect bacteria), and allow the bacteria to fight off viruses they have already encountered. This is an incredibly interesting piece of research and demonstrates the applications of CRISPRs to tracing the virus exposure of individuals  and it indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes and human health.  Learn more...

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Cellular Computing - Google+

Cellular Computing - Google+ | Complex Insight  - Understanding our world | Scoop.it
Cellular Computing

is a new page on G+ where you can discuss exiting concepts and publication around cellular computer. Have a look! Really cool material.....

https://plus.google.com/u/0/b/106140549977596536572/


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What's quantum physics got to do with biology?

Tonight at the World Science Festival, astrophysicist Paul Davies and quantum computing innovator Seth Lloyd will talk about the growing field of quantum biology—why it works, what it means, and how it might shape our future. The Bad News: The Festival is happening in New York City and tonight's panel is sold out. The Good News: You can watch a live webcast of the event online at 8:00 Eastern time.  Learn more

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New blood analysis chip could lead to disease diagnosis in minutes

New blood analysis chip could lead to disease diagnosis in minutes | Complex Insight  - Understanding our world | Scoop.it

This UC Berkelyreport from 2011 highlights the development of the basic mechanics of a lab on a chip. This  major milestone in microfluidics could soon lead to stand-alone, self-powered chips that can diagnose diseases within minutes. Learn more...

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Biotechnology innovation for inclusive growth: a study of Indian policies to foster accelerated technology adaptation for affordable development - Vijayaraghavan & Dutz (2012) - World Bank

The recent withholding of approval for transgenic eggplant in India by the Minister for Environment highlights the complications in bringing consensus in regulatory processes. In principle, Indian ability to effectively regulate biotechnology-derived products in healthcare and agriculture should provide a competitive advantage given the lower costs in carrying out such validation, driven by abundant available scientific and clinical labor and the consequent lower total costs of various validation procedures. Currently, the cost of regulations in OECD countries typically leads the private sector to confine regulatory validation to products that have a sufficiently large global market potential. This is a key reason for large multinationals and industrialized country public research bodies not to advance research for neglected diseases, small acreage crops, and low-value agriculture products. If India gains sufficient regulatory capacity, then the products approved in India have the potential to reach other developing countries that have similar product needs in the areas of health and agriculture.


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First ever biological amplifier created by Imperial scientists

First ever biological amplifier created by Imperial scientists | Complex Insight  - Understanding our world | Scoop.it

cientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

 Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals. Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli). 
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by Gail Wilson

"Scientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals.
Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli). 

The team say this ‘bio-amplifier’ might be used in microscopic cellular sensors , which scientists have already developed, that could detect minute traces of chemicals and toxins, to make them more sensitive. Ultimately, this could lead to new types of sensors to detect harmful toxins or diseases in our bodies and in the environment before they do any damage.
In laboratory tests, the team’s bio-amplifier was able to significantly boost the detection limit and sensitivity of a sensor designed to detect the toxin arsenic. The device is also modular, which means that the devices can be easily introduced in different genetic networks, and can potentially be used to increase the sensitivity and accuracy of a broad range of other genetic sensors to detect pathogens and toxins.
The results of the study are published in the journal Nucleic Acids Research. 
Dr Baojun Wang, who is now based at the University of Edinburgh, but carried out the study while in the Division of Cell and Molecular Biology at Imperial, said: “One potential use of this technology would be to deploy microscopic sensors equipped with our bio-amplifier component into a water network. Swarms of the sensors could then detect harmful or dangerous toxins that might be hazardous to our health. The bio-amplifiers in the sensors enable us to detect even minute amounts of dangerous toxins, which would be of huge benefit to water quality controllers.”
Scientists have previously known that cells have their own inbuilt amplifiers to first detect and then boost biological signals, which are crucial for survival and reproduction. They have been attempting to understand how they work in more detail so as to remodel them for other applications. However the challenge for scientists has been engineering a device that can predictably amplify signals without distortion or feedback.
In the study, scientists first re-engineered genes involved in a special cell network called hrp (hypersensitive response and pathogenicity), which have naturally occurring amplifying proteins that function just like an electronic amplifier. They then cloned these amplifying components and inserted them into the harmless gut bacteria E. coli, fitting it with a synthetic arsenic input sensor and a fluorescent green protein gene as the output.  ..."


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Will 'big data' prevent disease?

Will 'big data' prevent disease? | Complex Insight  - Understanding our world | Scoop.it
How the blistering pace of technological change could have a profound impact on healthcare.
ComplexInsight's insight:

Good article from the BBC Future health series. Video is worth watching if you want an insight into how new technologies will impact healthcare.

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Cancers Genomes and their Implications for Curing Cancer (by Bert Vogelstein, JHU)

The full lecture title is "Cancers - Their Genomes, Microenvironments, and Susceptibility to Bacteria-based Therapies" by Bert Vogelstein. The Johns Hopkins Center for Biotechnology Education and the Department of Biology in the Krieger School of Arts and Sciences hosted the American Society for Microbiology's Conference for Undergraduate Educators (ASMCUE) on the Homewood campus. Bert Vogelstein gave the closing plenary lecture, "Cancers - Their Genomes, Microenvironments, and Susceptibility to Bacteria-based Therapies". He teaches at John Hopkins University.

ASMCUE, now in its 18th year, is a professional development conference for approximately 300 educators. Each year, its steering committee organizes a program that offers access to premier scientists in diverse specialties and to educators leading biology education reform efforts. For more information on the conference, go to http://www.asmcue.org/page02d.shtml


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Computer Simulation Cracks Chicken-Egg Puzzle : Discovery News

Computer Simulation Cracks Chicken-Egg Puzzle : Discovery News | Complex Insight  - Understanding our world | Scoop.it

New computer technology cracks the age-old riddle, demonstrating how a protein kickstarts eggshell formation. Researchers at the Universities of Sheffield and Warwick, in northern and central England, demonstrate how vocledidin-17 (OC-17), plays a part in eggshell formation. In a computer simulation, the OC-17 protein acted as a catalyst to kickstart the formation of crystals that make up an eggshell by clamping itself on to calcium carbonate particles. In otherwords the chicken came first. Click on image or title to learn more...

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Researchers closer to understanding how proteins regulate immune system

Researchers closer to understanding how proteins regulate immune system | Complex Insight  - Understanding our world | Scoop.it

Researchers have revealed how white blood cells move to infection or inflammation in the body; findings which could help lead to developing drug therapies for immune system disorders. Click on the image or title to learn more.

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Flu immunity is affected by how many viruses actually cause the infection

Flu immunity is affected by how many viruses actually cause the infection | Complex Insight  - Understanding our world | Scoop.it

Both the number of viruses in initial flu infection, and the virus type, affects the patient's outcome. Mice infected by high concentrations developed immunity, and generated immune cells in the lungs to fight other strains. Mice that were infected with a relatively low concentration of the virus developed weaker immunity against the strain that infected them, did not build up this crucial population of immune cells in the lungs, and showed only delayed immunity toward other flu strains. This discovery could pave the way for new prophylactic strategies to fight flu infections and provides a novel basis for vaccine design. Learn more by clicking on the image or headline.

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Scientists Tie DNA Repair to Key Cell Signaling Network - Bioscience Technology

Scientists Tie DNA Repair to Key Cell Signaling Network - Bioscience Technology | Complex Insight  - Understanding our world | Scoop.it

University of Texas Medical Branch at Galveston researchers have found a surprising connection between a key DNA-repair process and a cellular signaling network linked to aging, heart disease, cancer and other chronic conditions. The discovery promises to open up an important new area of research — one that could ultimately yield novel treatments for a wide variety of diseases. Learn more...


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Biologists grow human-eye precursor from stem cells

Biologists grow human-eye precursor from stem cells | Complex Insight  - Understanding our world | Scoop.it

A stem-cell biologist has had an eye-opening success in his latest effort to mimic mammalian organ development in vitro. Yoshiki Sasai of the RIKEN Center for Developmental Biology (CBD) in Kobe, Japan, has grown the precursor of a human eye in the lab. Learn more...

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Humanoid Robot Swarm Synchronized Using Quorum Sensing - Technology Review

Humanoid Robot Swarm Synchronized Using Quorum Sensing  - Technology Review | Complex Insight  - Understanding our world | Scoop.it

Proof-of-principle experiment shows how humanoid robots can co-operate on a large scale by copying the behavior of social insects and bacterial colonies. - learn more.


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Bacterial signaling systems as platforms for rational design of new generations of biosensors

Bacterial signaling systems as platforms for rational design of new generations of biosensors

by
Checa SK, Zurbriggen MD, Soncini FC.
"Bacterial signal-responsive regulatory circuits have been employed as platform to design and construct whole-cell bacterial biosensors for reporting toxicity. A new generation of biosensors with improved performance and a wide application range has emerged after the application of synthetic biology concepts to biosensor design. Site-directed mutagenesis, directed evolution and domain swapping were applied to upgrade signal detection or to create novel sensor modules. Rewiring of the genetic circuits allows improving the determinations and reduces the heterogeneity of the response between individual reporter cells. Moreover, the assembly of natural or engineered modules to biosensor platforms provides innovative outputs, expanding the range of application of these devises, from monitoring toxics and bioremediation to killing targeted cells."
http://1.usa.gov/JTBbQj


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Scientists identify mechanisms in aspirin that help protect against cancer

Scientists identify mechanisms in aspirin that help protect against cancer | Complex Insight  - Understanding our world | Scoop.it

(via Medical Xpress)  Recent clinical studies have indicated that long-term usage of non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin can significantly reduce the risk of various cancers — some up to 30 per cent.  Previous studies have shown that cancer cells are less likely to divide if the white blood cells can be prevented from contacting the precursor cancer cells, suggesting that white blood cells – the immune cells – have the ability to promote disease by providing some kind of growth signal. A new study published in Current Biology from teams at Bristol and Sheffield Universities in the UK , show that at least in part, taking drugs like aspirin, which are generally taken for cardiovascular problems, prevent the development of cancer by starving the cancer cells of this source of white blood cell early-growth support. Learn more...

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Microfluidics-based diagnostics of infectious diseases in the developing world

Microfluidics-based diagnostics of infectious diseases in the developing world | Complex Insight  - Understanding our world | Scoop.it

This paper from 2010 gives a background on development of microfluidics-based diagnostics of infectious diseases.  So called Mchip technologies offer the promise of  portable advanced disease assay methods for less than $100. This paper covers the background of how the devices work. If you do not have a subscription to Nature you will have to pay for full access. Read more...

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