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Complex Insight  - Understanding our world
Latest news on complex systems in life sciences, engineering, education and government
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Hierarchical Modeling for Synthetic Biology

WE are huge fans of TinkerCell - its a great application, awesome open source framework and very useful too. This article scooped by the SynBio cool folks at the Leukippo Institute on TinkerCell by Deepak Chandran and Herbert M Sauro caught our eye.

 

"One of the characteristics of Synthetic Biology is that it often combines mathematical modeling with experimental work. The link between modeling and experiments is carried out by human researchers who have a conceptual understanding of the underlying biological system. At present, there is no method for representing a conceptual description that can be used to connect mathematical models and experimental data, especially sequence annotations, pertaining to the same underlying biological system. One reason for this limitation is that there can exist different mathematical models of the same biological system. In such cases, the same annotation in a DNA sequence would map differently to different models of the same system. In order to enable software support for synthetic biology, a software framework is needed such that it is able to capture a conceptual description of a biological system, including quantitative values, without confining itself to one mathematical model. The novel use of hierarchical modeling inside TinkerCell (www.tinkercell.com) provides one potential software solution for representing a "conceptual diagram" of a biological system. The conceptual diagram does not assume any underlying model. Rather, the diagram is mapped automatically to one of several models. The diagram can then contain information relevant for both modeling and experimental work. Computer-aided design (CAD) can be very useful to synthetic biology. CAD allows engineers to spend more effort at the design stage and less at the construction stage by automatically performing many tasks that are currently performed by human researchers. The ability to automatically link models and experimental results will be one step in the development of a practical CAD systems for synthetic biology."

http://bit.ly/SSDHaX


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The Future of Medical Visualisation - Technology Review

The Future of Medical Visualisation - Technology Review | Complex Insight  - Understanding our world | Scoop.it

Medicine has been revolutionised by 3D imaging techniques. In the last five years, commercial CT scanners that can create 3D videos of a beating heart or new diffusion imaging techniques that enable imaging of  nerve bundles and muscle fibres have started to become available. A great tech piece in Technology Review covers where medical imaging is going next. Certainly worth reading. Click on the image or the title to learn more...

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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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Stop and go: 'Traffic policeman' protein directs crucial step in cell division

A traffic policeman standing at a busy intersection directing the flow of vehicles may be a rare sight these days, but a similar scene appears to still frequently play out in our cells. A protein called Lem4 directs a crucial step of cell division by preventing the progress of one molecule while waving another through, scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have found. The study is published online today in Cell. Click on the 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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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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Cancer, Data and the Fallacy of the $1000 Genome - Forbes

Cancer, Data and the Fallacy of the $1000 Genome - Forbes | Complex Insight  - Understanding our world | Scoop.it

Article based on  a talk given by Mark Boguski of Harvard Medical School at a recent healthcare conference in Boston.  Article is by Jim Golden a practising LIfe Science data scientist and worth reading. 

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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...


Via Dr Richard Badge
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Emergence of drug resistance to ARVs has potential to 'curb, and even reverse' gains against HIV

"In sub-Saharan Africa, the region with the highest HIV/AIDS burden, high-level political commitment and substantial international funding have led to an unparalleled scale-up of access to treatment over the past eight years," they write, adding, "However, little attention has been paid to the potential emergence and spread of drug-resistant HIV and its public health implications." Learn more..

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Why health IT systems integrate poorly today, and what future EHRs can do about it - O'Reilly Radar

Why health IT systems integrate poorly today, and what future EHRs can do about it - O'Reilly Radar | Complex Insight  - Understanding our world | Scoop.it

New Internet-centric approaches to health IT systems are needed, and the government should be mandating a more modern open style of data exchange that breaks through monolithic systems. Worth reading - the challenge of proprietary vendors versus open systems is going to be a central theme in healthcare, smart cities, and internet of things. This article explains the healthcare IT situation in the US. Worth reading...

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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


Via Gerd Moe-Behrens
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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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Mathematical Model Developed to Predict Malaria Outbreaks: Open Malaria Warning (OMaWa)

Mathematical Model Developed to Predict Malaria Outbreaks: Open Malaria Warning (OMaWa) | Complex Insight  - Understanding our world | Scoop.it

Ethiopian and Norwegian researchers have developed a mathematical model that can identify conditions that increase the likelihood of a malaria outbreak up to two months ahead of its occurrence.The computer model, Open Malaria Warning (OMaWa), incorporates hydrological, meteorological, mosquito-breeding and land-use data to determine when and where outbreaks are likely to occur. Unlike earlier models which simplified key components of the malariy outbreak cycle - the OmaWa model is delivering better results. Learn more..


Via Ashish Umre, Frédéric Amblard
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Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity

Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity | Complex Insight  - Understanding our world | Scoop.it

Paper by Miller M, Hafner M, Sontag E, Davidsohn N, Subramanian S, Purnick PE, Lauffenburger D, Weiss R.

"Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of β-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation) are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for 'synthetic cellular heterogeniety' that function to generate beneficial population diversity..." More at: http://bit.ly/P3S8nP


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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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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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NSF selects UAB biologist for prestigious Tree of Life team

NSF selects UAB biologist for prestigious Tree of Life team | Complex Insight  - Understanding our world | Scoop.it

UAB biologist Robert Thacker, Ph.D., is part of an interdisciplinary team developing a digital Tree of Life that will enable scientists to see the relationships between organisms at a glance. 

The project, Arbor: Comparative Analysis Workflows for the Tree of Life, is part of the National Science Foundation’s $13 million Assembling, Visualizing and Analyzing the Tree of Life program, AVAToL. The Arbor team will receive $4 million; $500,000 is dedicated to the work of Thacker, a professor in the UAB Department of Biology, whose focus is symbiosis research in marine invertebrates and sponges. “The idea is that we will be able to accelerate science quickly and easily by sharing data and the way it is analyzed. And that will encourage scientists to try new ideas, find new answers and enhance the quality of research in multiple fields of science,” said Thacker.

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Accelrys Discovery Studio 3.5 Released

Accelrys Discovery Studio 3.5 Released | Complex Insight  - Understanding our world | Scoop.it

We use Kepler for some open workflow tasks however a number of life scientists we know use Pipeline Pilot.  Accelrys’  recently released Discovery Studio® a  complete modeling and simulation solution  for both small molecules and macromolecules-based drug design. Based on Pipeline Pilot, Discovery Studio enables scientists to automate routine tasks, integrate third party applications and  deploy models out to research colleagues. IF you are automating workflows in Life Science environments it might be worth a look. 

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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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Video: Synthetic Biologist Karmella Haynes | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future

Video: Synthetic Biologist Karmella Haynes | The Synthetic Bestiary – Synthetic Biology, Genetic Engineering, and The Future | Complex Insight  - Understanding our world | Scoop.it

 Good introduction to synthetic biology from practioner Karmella Haynes, a post doc researcher at Harvard. 


Via Gerd Moe-Behrens
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SMU biochemist creates dynamic model of human P-glycoprotein

SMU biologists Pia Vogel and John Wise are using the computational power of SMU's high-performance supercomputer to screen millions of drug compounds. A key aspect of their approach is to animate the protien structure to give a dynamic moving model of the protien which aids in understanding. Interestingly SMU's approach is using highend computer visualization also echoed in the approach of the open source bioBlend project that combines the open source Blender and Python libs for parsing protein database info. Click image for more on SMU project and see bioblender.eu for more on BioBlender.

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Engineering mosquitos to reject malaria | Ars Technica

Engineering mosquitos to reject malaria | Ars Technica | Complex Insight  - Understanding our world | Scoop.it
via RKelwick

 

by
John Timmer
"Pests that carry a human antibody make poor hosts for parasites.
One of the easiest and often most effective means of controlling the spread of malaria is to control the mosquitos that carry it to humans. Unfortunately, that has proven to be just as much of an evolutionary arms race as targeting malaria itself; mosquitos evolve resistance to pesticides almost as quickly as malaria has evolved resistance to drugs.

Recent efforts have focused on forms of control that don't impose a huge fitness burden on the mosquito population. This general approach has been tested in the wild on the mosquitos that carry Dengue fever, which scientists infected with bacteria that block the spread of the virus. Now, researchers are reporting that they've developed genetically modified mosquitos that turn mosquitos into a dead-end for the malarial parasite. Their method: have the mosquitos express antibodies against the parasite whenever it feeds on blood.

Antibodies have a relatively poor history when it comes to targeting malaria in humans. Vaccines against the parasite tend to be ineffective, because Plasmodium falciparum has evolved ways of evading an immune response, often completely changing the proteins that coat its surface in order to keep antibodies from recognizing it. But these changes are only triggered once the parasite is already inside the human body...."
http://bit.ly/LkMXEm


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Temporal percolation of the susceptible network in an epidemic spreading

L. D. Valdez, P. A. Macri, L. A. Braunstein
(Submitted on 13 Jun 2012)
In this work, we study the evolution of the susceptible individuals during the spread of an epidemic modeled by the susceptible-infected-recovered (SIR) process spreading on top of complex networks. Using a edge-based compartmental approach and percolation tools, we find that the network composed by susceptible individuals undergoes a dynamic node percolation transition with a time dependent control parameter. We show that there exists a critical time $t_c$ above which the giant susceptible cluster is destroyed. As a consequence, in order to protect a large fraction of the susceptible individuals, any mitigation strategy should be implemented before this critical time $t_c$. Our theoretical results are confirmed by extensive simulations of the SIR process.


Via Frédéric Amblard
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Mind Wobbles - A Totally Awesome Systems Biology Blog by Allyson Lister, Newcastle Uni.

Mind Wobbles - A Totally Awesome Systems Biology Blog by Allyson Lister, Newcastle Uni. | Complex Insight  - Understanding our world | Scoop.it

Awesome post on systems biology by Allyson Lister  a PhD student at Newcastle University. Her Blog "The Mind Wobbles" - should be high on systems biologists and computational modellers reading list.

 

Sample: There are four main areas of study in systems biology research: (i) the structure (e.g. interactions and pathways) of a system; (ii) how a system behaves over time, or its dynamics; (iii) the method of controlling and modulating the system; and (iv) the design method, or the deliberate progress using well defined design principles. These four properties are strongly tied to the quantitative modelling aspect of systems biology, and illustrate the importance of such models. However, models are of limited use to either people or computers if they do not have structured biological annotations to provide context. For instance, until SBML  models are annotated by the BioModels team, elements often contain short-hand, biologically irrelevant names and descriptions in computationally incompatible free text. While attaching additional biological knowledge to quantitative models is not a requirement for their simulation, without such annotations model sharing, interpretation of simulation results, integration and reuse becomes nearly impossible [9]. Therefore the addition of biologically relevant, computationally accessible metadata will not only enhance the semantics of a model but provide a method of unambiguously identifying its elements.  Read More...

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