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‘Biohackers’ go solo in quest to find cures - San Francisco Business Times

‘Biohackers’ go solo in quest to find cures - San Francisco Business Times | SynBioFromLeukipposInstitute | Scoop.it
Ryan Bethencourt is hacking his way toward saving lives.
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Battle of the Next-Generation DNA Sequencers Heating Up | Singularity Hub

Battle of the Next-Generation DNA Sequencers Heating Up | Singularity Hub | SynBioFromLeukipposInstitute | Scoop.it
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A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology : Statistical Applications in Genetics and Molecular Bi...

A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology : Statistical Applications in Genetics and Molecular Bi... | SynBioFromLeukipposInstitute | Scoop.it

By

Grzegorczyk, Marco / Husmeier, Dirk

"An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment."
http://bit.ly/QaeBH8

 
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Regulation of cell behavior and tissue patterning by bioelectrical signals: challenges and opportunities for biomedical engineering

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Levin M, Stevenson CG.

"Achieving control over cell behavior and pattern formation requires molecular-level understanding of regulatory mechanisms. Alongside transcriptional networks and biochemical gradients, there functions an important system of cellular communication and control: transmembrane voltage gradients (V(mem)). Bioelectrical signals encoded in spatiotemporal changes of V(mem) control cell proliferation, migration, and differentiation. Moreover, endogenous bioelectrical gradients serve as instructive cues mediating anatomical polarity and other organ-level aspects of morphogenesis. In the past decade, significant advances in molecular physiology have enabled the development of new genetic and biophysical tools for the investigation and functional manipulation of bioelectric cues. Recent data implicate V(mem) as a crucial epigenetic regulator of patterning events in embryogenesis, regeneration, and cancer. We review new conceptual and methodological developments in this fascinating field. Bioelectricity offers a novel way of quantitatively understanding regulation of growth and form in vivo, and it reveals tractable, powerful control points that will enable truly transformative applications in bioengineering, regenerative medicine, and synthetic biology."
http://1.usa.gov/MPjIVB

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Cell - A Whole-Cell Computational Model Predicts Phenotype from Genotype

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Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Miriam V. Gutschow, Jared M. Jacobs, Benjamin Bolival, Nacyra Assad-Garcia, John I. Glass, Markus W. Covert

Highlights
An entire organism is modeled in terms of its molecular components
Complex phenotypes can be modeled by integrating cell processes into a single model
Unobserved cellular behaviors are predicted by model of M. genitalium
New biological processes and parameters are predicted by model of M. genitalium
Summary

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery."
http://bit.ly/NnoQWI

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Your Laptop Can Now Analyze Big Data - Technology Review

Your Laptop Can Now Analyze Big Data - Technology Review | SynBioFromLeukipposInstitute | Scoop.it
New software makes it possible to do in minutes on a small computer what used to be done by large clusters of computers.
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Introduction to bioengineering from Ginkgo Bioworks.

 http://bit.ly/MblXUy

 
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Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity

Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity | SynBioFromLeukipposInstitute | Scoop.it

*Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity*

by
Hans C. Bernstein, Steven D. Paulson, Ross P. Carlson

"Synthetic Escherichia coli consortia engineered for syntrophy demonstrated enhanced biomass productivity relative to monocultures. Binary consortia were designed to mimic a ubiquitous, naturally occurring ecological template of primary productivity supported by secondary consumption. The synthetic consortia replicated this evolution-proven strategy by combining a glucose positive E. coli strain, which served as the system's primary producer, with a glucose negative E. coli strain which consumed metabolic byproducts from the primary producer. The engineered consortia utilized strategic division of labor to simultaneously optimize multiple tasks enhancing overall culture performance. Consortial interactions resulted in the emergent property of enhanced system biomass productivity which was demonstrated with three distinct culturing systems: batch, chemostat and biofilm growth. Glucose-based biomass productivity increased by ∼15, 20 and 50% compared to appropriate monoculture controls for these three culturing systems, respectively. Interestingly, the consortial interactions also produced biofilms with predictable, self-assembling, laminated microstructures. This study establishes a metabolic engineering paradigm which can be easily adapted to existing E. coli based bioprocesses to improve productivity based on a robust ecological theme."

http://bit.ly/MyhfF5

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Bioprinting Humanity: Where It's Headed

Bioprinting Humanity: Where It's Headed | SynBioFromLeukipposInstitute | Scoop.it
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Top Universities Test the Online Appeal of Free

Top Universities Test the Online Appeal of Free | SynBioFromLeukipposInstitute | Scoop.it
Online courses have been around for years, but now big-name colleges and competing software platforms have entered the field, which is evolving with astonishing speed.
 
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Holy Genetically-Engineered Organisms Batman - Synthetic Biology Has A Banner Month! - Forbes

Holy Genetically-Engineered Organisms Batman - Synthetic Biology Has A Banner Month! - Forbes | SynBioFromLeukipposInstitute | Scoop.it

by

Steven Kotler

"It’s been a good month for synthetic biology. A few weeks ago, in a great talk (on the concept of “singularities”) given to METal International in Los Angeles, biophysicist +Reese Jones showed footage of the world’s first DNA laser printer at work.

You heard me right—a DNA laser printer. Created by the San Francisco-based company Cambrian Genomics (Jones is one of the founders), a DNA laser printer works just like a normal laser printer—only replace the traditional ink with genetic code.

Essentially, what Craig Venter and Blue Heron Technologies pulled off with the world’s first synthetic genome (where chemical synthesis produced 1000-base long strands of DNA which were then stitched together to form a 1,000,000-base long novel organism) was synthesis 1.0.

The DNA Laser Printer, meanwhile, is Synthesis 2.0.

Here’s why. Traditional DNA synthesis (chemical synthesis) has a 99 percent accuracy rate per 100 pairs—an impossible to manage error rate when synthesizing anything larger than a virus. But the DNA laser printer is always 100 percent accurate—hypothetically to any strand length.

And while the technology is not yet market ready (so nobody really wants to talk numbers), it bodes well for a radical shift in cost. Right now, synethesizing really short strands of DNA is about 25 cents a base (for simple work). More complex assemblies can still be as high as a $1 a base....."
http://onforb.es/M9t8g5

 
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Team:NRP-UEA-Norwich - 2012.igem.org

Team:NRP-UEA-Norwich - 2012.igem.org | SynBioFromLeukipposInstitute | Scoop.it

Aug 17th Hangout with the UK iGEM Synthetic Biology Teams at Google Campus London http://bit.ly/LH2jD7

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Stanford's computational cell model lets scientists experiment virtually

Stanford's computational cell model lets scientists experiment virtually | SynBioFromLeukipposInstitute | Scoop.it

Stanford scientists have created a full computational model of the Mycoplasma genitalium bacteria, which will rapidly speed up experiments that would otherwise involve time-consuming alterations to...

 
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Towards the Recapitulation of Ancient History in the Laboratory: Combining SynBio with Experimental Evolution

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Betül K. Arslan and Eric A. Gaucher

"One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral sequence reconstruction with synthetic biology allows us to resurrect the past within a modern context and has expanded our understanding of protein functionality within a historical context. Experimental evolution, on the other hand, provides us with the ability to study evolution in action, under controlled conditions in the laboratory. Here we describe a novel experimental setup that integrates two disparate fields - ancestral sequence reconstruction and experimental evolution. This allows us to rewind and replay the evolutionary history of ancient biomolecules in the laboratory. We anticipate that our combination will provide a deeper understanding of the underlying roles that contingency and determinism play in shaping evolutionary processes."
http://bit.ly/PrInoe

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TEDxMontreal - Yasaman Sheri - Synthetic biology and mass production

Industrial designer Yasaman Sheri considers the future of synthetic biology, biotechnology and mass production. About TEDx, x = independently organized event...
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Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation

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Kashida S, Inoue T, Saito H.

"The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to constructing efficient molecular devices that function in living cells. Here, we demonstrate a 3D structure-based molecular design principle for constructing short hairpin RNA (shRNA)-mediated genetic information converters; these converters respond to specific proteins and trigger the desired gene expression by modulating the function of the RNA-processing enzyme Dicer. The inhibitory effect on Dicer cleavage against the shRNA designed to specifically bind to U1A spliceosomal protein was correlated with the degree of steric hindrance between Dicer and the shRNA-protein complex in vitro: The level of the hindrance was predicted based on the models. Moreover, the regulation of gene expression was achieved by using the shRNA converters designed to bind to the target U1A or nuclear factor-κB (NF-κB) p50 proteins expressed in human cells. The 3D molecular design approach is widely applicable for developing new devices in synthetic biology."
http://1.usa.gov/OGlXOS

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Data for doctors: Big data meets a big business

Data for doctors: Big data meets a big business | SynBioFromLeukipposInstitute | Scoop.it
Forget the division between structured and unstructured data.
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Reshma Shetty - Ginkgo BioWorks - videolectures.net

Reshma Shetty - Ginkgo BioWorks - videolectures.net | SynBioFromLeukipposInstitute | Scoop.it

Great talk by Reshma Shetty.
http://videolectures.net/reshma_shetty/

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Fluorine: A new element in protein design

Fluorine: A new element in protein design | SynBioFromLeukipposInstitute | Scoop.it

Introducing noncanonical amino acids into proteins:

*Fluorine: A new element in protein design*

Review
by
Benjamin C. Buer, E. Neil G. Marsh

"Fluorocarbons are quintessentially man-made molecules, fluorine being all but absent from biology. Perfluorinated molecules exhibit novel physicochemical properties that include extreme chemical inertness, thermal stability, and an unusual propensity for phase segregation. The question we and others have sought to answer is to what extent can these properties be engineered into proteins? Here, we review recent studies in which proteins have been designed that incorporate highly fluorinated analogs of hydrophobic amino acids with the aim of creating proteins with novel chemical and biological properties. Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure and biological activity. Most studies have focused on small proteins that can be produced by peptide synthesis as synthesis of large proteins containing specifically fluorinated residues remains challenging. However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design."

http://bit.ly/OcVh6w

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Stanford faculty is embracing online teaching opportunities

The team leading Stanford's online education initiative announces seed grants to faculty members across campus for course development.
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Stealthy Gen9 Rolls Out BioFab for Large-Scale Gene Manufacturing | Xconomy

Stealthy Gen9 Rolls Out BioFab for Large-Scale Gene Manufacturing | Xconomy | SynBioFromLeukipposInstitute | Scoop.it

by

Arlene Weintraub

"For the past three years, Cambridge, MA-based Gen9 has been quietly building something that its founders believe has been sorely lacking in biotech: an affordable and efficient way to synthesize genes on a massive scale. Those founders are pioneers in the field of synthetic biology: Joseph Jacobson, an MIT professor and specialist in the field of using biology to create machines; George Church, genetics professor at Harvard Medical School and one of the original developers of genomic sequencing tools; and Drew Endy, a Stanford faculty member who specializes in bioengineering....."

http://bit.ly/NA6HlU

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synbioleap

synbioleap | SynBioFromLeukipposInstitute | Scoop.it

LeAP is a workshop to develop your ideas for how synthetic biology can best advance Oct 1-5 Warrenton, Va http://bit.ly/MJngIP

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