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3quarksdaily: Synthetic Biology: Engineering Life To Examine It

3quarksdaily: Synthetic Biology: Engineering Life To Examine It | Bioinformatics Training | Scoop.it

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Socrates Logos's curator insight, January 7, 5:33 AM

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Jalees Rehman

*Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two repressors (genes that encode for proteins which suppress the expression of genes) as well as a gene encoding for green fluorescent protein that served as a read-out for the system. The repressors used were sensitive to either selected chemicals or temperature. In one of the experiments, the system was turned ON by adding the chemical IPTG (a modified sugar) and nearly all the cells became green fluorescent within five to six hours. Upon raising the temperature to activate the temperature-sensitive repressor, the cells began losing their green fluorescence within an hour and returned to the OFF state. Many labs had used chemical or temperature switches to turn gene expression on in the past, but this paper was the first to assemble multiple genes together and construct a switch which allowed switching cells back and forth between stable ON and OFF states.

 Dna-163466_640 The same issue of Nature contained a second land-mark paper which also described the engineering of gene circuits. The researchers Michael Elowitz and Stanislas Leibler describe the generation of an engineered gene oscillator in their article "A synthetic oscillatory network of transcriptional regulators". By introducing three repressor genes which constituted a negative feedback loop and a green fluorescent protein as a marker of the oscillation, the researchers created a molecular clock in bacteria with an oscillation period of roughly 150 minutes. The genes and proteins encoded by the genes were not part of any natural biological clock and none of them would have oscillated if they had been introduced into the bacteria on their own. The beauty of the design lay in the combination of three serially repressing genes and the periodicity of this engineered clock reflected the half-life of the protein encoded by each gene as well as the time it took for the protein to act on the subsequent member of the gene loop.  Both papers described the introduction of plasmids encoding for multiple genes into bacteria but this itself was not novel. In fact, this has been a routine practice since the 1970s for many molecular biology laboratories. The panache of the work lay in the construction of functional biological modules consisting of multiple genes which interacted with each other in a controlled and predictable manner. Since the publication of these two articles, hundreds of scientific papers have been published which describe even more intricate engineered gene circuits. These newer studies take advantage of the large number of molecular tools that have become available to query the genome as well as newer DNA plasmids which encode for novel biosensors and regulators. Synthetic biology is an area of science devoted to engineering novel biological circuits, devices, systems, genomes or even whole organisms. This rather broad description of what "synthetic biology" encompasses reflects the multidisciplinary nature of this field which integrates ideas derived from biology, engineering, chemistry and mathematical modeling as well as a vast arsenal of experimental tools developed in each of these disciplines. Specific examples of "synthetic biology" include the engineering of microbial organisms that are able to mass produce fuels or other valuable raw materials, synthesizing large chunks of DNA to replace whole chromosomes or even the complete genome in certain cells, assembling synthetic cells or introducing groups of genes into cells so that these genes can form functional circuits by interacting with each other. Synthesis in the context of synthetic biology can signify the engineering of artificial genes or biological systems that do not exist in nature (i.e. synthetic = artificial or unnatural), but synthesis can also stand for integration and composition, a meaning which is closer to the Greek origin of the word.  It is this latter aspect of synthetic biology which makes it an attractive area for basic scientists who are trying to understand the complexity of biological organisms. Instead of the traditional molecular biology focus on studying just one single gene and its function, synthetic biology is engineering biological composites that consist of multiple genes and regulatory elements of each gene. This enables scientists to interrogate the interactions of these genes, their regulatory elements and the proteins encoded by the genes with each other. Synthesis serves as a path to analysis. One goal of synthetic biologists is to create complex circuits in cells to facilitate biocomputing, building biological computers that are as powerful or even more powerful that traditional computers. While such gene circuits and cells that have been engineered have some degree of memory and computing power, they are no match for the comparatively gigantic computing power of even small digital computers. Nevertheless, we have to keep in mind that the field is very young and advances are progressing at a rapid pace. One of the major recent advances in synthetic biology occurred in 2013 when an MIT research team led by Rahul Sarpeshkar and Timothy Lu at MIT created analog computing circuits in cells. Most synthetic biology groups that engineer gene circuits in cells to create biological computers have taken their cues from contemporary computer technology. Nearly all of the computers we use are digital computers, which process data using discrete values such as 0's and 1's. Analog data processing on the other hand uses a continuous range of values instead of 0's and 1's. Digital computers have supplanted analog computing in nearly all areas of life because they are easy to program, highly efficient and process analog signals by converting them into digital data. Nature, on the other hand, processes data and information using both analog and digital approaches. Some biological states are indeed discrete, such as heart cells which are electrically depolarized and then repolarized in periodical intervals in order to keep the heart beating. Such discrete states of cells (polarized / depolarized) can be modeled using the ON and OFF states in the biological circuit described earlier. However, many biological processes, such as inflammation, occur on a continuous scale. Cells do not just exist in uninflamed and inflamed states; instead there is a continuum of inflammation from minimal inflammatory activation of cells to massive inflammation. Environmental signals that are critical for cell behavior such as temperature, tension or shear stress occur on a continuous scale and there is little evidence to indicate that cells convert these analog signals into digital data. Most of the attempts to create synthetic gene circuits and study information processing in cells have been based on a digital computing paradigm. Sarpeshkar and Lu instead wondered whether one could construct analog computation circuits and take advantage of the analog information processing systems that may be intrinsic to cells. The researchers created an analog synthetic gene circuit using only three proteins that regulate gene expression and the fluorescent protein mCherry as a read-out. This synthetic circuit was able to perform additions or ratiometric calculations in which the cumulative fluorescence of the mCherry was either the sum or the ratio of selected chemical input concentrations. Constructing a digital circuit with similar computational power would have required a much larger number of components.  The design of analog gene circuits represents a major turning point in synthetic biology and will likely spark a wave of new research which combines analog and digital computing when trying to engineer biological computers. In our day-to-day lives, analog computers have become more-or-less obsolete. However, the recent call for unconventional computing research by the US Defense Advanced Research Projects Agency (DARPA) is seen by some as one indicator of a possible paradigm shift towards re-examining the value of analog computing. If other synthetic biology groups can replicate the work of Sarpeshkar and Lu and construct even more powerful analog or analog-digital hybrid circuits, then the renaissance of analog computing could be driven by biology.  It is difficult to make any predictions regarding the construction of biological computing machines which rival or surpass the computing power of contemporary digital computers. What we can say is that synthetic biology is becoming one of the most exciting areas of research that will provide amazing insights into the complexity of biological systems and may provide a path to revolutionize biotechnology..."


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Sandrine Palcy's curator insight, January 9, 5:11 AM

From computing biology to biology for computing...!

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Bioinformatics, blended with education and health sciences subjects
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GTPB: TA-AFADM1 Transcriptome Assembly, Automatic Annotation and Data Mining

GTPB: TA-AFADM1 Transcriptome Assembly, Automatic Annotation and Data Mining | Bioinformatics Training | Scoop.it

This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome.

The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data.

 

With Stefan Goetz and Riccardo Alese Cigliano

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This  is a new edition of a combined RNAseq and Automatic Functional Annotation hands-on training course, successfully held here several times.

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Balti and Bioinformatics “On Air” Wednesday September 10th 2014 - Oxford Nanopore sequencing talks


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Analyzing Family Genomics Reveals New Culprit in Rare Disease

Analyzing Family Genomics Reveals New Culprit in Rare Disease | Bioinformatics Training | Scoop.it
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Adams-Oliver syndrome (AOS) is a rare congenital disease characterized by scalp lesions and limb defects. Additional vascular abnormalities and heart defects can lead to early death in some patients.
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That’s Not #Funny: Higher Ed’s Least Clever Twitter Accounts

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Earlier this month, a puckish Twitter user going by the handle @ProfJeffJarvis managed to provoke two actual professors into fits of outrage.
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Collaborative That Once Criticized Software Companies Becomes One

Collaborative That Once Criticized Software Companies Becomes One | Bioinformatics Training | Scoop.it
Ten years ago, a group of universities started a collaborative software project touted as an alternative to commercial software companies, which were criticized as too costly.
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As many academics as possible should be running Kuali's test drives: students, teachers, trainers, administrative staff members, librarians,etc.

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Evolution in the Anthropocene: Population Genomics of NYC Wildlife

This presentation describes ongoing efforts to develop white-footed mice (and a few other species) in New York City as models for examining the evolutionary implications of urbanization. Also...
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Tracking Cells from Well to Diseased

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KUOW's Marcie Sillman and producer Amina Al-Sadi interviewed Dr. Lee Hood about P4 medicine and the 100K Wellness Project. This 29-minute recording is a great conversation about Lee's vision for how to turn healthcare on its head.
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New $10.9 Million Grant from NIH

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The NIH's National Institute of General Medical Scienes has issued a Biotechnology Resource Grant of $10.9 million over five years to the National Center for Dynamic Interactome Research (ncdir.org) project.
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Genomics of Microbes and Microbiomes - Julia Segre

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A History of Bioinformatics (in the Year 2039)

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039.
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Excellent content, very smart idea for a talk, exceptional cvalue for newcomers to Bioinformatics.

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Careers in Bioinformatics and Precision Medicine - Career Development Week

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Must Read Report: The Internet’s Latest Disruption – Knowledge.

Must Read Report: The Internet’s Latest Disruption – Knowledge. | Bioinformatics Training | Scoop.it
Know or die: risk and opportunity of Knowledge 2.0
“And the web stormed the enterprise and disrupted roles, tasks and jobs: it cast speed, openness, flexibility and efficiency throughout, sparing no business processes: manufacturing, logistic, accounting, customer relation management, lead generation…”
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Google Will Finance Carnegie Mellon’s MOOC Research

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Balti and Bioinformatics - Yannick Wurm - YouTube

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Application Note about the GOBLET Portal (open access)

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A global repository of bioinformatics training materials.

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How Streaming Media Threaten the Mission of Libraries

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Digital music has made it easier to buy and share recordings. But try telling that to librarians.
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New Structural Map Helps To Understand Aggressive Tumors

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Aggressive tumor growth is linked to high activity of a macromolecular assembly called RNA polymerase I.
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Why Students Should Own Their Educational Data

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Designing a textbook or lecture with the average student in mind may sound logical. But L.
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Pimp your brain: Bioinformatics

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformat...
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James Hane's curator insight, August 26, 2:41 AM

youtube captions make for an interesting read

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BIOCELLION: New Supercomputer Software Framework Models Biological Systems at Unprecedented Scales

BIOCELLION: New Supercomputer Software Framework Models Biological Systems at Unprecedented Scales | Bioinformatics Training | Scoop.it
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Can You Really Teach a MOOC in a Refugee Camp?

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Two men living in Dadaab, a refugee camp in Kenya, would watch lecture videos and take online quizzes at a nearby United Nations compound.
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Are Courses Outdated? MIT Considers Offering ‘Modules’ Instead

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People now buy songs, not albums. They read articles, not newspapers. So why not mix and match learning “modules” rather than lock into 12-week university courses?
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Not too late to discover this.

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ISB Researchers Help Identify Four New Subtypes of Gastric Cancer That May Lead to New Targeted Treatments

ISB Researchers Help Identify Four New Subtypes of Gastric Cancer That May Lead to New Targeted Treatments | Bioinformatics Training | Scoop.it
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Jon Spaihts: Hollywood’s go-to science fiction screenwriter on the importance of science in filmmaking

Jon Spaihts: Hollywood’s go-to science fiction screenwriter on the importance of science in filmmaking | Bioinformatics Training | Scoop.it
Hollywood’s go-to science fiction writer.

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L’université de demain : des cours gratuits, à toute heure...

L’université de demain : des cours gratuits, à toute heure... | Bioinformatics Training | Scoop.it
Des cours dispensés la nuit ou sans horaire fixe, des bibliothèques virtuelles, des ressources pédagogiques et l’accès au matériel gratuits…...

 


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juandoming's curator insight, July 19, 12:43 PM

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