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Synthetic biology in China – Foundation and Initiation - free slide submission, upload slide - Medical, weSRCH

Synthetic biology in China – Foundation and Initiation - free slide submission, upload slide - Medical, weSRCH | Biomedical synthetic biology | Scoop.it

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Programmable bacteria detect and record an environmental signal in the mammalian gut

Programmable bacteria detect and record an environmental signal in the mammalian gut | Biomedical synthetic biology | Scoop.it

The mammalian gut is a dynamic community of symbiotic microbes that interact with the host to impact health, disease, and metabolism. We constructed engineered bacteria that survive in the mammalian gut and sense, remember, and report on their experiences. Based on previous genetic memory systems, we constructed a two-part system with a “trigger element” in which the lambda Cro gene is transcribed from a tetracycline-inducible promoter, and a “memory element” derived from the cI/Cro region of phage lambda. The memory element has an extremely stable cI state and a Cro state that is stable for many cell divisions. When Escherichia coli bearing the memory system are administered to mice treated with anhydrotetracycline, the recovered bacteria all have switched to the Cro state, whereas those administered to untreated mice remain in the cI state. The trigger and memory elements were transferred from E. coli K12 to a newly isolated murine E. coli strain; the stability and switching properties of the memory element were essentially identical in vitro and during passage through mice, but the engineered murine E. coli was more stably established in the mouse gut. This work lays a foundation for the use of synthetic genetic circuits as monitoring systems in complex, ill-defined environments, and may lead to the development of living diagnostics and therapeutics.

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Perspective: Synthetic biology revives antibiotics

Perspective: Synthetic biology revives antibiotics | Biomedical synthetic biology | Scoop.it
Re-engineering natural products provides a new route to drug discovery, says Gerard Wright.
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Realizing the potential of synthetic biology

Synthetic biology, despite still being in its infancy, is increasingly providing valuable information for applications in the clinic, the biotechnology industry and in basic molecular research. Both its unique potential and the challenges it presents have brought together the expertise of an eclectic group of scientists, from cell biologists to engineers. In this Viewpoint article, five experts discuss their views on the future of synthetic biology, on its main achievements in basic and applied science, and on the bioethical issues that are associated with the design of new biological systems.

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What should we focus on in synthetic biology?

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Cell - Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

Cell - Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos | Biomedical synthetic biology | Scoop.it

Monkeys serve as important model species for studying human diseases and developing therapeutic strategies, yet the application of monkeys in biomedical researches has been significantly hindered by the difficulties in producing animals genetically modified at the desired target sites. Here, we first applied the CRISPR/Cas9 system, a versatile tool for editing the genes of different organisms, to target monkey genomes. By coinjection of Cas9 mRNA and sgRNAs into one-cell-stage embryos, we successfully achieve precise gene targeting in cynomolgus monkeys. We also show that this system enables simultaneous disruption of two target genes (Ppar-γ and Rag1) in one step, and no off-target mutagenesis was detected by comprehensive analysis. Thus, coinjection of one-cell-stage embryos with Cas9 mRNA and sgRNAs is an efficient and reliable approach for gene-modified cynomolgus monkey generation.

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A robust TALENs system for highly efficient mammalian genome editing - Sci. Reports

A robust TALENs system for highly efficient mammalian genome editing - Sci. Reports | Biomedical synthetic biology | Scoop.it

(via T. Lahaye, thx)

Feng et al, 2013

Currently, for genomic editing in cultured cells, two plasmids encoding a pair of TALENs are co-transfected, followed by limited dilution to isolate cell colonies with the intended genomic manipulation. However, uncertain transfection efficiency becomes a bottleneck, especially in hard-to-transfect cells, reducing the overall efficiency of genome editing. We have developed a robust TALENs system in which each TALEN plasmid also encodes a fluorescence protein. Thus, cells transfected with both TALEN plasmids, a prerequisite for genomic editing, can be isolated by fluorescence-activated cell sorting. Our improved TALENs system can be applied to all cultured cells to achieve highly efficient genomic editing. Furthermore, an optimized procedure for genomic editing using TALENs is also presented. We expect our system to be widely adopted by the scientific community.


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Genetic Screens in Human Cells Using the CRISPR-Cas9 System

Genetic Screens in Human Cells Using the CRISPR-Cas9 System | Biomedical synthetic biology | Scoop.it

The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library. sgRNA expression cassettes were stably integrated into the genome, which enabled a complex mutant pool to be tracked by massively parallel sequencing. We used a library containing 73,000 sgRNAs to generate knockout collections and performed screens in two human cell lines. A screen for resistance to the nucleotide analog 6-thioguanine identified all expected members of the DNA mismatch repair pathway, whereas another for the DNA topoisomerase II (TOP2A) poison etoposide identified TOP2A, as expected, and also cyclin-dependent kinase 6, CDK6. A negative selection screen for essential genes identified numerous gene sets corresponding to fundamental processes. Last, we show that sgRNA efficiency is associated with specific sequence motifs, enabling the prediction of more effective sgRNAs. Collectively, these results establish Cas9/sgRNA screens as a powerful tool for systematic genetic analysis in mammalian cells.

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Another paper, which describes using CRISPR-Cas for human cell screening! 

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New paradigm for tumor theranostic methodology using bacteria-based microrobot : Scientific Reports : Nature Publishing Group

New paradigm for tumor theranostic methodology using bacteria-based microrobot : Scientific Reports : Nature Publishing Group | Biomedical synthetic biology | Scoop.it

We propose a bacteria-based microrobot (bacteriobot) based on a new fusion paradigm for theranostic activities against solid tumors. We develop a bacteriobot using the strong attachment of bacteria to Cy5.5-coated polystyrene microbeads due to the high-affinity interaction between biotin and streptavidin. The chemotactic responses of the bacteria and the bacteriobots to the concentration gradients of lysates or spheroids of solid tumors can be detected as the migration of the bacteria and/or the bacteriobots out of the central region toward the side regions in a chemotactic microfluidic chamber. The bacteriobots showed higher migration velocity toward tumor cell lysates or spheroids than toward normal cells. In addition, when only the bacteriobots were injected to the CT-26 tumor mouse model, Cy5.5 signal was detected from the tumor site of the mouse model. In-vitroand in-vivo tests verified that the bacteriobots had chemotactic motility and tumor targeting ability. The new microrobot paradigm in which bacteria act as microactuators and microsensors to deliver microstructures to tumors can be considered a new theranostic methodology for targeting and treating solid tumors.

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Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System | Biomedical synthetic biology | Scoop.it

The spatiotemporal organization and dynamics of chromatin play critical roles in regulating genome function. However, visualizing specific, endogenous genomic loci remains challenging in living cells. Here, we demonstrate such an imaging technique by repurposing the bacterial CRISPR/Cas system. Using an EGFP-tagged endonuclease-deficient Cas9 protein and a structurally optimized small guide (sg) RNA, we show robust imaging of repetitive elements in telomeres and coding genes in living cells. Furthermore, an array of sgRNAs tiling along the target locus enables the visualization of nonrepetitive genomic sequences. Using this method, we have studied telomere dynamics during elongation or disruption, the subnuclear localization of the MUC4 loci, the cohesion of replicated MUC4 loci on sister chromatids, and their dynamic behaviors during mitosis. This CRISPR imaging tool has potential to significantly improve the capacity to study the conformation and dynamics of native chromosomes in living human cells.

omni's insight:

Another nice tool developed from CRISPR-Cas!

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The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements | Biomedical synthetic biology | Scoop.it

Although emerging evidence suggests that transposable elements (TEs) have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized. Here we show that TEs have contributed to the human genome nearly half of its active elements. Using DNase I hypersensitivity data sets from ENCODE in normal, embryonic, and cancer cells, we found that 44% of open chromatin regions were in TEs and that this proportion reached 63% for primate-specific regions. We also showed that distinct subfamilies of endogenous retroviruses (ERVs) contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily–transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation. We also showed that thousands of ERV–derived sequences were activated in a cell type–specific manner, especially in embryonic and cancer cells, and we demonstrated that this activity was associated with cell type–specific expression of neighboring genes. Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.

 

 


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Association of Nut Consumption with Total and Cause-Specific Mortality — NEJM

Association of Nut Consumption with Total and Cause-Specific Mortality — NEJM | Biomedical synthetic biology | Scoop.it
BACKGROUND

Increased nut consumption has been associated with a reduced risk of major chronic diseases, including cardiovascular disease and type 2 diabetes mellitus. However, the association between nut consumption and mortality remains unclear.

 

RESULTS

During 3,038,853 person-years of follow-up, 16,200 women and 11,229 men died. Nut consumption was inversely associated with total mortality among both women and men, after adjustment for other known or suspected risk factors. The pooled multivariate hazard ratios for death among participants who ate nuts, as compared with those who did not, were 0.93 (95% confidence interval [CI], 0.90 to 0.96) for the consumption of nuts less than once per week, 0.89 (95% CI, 0.86 to 0.93) for once per week, 0.87 (95% CI, 0.83 to 0.90) for two to four times per week, 0.85 (95% CI, 0.79 to 0.91) for five or six times per week, and 0.80 (95% CI, 0.73 to 0.86) for seven or more times per week (P<0.001 for trend). Significant inverse associations were also observed between nut consumption and deaths due to cancer, heart disease, and respiratory disease.

 
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Good news for me ( I am a nuts lover)!

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TALE: A tale of genome editing

TALE: A tale of genome editing | Biomedical synthetic biology | Scoop.it

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Socrates Logos's curator insight, December 3, 2013 11:55 AM

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Zhang M, Wang F, Li S, Wang Y, Bai Y, Xu X.

"Transcription activator-like effectors (TALEs), first identified in Xanthomonas bacteria, are naturally occurring or artificially designed proteins that modulate gene transcription. These proteins recognize and bind DNA sequences based on a variable numbers of tandem repeats. Each repeat is comprised of a set of ∼34 conserved amino acids; within this conserved domain, there are usually two amino acids that distinguish one TALE from another. Interestingly, TALEs have revealed a simple cipher for the one-to-one recognition of proteins for DNA bases. Synthetic TALEs have been used to successfully target genes in a variety of species, including humans. Depending on the type of functional domain that is fused to the TALE of interest, these proteins can have diverse biological effects. For example, after binding DNA, TALEs fused to transcriptional activation domains can function as robust transcription factors (TALE-TFs), while fused to restriction endonucleases (TALENs) can cut DNA. Targeted genome editing, in theory, is capable of modifying any endogenous gene sequence of interest; this can be performed in cells or organisms, and may be applied to clinical gene-based therapies in the future. With current technologies, highly accurate, specific, and reliable gene editing cannot be achieved. Thus, recognition and binding mechanisms governing TALE biology are currently hot research areas. In this review, we summarize the major advances in TALE technology over the past several years with a focus on the interaction between TALEs and DNA, TALE design and construction, potential applications for this technology, and unique characteristics that make TALEs superior to zinc finger endonucleases."

 http://bit.ly/IErZ3z

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Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs | Biomedical synthetic biology | Scoop.it

Small regulatory RNAs (sRNAs) regulate gene expression in bacteria. We designed synthetic sRNAs to identify and modulate the expression of target genes for metabolic engineering in Escherichia coli. Using synthetic sRNAs for the combinatorial knockdown of four candidate genes in 14 different strains, we isolated an engineered E. coli strain (tyrR- and csrA-repressed S17-1) capable of producing 2 g per liter of tyrosine. Using a library of 130 synthetic sRNAs, we also identified chromosomal gene targets that enabled substantial increases in cadaverine production. Repression of murE led to a 55% increase in cadaverine production compared to the reported engineered strain (XQ56 harboring the plasmid p15CadA)1. The design principles and the engineering strategy using synthetic sRNAs reported here are generalizable to other bacteria and applicable in developing superior producer strains. The ability to fine-tune target genes with designed sRNAs provides substantial advantages over gene-knockout strategies and other large-scale target identification strategies owing to its easy implementation, ability to modulate chromosomal gene expression without modifying those genes and because it does not require construction of strain libraries.

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omni's comment, December 4, 2013 8:31 PM
Thank you for nominating this biomedical synthetic biology as a noteworthy topic. I will keep on contribute to this community.
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Efficient engineering of a bacteriophage genome usi... [RNA Biol. 2014] - PubMed - NCBI

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are targeted by the CRISPR-Cas system, thus enabling isolation of the desired recombinant phages. This method broadens CRISPR Cas-based editing to phages and uses a CRISPR-Cas type other than type II. The method may be adjusted to genetically engineer any bacteriophage genome.

omni's insight:

CRISPR used for engineering Phage!

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Synthetic biology: Cultural divide

Synthetic biology: Cultural divide | Biomedical synthetic biology | Scoop.it
Synthetic biology is facing a tug of war over whether to patent its discoveries or embrace open-source innovation.
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Open-souce or Patent?

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Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go

Integrating Biological Redesign:  Where Synthetic Biology Came From and Where It Needs to Go | Biomedical synthetic biology | Scoop.it

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Socrates Logos's curator insight, June 16, 5:13 PM

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Jeffrey C. Way, James J. Collins, Jay D. Keasling, and Pamela A. Silver

"Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standard- ized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field’s accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering."

http://bit.ly/1pC96Se

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Synthetic biology: How best to build a cell

Synthetic biology: How best to build a cell | Biomedical synthetic biology | Scoop.it
Experts weigh in on the biggest obstacles in synthetic biology — from names to knowledge gaps — and what it will take to overcome them.
omni's insight:

Synthetic biology requires more supports! 

 

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New Centre for Doctoral Training in Synthetic Biology announced

New Centre for Doctoral Training in Synthetic Biology announced | Biomedical synthetic biology | Scoop.it

The EPSRC Centre for Doctoral Training in Synthetic Biology will combine world-leading expertise in engineering and the physical and life sciences at the Universities of Oxford, Bristol and Warwick to create the next generation of industrial and academic leaders in the important new field of synthetic biology.


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Interactions in the microbiome: communities of organisms and communities of genes - Boon - 2013 - FEMS Microbiology Reviews - Wiley Online Library

Interactions in the microbiome: communities of organisms and communities of genes - Boon - 2013 - FEMS Microbiology Reviews - Wiley Online Library | Biomedical synthetic biology | Scoop.it

A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term ‘community’ is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to the mechanistically driven question of ‘How will they respond?’


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Christopher Voigt, Synthetic Biology Primer and Status

November 5, 2013: Introduced by moderator Anne-Marie Mazza of The National Academies, Christopher "Chris" Voigt of MIT and Editor-in-Chief of the journal ACS Synthetic…
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Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders | Biomedical synthetic biology | Scoop.it

Neurodevelopmental disorders, including autism spectrum disorder (ASD), are defined by core behavioral impairments; however, subsets of individuals display a spectrum of gastrointestinal (GI) abnormalities. We demonstrate GI barrier defects and microbiota alterations in the maternal immune activation (MIA) mouse model that is known to display features of ASD. Oral treatment of MIA offspring with the human commensalBacteroides fragilis corrects gut permeability, alters microbial composition, and ameliorates defects in communicative, stereotypic, anxiety-like and sensorimotor behaviors. MIA offspring display an altered serum metabolomic profile, and B. fragilis modulates levels of several metabolites. Treating naive mice with a metabolite that is increased by MIA and restored by B. fragilis causes certain behavioral abnormalities, suggesting that gut bacterial effects on the host metabolome impact behavior. Taken together, these findings support a gut-microbiome-brain connection in a mouse model of ASD and identify a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders.

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Nature Communications: Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides (2013)

Nature Communications: Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides (2013) | Biomedical synthetic biology | Scoop.it

Bacterial Type III Secretion Systems deliver effectors into host cells to manipulate cellular processes to the advantage of the pathogen. Many host targets of these effectors are found on membranes. Therefore, to identify their targets, effectors often use specialized membrane-localization domains to localize to appropriate host membranes. However, the molecular mechanisms used by many domains are unknown. Here we identify a conserved bacterial phosphoinositide-binding domain (BPD) that is found in functionally diverse Type III effectors of both plant and animal pathogens. We show that members of the BPD family functionally bind phosphoinositides and mediate localization to host membranes. Moreover, NMR studies reveal that the BPD of the newly identified Vibrio parahaemolyticus Type III effector VopR is unfolded in solution, but folds into a specific structure upon binding its ligand phosphatidylinositol-(4,5)-bisphosphate. Thus, our findings suggest a possible mechanism for promoting refolding of Type III effectors after delivery into host cells.


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Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells | Biomedical synthetic biology | Scoop.it

The simplicity of programming the CRISPR-associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on a genome-wide scale. We show that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells. First, we used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells. Next, in a melanoma model, we screened for genes whose loss is involved in resistance to vemurafenib, a therapeutic that inhibits mutant protein kinase BRAF. Our highest-ranking candidates include previously validated genes NF1 andMED12 as well as novel hits NF2, CUL3, TADA2B, and TADA1. We observe a high level of consistency between independent guide RNAs targeting the same gene and a high rate of hit confirmation, demonstrating the promise of genome-scale screening with Cas9.

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Get an idea from this paper! 

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Cell Stem Cell - Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients

Cell Stem Cell - Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients | Biomedical synthetic biology | Scoop.it

Single murine and human intestinal stem cells can be expanded in culture over long time periods as genetically and phenotypically stable epithelial organoids. Increased cAMP levels induce rapid swelling of such organoids by opening the cystic fibrosis transmembrane conductor receptor (CFTR). This response is lost in organoids derived from cystic fibrosis (CF) patients. Here we use the CRISPR/Cas9 genome editing system to correct the CFTR locus by homologous recombination in cultured intestinal stem cells of CF patients. The corrected allele is expressed and fully functional as measured in clonally expanded organoids. This study provides proof of concept for gene correction by homologous recombination in primary adult stem cells derived from patients with a single-gene hereditary defect.

omni's insight:

CRISPR goes for biomedical applications!

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CRISPR technology leaps from lab to industry

CRISPR technology leaps from lab to industry | Biomedical synthetic biology | Scoop.it

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Socrates Logos's curator insight, December 4, 2013 3:27 PM

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Helen Shen

"Scientists launch company to develop the therapeutic potential of gene-snipping enzymes.

Instead of taking prescription pills to treat their ailments, patients may one day opt for genetic 'surgery' — using an innovative gene-editing technology to snip out harmful mutations and swap in healthy DNA.

The system, called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), has exploded in popularity in the past year, with genetic engineers, neuroscientists and even plant biologists viewing it as a highly efficient and precise research tool. Now, the gene-editing system has spun out a biotechnology company that is attracting attention from investors as well.

Editas Medicine, based in Cambridge, Massachusetts, announced its launch on 25 November with an initial US$43 million venture capital investment. The company, founded by five leading CRISPR researchers, aims to develop therapies that directly modify disease-related genes. "This is a platform that could have a profound impact on a variety of genetic disorders," says interim president Kevin Bitterman, a venture capitalist at Polaris Partners in Waltham, Massachusetts, which is one of Editas' backers. The nicest cutCRISPR piggybacks on an immune strategy that bacteria use to detect and chop up foreign DNA. The DNA-cutting enzyme Cas9 finds its target with the help of an RNA guide sequence that researchers can now engineer to home in on potentially any gene of interest.

Editas is not disclosing its intended targets, but the technology might be tried first on diseases caused by a single faulty gene copy, says Feng Zhang, a neuroscientist at the Massachusetts Institute of Technology’s McGovern Institute for Brain Research in Cambridge, Massachusetts, and one of Editas’ founders. Simply disabling the disease-causing copy could clear the way for the good copy to take over. Treating conditions involving two dysfunctional gene copies will require correcting the gene by splicing in healthy DNA — a feat that Zhang says will require more work and engineering....."



http://bit.ly/1bhL7uM