SynBioFromLeukipposInstitute

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Gibson DG.

"The yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp and can be as long as 200 nucleotides in length to produce kilobase-sized synthetic DNA molecules. A protocol for designing the oligonucleotides to be assembled, transforming them into yeast, and confirming their assembly is described here. This straightforward scheme for assembling chemically synthesized oligonucleotides can be a useful tool for building synthetic DNA molecules."

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Cello J, Mueller S.

"Making use of the nucleotides sequence of the RNA genome (7,440 nt) of poliovirus, synthetic deoxyoligonucleotides, 60-70 nt in length are synthesized. The oligonucleotides that map to adjacent segments in the genome are designed such that they are of plus- and minus-strand polarity with the overlapping complementary sequences at their termini. The oligonucleotides are assembled by asymmetric PCR, and then, the segments are ligated directly into a plasmid. The segments are assembled stepwise via common unique restriction endonuclease cleavage sites to yield a full-length poliovirus complementary DNA (cDNA), carrying a phage T7 RNA polymerase promoter at the (left) 5' end. Genomic RNA is generated with a phage T7 RNA polymerase. The viral RNA is incubated in a cell-free extract, where it is translated and replicated, resulting in the de novo synthesis of poliovirus (PV). Finally, in vivo and in vitro experiments are carried out to confirm that infectious material isolated from the cell-free extract is indeed infectious PV.All components of the synthetic PV are generated by biochemical means. No virus-related structure or component that may have been generated previously in vivo is used as template or as building block for the viral particles. Our work shows that it is possible to synthesize an infectious agent in test tube by solely following instructions from a written sequence."

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Takafumi Miyamoto, Robert DeRose, Allison Suarez, Tasuku Ueno Melinda Chen, Tai-ping Sun, Michael J Wolfgang, Chandrani Mukherjee, David J Meyers & Takanari Inoue
"Using a newly synthesized gibberellin analog containing an acetoxymethyl group (GA3-AM) and its binding proteins, we developed an efficient chemically inducible dimerization (CID) system that is completely orthogonal to existing rapamycin-mediated protein dimerization. Combining the two systems should allow applications that have been difficult or impossible with only one CID system. By using both chemical inputs (rapamycin and GA3-AM), we designed and synthesized Boolean logic gates in living mammalian cells. These gates produced output signals such as fluorescence and membrane ruffling on a timescale of seconds, substantially faster than earlier intracellular logic gates. The use of two orthogonal dimerization systems in the same cell also allows for finer modulation of protein perturbations than is possible with a single dimerizer."
http://bit.ly/Ke0363

comment:
Cellular Computers? Scientists Train Cells to Perform Boolean Functions
"Johns Hopkins scientists have engineered cells that behave like AND and OR Boolean logic gates, producing an output based on one or more unique inputs. This feat, published in the May issue of Nature Chemical Biology, could eventually help researchers create computers that use cells as tiny circuits. Study leader Takanari Inoue, Ph.D., an assistant professor in the Department of Cell Biology and member of the Institute of Basic Biomedical Sciences' Center for Cell Dynamics at the Johns Hopkins University School of Medicine, explains that many researchers are striving to mimic devices in everyday use by engineering new qualities into biological materials, including biomolecules and cells. Several of those engaged in this relatively new field, known as synthetic biology, have tried to create biological computers....."
http://bit.ly/KyhkWv

"New study creates cells that act like circuits, a step toward developing cellular computers

Johns Hopkins scientists have engineered cells that behave like AND and OR Boolean logic gates, producing an output based on one or more unique inputs. This feat, published in the May issue of Nature Chemical Biology, could eventually help researchers create computers that use cells as tiny circuits.

Study leader Takanari Inoue, Ph.D., an assistant professor in the Department of Cell Biology and member of the Institute of Basic Biomedical Sciences’ Center for Cell Dynamics at the Johns Hopkins University School of Medicine, explains that many researchers are striving to mimic devices in everyday use by engineering new qualities into biological materials, including biomolecules and cells. Several of those engaged in this relatively new field, known as synthetic biology, have tried to create biological computers.

At the heart of both the biological and the more everyday silicon-based variety of computers are Boolean logic gates, which produce responses that vary depending on what type and how many inputs they receive. For example, AND gates need two unique inputs to generate an output. In contrast, OR gates generate an output based on whether they receive one input, or another, or both......."
http://bit.ly/JQDxMA

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Katherine A Riccione, Robert P Smith, Anna J Lee, and Lingchong You
"The survival of cells and organisms requires proper responses to environmental signals. These responses are governed by cellular networks, which serve to process diverse environmental cues. Biological networks often contain recurring network topologies called ‘motifs’. It has been recognized that the study of such motifs allows one to predict the response of a biological network, and thus cellular behavior. However, studying a single motif in complete isolation of all other network motifs in a natural setting is difficult. Synthetic biology has emerged as a powerful approach to understanding the dynamic properties of network motifs. In addition to testing existing theoretical predictions, construction and analysis of synthetic gene circuits has led to the discovery of novel motif dynamics such as how the combination of simple motifs can lead to autonomous dynamics or how noise in transcription and translation can affect the dynamics of a motif. Here, we review developments in synthetic biology as they pertain to increasing our understanding of cellular information processing. We highlight several types of dynamic behaviors that diverse motifs can generate, including the control of input/output responses, the generation of autonomous spatial and temporal dynamics, as well as the influence of noise in motif dynamics and cellular behavior."

http://pubs.acs.org/doi/abs/10.1021/sb300044r

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 Berla BM, Pakrasi HB.

"We analyzed DNA microarrays to identify highly expressed genes during stationary phase of Synechocystis sp. PCC 6803. Many identified genes are on endogenous plasmids, with copy numbers between 0.4 and 7 per chromosome. The promoters of such genes will be useful parts for synthetic biology applications in this phototrophic host."

http://1.usa.gov/KYf7Ar

Logic gates based on ion transistors
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Klas Tybrandt, Robert Forchheimer & Magnus Berggren
"Precise control over processing, transport and delivery of ionic and molecular signals is of great importance in numerous fields of life sciences. Integrated circuits based on ion transistors would be one approach to route and dispense complex chemical signal patterns to achieve such control. To date several types of ion transistors have been reported; however, only individual devices have so far been presented and most of them are not functional at physiological salt concentrations. Here we report integrated chemical logic gates based on ion bipolar junction transistors. Inverters and NAND gates of both npn type and complementary type are demonstrated. We find that complementary ion gates have higher gain and lower power consumption, as compared with the single transistor-type gates, which imitates the advantages of complementary logics found in conventional electronics. Ion inverters and NAND gates lay the groundwork for further development of solid-state chemical delivery circuits." http://bit.ly/KqX9tf

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Luo Z, Zhang S.

"Chirality is absolutely central in chemistry and biology. The recent findings of chiral self-assembling peptides' remarkable chemical complementarity and structural compatibility make it one of the most inspired designer materials and structures in nanobiotechnology. The emerging field of designer chemistry and biology further explores biological and medical applications of these simple d,l- amino acids through producing marvellous nanostructures under physiological conditions. These self-assembled structures include well-ordered nanofibers, nanotubes and nanovesicles. These structures have been used for 3-dimensional tissue cultures of primary cells and stem cells, sustained release of small molecules, growth factors and monoclonal antibodies, accelerated wound-healing in reparative and regenerative medicine as well as tissue engineering. Recent advances in molecular designs have also led to the development of 3D fine-tuned bioactive tissue culture scaffolds. They are also used to stabilize membrane proteins including difficult G-protein coupled receptors for designing nanobiodevices. One of the self-assembling peptides has been used in human clinical trials for accelerated wound-healings. It is our hope that these peptide materials will open doors for more and diverse clinical uses. The field of chiral self-assembling peptide nanobiotechnology is growing in a number of directions that has led to many surprises in areas of novel materials, synthetic biology, clinical medicine and beyond."

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Benders GA.

"Many bacterial and archaeal genomes are of a similar size to molecules that have been cloned in the yeast Saccharomyces cerevisiae and thus might be clonable as single, circular episomes in this host. Yeast offers a variety of efficient tools for the manipulation and study of cloned DNA. One strategy to clone a genome in yeast is to cotransform yeast spheroplasts with the genome of interest and a linear yeast vector whose termini are homologous to a spot in the genome. Clones are selected on auxotrophic medium and then screened for completeness and size; they may also be sequenced."

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Richardson SM, Liu S, Boeke JD, Bader JS.
"The manual design of synthetic genes is a tedious and error-prone process-even for very short genes-and it becomes completely infeasible when multiple synthetic genes are needed. GeneDesign is a set of modules that automate batch nucleotide manipulation. Here, we explain the installation, configuration, and use of GeneDesign as part of a synthetic design workflow."
http://1.usa.gov/LZunjc

the app can be found here: http://genedesign.thruhere.net/gd/

/PRNewswire-Asia/ -- GenScript USA Inc., a leading biotech company, has announced the opening of a new R&D facility in Nanjing, China.

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Kolganova NA, Shchyolkina AK, Chudinov AV, Zasedatelev AS, Florentiev VL, Timofeev EN.
"Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine."
http://1.usa.gov/L6b85g

Awesome app. I tested a pre release version. Just great! http://genomecompiler.com/

by
Zhengjun Guan ; Lei Pei ; Markus Schmidt ; Wei Wei
"While having developed into one of the most dynamic fields of the life sciences, synthetic biology may pose potential risks to the environment and human health. Based on current national and international risk assessment methods and current regulation of synthetic biology, we reviewed risk assessment in relation to synthetic biology’s research subfields (such as DNA-based biocircuits, minimal genome, protocells and chemical synthetic biology), its relation with biosafety engineering, its effect on ELSI (Ethics, Legal and Social Implications) and recent biosecurity challenges, such as biopunk (or biohackery), garage biology, do-it-yourself biology and bioterrorism. Additionally, we investigated existing strategies for management of synthetic biology research, focusing on self-regulatory or technology-focused methods and using the 5P (the principal investigator, the project, the premises, the provider of genetic material and its purchaser) strategy focusing in five different policy intervention points. Furthermore, we reviewed the current research and development of synthetic biology and its current biosafety regulations in China. Finally, we recommended management strategies to guide future research in synthetic biology with necessary amendments, including the establishment of regulations with a core of safety assessment, synthetic biology-specific good laboratory practice guidelines, and arguments for the reinforcement of internal regulation at the institution level and more active public outreach efforts for biosafety." http://www.doaj.org/doaj?func=abstract&id=1027935

DNA synthesis, assembly and applications in synthetic biology

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Ma S, Tang N, Tian J.
"The past couple of years saw exciting new developments in microchip-based gene synthesis technologies. Such technologies hold the potential for significantly increasing the throughput and decreasing the cost of gene synthesis. Together with more efficient enzymatic error correction and genome assembly methods, these new technologies are pushing the field of synthetic biology to a higher level."
http://1.usa.gov/LDsxEX

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Shuler ML, Foley P, Atlas J.
"One important aim of synthetic biology is to develop a self-replicating biological system capable of performing useful tasks. A mathematical model of a synthetic organism would greatly enhance its value by providing a platform in which proposed modifications to the system could be rapidly prototyped and tested. Such a platform would allow the explicit connection of genomic sequence information to physiological predictions. As an initial step toward this aim, a minimal cell model (MCM) has been formulated. The MCM is defined as a model of a hypothetical cell with the minimum number of genes necessary to grow and divide in an optimally supportive culture environment. It is chemically detailed in terms of genes and gene products, as well as physiologically complete in terms of bacterial cell processes (e.g., DNA replication and cell division). A mathematical framework originally developed for modeling Escherichia coli has been used to build the platform MCM. A MCM with 241 product-coding genes (those which produce protein or stable RNA products) is presented. This gene set is genomically complete in that it codes for all the functions that a minimal chemoheterotrophic bacterium would require for sustained growth and division. With this model, the hypotheses behind a minimal gene set can be tested using a chemically detailed, dynamic, whole-cell modeling approach. Furthermore, the MCM can simulate the behavior of a whole cell that depends on the cell's (1) metabolic rates and chemical state, (2) genome in terms of expression of various genes, (3) environment both in terms of direct nutrient starvation and competitive inhibition leading to starvation, and (4) genomic sequence in terms of the chromosomal locations of genes."
http://1.usa.gov/JSYSTM

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Redi CA, Capanna E.

"The study of genome size (GS) and its variation is so fascinating to the scientific community because it constitutes the link between the present-day analytical and molecular studies of the genome and the old trunk of the holistic and synthetic view of the genome. The GS of several taxa vary over a broad range and do not correlate with the complexity of the organisms (the C-value paradox). However, the biology of transposable elements has let us reach a satisfactory view of the molecular mechanisms that give rise to GS variation and novelties, providing a less perplexing view of the significance of the GS (C-enigma). The knowledge of the composition and structure of a genome is a pre-requisite for trying to understand the evolution of the main genome signature: its size. The radiation of mammals provides an approximately 180-million-year test case for theories of how GS evolves. It has been found from data-mining GS databases that GS is a useful cyto-taxonomical instrument at the level of orders/superorders, providing genomic signatures characterizing Monotremata, Marsupialia, Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. A hypothetical ancestral mammalian-like GS of 2.9-3.7 pg has been suggested. This value appears compatible with the average values calculated for the high systematic levels of the extant Monotremata (∼2.97 pg) and Marsupialia (∼4.07 pg), suggesting invasion of mobile DNA elements concurrently with the separation of the older clades of Afrotheria (∼5.5 pg) and Xenarthra (∼4.5 pg) with larger GS, leaving the Euarchontoglires (∼3.4 pg) and Laurasiatheria (∼2.8 pg) genomes with fewer transposable elements. However, the paucity of GS data (546 mammalian species sized from 5,488 living species) for species, genera, and families calls for caution. Considering that mammalian species may be vanished even before they are known, GS data are sorely needed to phenotype the effects brought about by their variation and to validate any hypotheses on GS evolution in mammals."