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Table of Contents for Cell,
Volume 131, Issue 2. October 19, 2007
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Analysis
From Bench to Business and Back Again
K. Wilan

Essay
Presenilin: Running with Scissors in the Membrane
D.J. Selkoe and M.S. Wolfe

Previews
A Backup DNA Repair Pathway Moves to the Forefront
A. Nussenzweig and M.C. Nussenzweig

When Two Is Better Than One
C.C. Babbitt, R. Haygood, and G.A. Wray

Retinoblastoma Teaches a New Lesson
H. te Riele

The Chromosomal Passenger Complex: One for All and All for One
S. Ruchaud, M. Carmena, and W.C. Earnshaw

How Mice Cope with Stressful Social Situations
S.E. Hyman

Taking Neural Crest Stem Cells to New Heights
E. Kokovay and S. Temple

Cordon-Bleu: A New Taste in Actin Nucleation
B. Winckler and D.A. Schafer

Review
Developmental Origin of Fat: Tracking Obesity to Its Source
S. Gesta, Y.-H. Tseng, and C.R. Kahn

SnapShot
Nuclear Transport
E.J. Tran, T.A. Bolger, and S.R. Wente

Articles
Regulation of Tumor Cell Mitochondrial Homeostasis by an Organelle-Specific Hsp90 Chaperone Network
B.H. Kang, J. Plescia, T. Dohi, J. Rosa, S.J. Doxsey, and D.C. Altieri

Molecular chaperones, especially members of the Hsp90 family, are thought to promote tumor cell survival, but this function is not well understood. Here, Kang et al. report that mitochondria of tumor cells, but not most normal tissues, contain Hsp90 and its related protein, TRAP-1. These molecules associate with Cyclophilin D - an immunophilin that normally initiates mitochondrial cell death - and inhibit its function. Furthermore, Hsp90 antagonists directed to mitochondria cause sudden collapse of mitochondrial function and selective tumor cell death. These organelle-specific antagonists may provide a new class of potent anticancer agents.

Structure of a Survivin-Borealin-INCENP Core Complex Reveals How Chromosomal Passengers Travel Together
A.A. Jeyaprakash, U.R. Klein, D. Lindner, J. Ebert, E.A. Nigg, and E. Conti

The chromosomal passenger complex (CPC), an essential regulator of mitosis, contains the kinase Aurora B and a regulatory complex (Survivin, Borealin, and INCENP). The CPC displays dynamic localization properties during cell division, and all three regulatory subunits are required for the spatial and temporal control of Aurora B activity. Jeyaprakash and colleagues solve the crystal structure of a minimal Survivin-Borealin-INCENP complex and use structure-based mutants to reveal that the association of all three subunits creates a composite molecular surface that bears the conserved residues required for localization. Thus, the regulatory core of the CPC functions as a single structural unit.

Recycling of Eukaryotic Posttermination Ribosomal Complexes
A.V. Pisarev, C.U.T. Hellen, and T.V. Pestova

To participate in multiple rounds of translation, ribosomes have to be recycled after translation termination. In prokaryotes, recycling requires ribosome recycling factor RRF. Eukaryotes lack an RRF homolog, and their recycling mechanism has been unknown. Pisarev et al. reconstitute eukaryotic recycling in vitro and show that it can be promoted by translation initiation factors. eIF3 plays the principal role in splitting posttermination complexes into 60S subunits and mRNA/tRNA-containing 40S subunits. Next, eIF1 mediates release of tRNA and eIF3j ensures subsequent mRNA dissociation. This study provides an unexpected function for translation initiation factors in ribosome recycling.

The Structural Basis for the Large Powerstroke of Myosin VI
J. Ménétrey, P. Llinas, M. Mukherjea, H.L. Sweeney, and A. Houdusse

Myosin VI moves along actin filaments in the opposite direction than other myosin motors and has a large step size (powerstroke). These properties stem from unique structural inserts within myosin VI. Now, Menetrey and colleagues solve the crystal structure of myosin VI in a state that represents the starting point for movement (pre-powerstroke). Myosin VI adopts a pre-powerstroke state in which the domain that positions the lever arm is rearranged compared to its position at the end of the powerstroke. These findings explain the directionality and large powerstroke of myosin VI.

RSUME, a Small RWD-Containing Protein, Enhances SUMO Conjugation and Stabilizes HIF-1α during Hypoxia
A. Carbia-Nagashima, J. Gerez, C. Perez-Castro, M. Paez-Pereda, S. Silberstein, G.K. Stalla, F. Holsboer, and E. Arzt

Conjugation of SUMO to various proteins regulates diverse cellular functions. Carbia-Nagashima et al. identify a protein RSUME that is induced by hypoxia in brain tumors. RSUME enhances the sumoylation of proteins including IκB and HIF-1α, which inhibits NF-κB activity and stabilizes HIF-1α, respectively. RSUME forms a heterodimer with the SUMO conjugase Ubc9 and enhances Ubc9 activity. These findings point to a central role of RSUME in potentiating sumoylation and hence in influencing critical regulatory pathways such as hypoxia and NF-κB signaling.

Self-Renewing Osteoprogenitors in Bone Marrow Sinusoids Can Organize a Hematopoietic Microenvironment
B. Sacchetti, A. Funari, S. Michienzi, S. Di Cesare, S. Piersanti, I. Saggio, E. Tagliafico, S. Ferrari, P.G. Robey, M. Riminucci, and P. Bianco

The identity and self-renewal capacity of the skeletal stem/progenitor cells in the bone marrow has long remained elusive. Here, Sacchetti et al. identify subendothelial, adventitial cells in bone marrow sinusoids as clonogenic osteoprogenitors. When explanted, these cells can generate bone and self-renew upon heterotopic transplantation in vivo. These transplanted cells also establish, through dynamic interactions with developing sinusoids, the hematopoietic microenvironment at heterotopic sites. Thus, subendothelial, adventitial cells of bone marrow sinusoids can act as organizers of the hematopoietic microenvironment.

Cordon-Bleu Is an Actin Nucleation Factor and Controls Neuronal Morphology
R. Ahuja, R. Pinyol, N. Reichenbach, L. Custer, J. Klingensmith, M.M. Kessels, and B. Qualmann

Despite the numerous crucial functions of actin filaments and the variety of different cellular actin structures formed, there are only a small number of factors known to nucleate filament formation. Here, Ahuja et al. describe the discovery and detailed characterization of a new type of nucleator, Cordon-bleu, which promotes formation of nonbundled, unbranched filaments and appears to be important for neuronal morphology. The results suggest that a minimal assembly of three actin monomers in crossfilament orientation is needed to kick-start spontaneous actin filament polymerization.

v-SNARE Actions during Ca2+ -Triggered Exocytosis
J. Kesavan, M. Borisovska, and D. Bruns

SNARE proteins mediate membrane fusion in various trafficking pathways. However, the degree to which SNAREs provide the force for vesicle fusion remains poorly understood. Using a combination of high-resolution techniques, Kesavan et al. examine calcium-dependent exocytosis in mouse chromaffin cells at the millisecond timescale. The authors show that the execution of pre- and postfusional steps during exocytosis depends on a short molecular distance between the SNARE domain and the transmembrane anchor of the vesicular SNARE protein synaptobrevin II. Thus vesicular SNARE proteins drive membrane fusion and continuous molecular "pulling" by SNAREs guide the vesicle through the consecutive stages of exocytosis.

Glia-like Stem Cells Sustain Physiologic Neurogenesis in the Adult Mammalian Carotid Body
R. Pardal, P. Ortega-Sáenz, R. Durán, and J. López-Barneo

Neurogenesis occurs in the adult mammalian brain, but whether neural stem cells exist in the peripheral nervous system is unknown. Pardal et al. now identify stem cells in the adult carotid body, an oxygen-sensing organ. Unexpectedly, these stem cells are glia-like cells, which were believed to have only a supportive role. Activated by low blood oxygen, these cells produce progenitors that differentiate into neuron-like glomus cells and produce dopamine and growth factors in vitro. Thus neurogenesis can occur in the adult peripheral nervous system and stem cell-derived glomus cells may be useful for cell therapy against Parkinson's disease.

Differentiated Horizontal Interneurons Clonally Expand to Form Metastatic Retinoblastoma in Mice
I. Ajioka, R.A.P. Martins, I.T. Bayazitov, S. Donovan, D.A. Johnson, S. Frase, S. Cicero, K. Boyd, S.S. Zakharenko, and M.A. Dyer

It is commonly believed that cell-cycle exit must precede differentiation, and that terminally differentiated cells do not proliferate. This principle extends to cancer as differentiated tumors are less aggressive than their undifferentiated counterparts. Now, Ajioka et al. show that a postmitotic differentiated neuron re-enters the cell cycle and clonally expands while maintaining all of its molecular and morphological features including neurites and synapses. Studying the mouse retina, the authors find that interneurons rapidly expand and form highly differentiated, yet extremely aggressive, retinoblastoma. These provocative findings provide a fresh look on the relationship between differentiation and proliferation during tumorigenesis.

Molecular Adaptations Underlying Susceptibility and Resistance to Social Defeat in Brain Reward Regions
V. Krishnan, M.-H. Han, D.L. Graham, O. Berton, W. Renthal, S.J. Russo, Q. LaPlant, A. Graham, M. Lutter, D.C. Lagace, S. Ghose, R. Reister, P. Tannous, T.A. Green, R.L. Neve, S. Chakravarty, A. Kumar, A.J. Eisch, D.W. Self, F.S. Lee, C.A. Tamminga, D.C. Cooper, H.K. Gershenfeld, and E.J. Nestler

Stress can precipitate conditions like depression in some individuals but not others, and mechanisms underlying these variations are poorly understood. Krishnan et al. investigate the adaptations in the brain that distinguish mice that are susceptible to a social stress (social defeat) from those that are resistant. Vulnerability is mediated by enhanced release of the growth factor BDNF in two limbic structures that mediate brain reward. Thus brain reward circuits are important in the susceptibility and resistance to stress, and these adaptations in mice may help to understand depression and resilience in humans.

Resource
Systematic Gene Expression Mapping Clusters Nuclear Receptors According to Their Function in the Brain
F. Gofflot, N. Chartoire, L. Vasseur, S. Heikkinen, D. Dembele, J. Le Merrer, and J. Auwerx

Nuclear receptors (NRs) are transcription factors that operate at the interface between genes and the environment. Although most NRs are present in the central nervous system, little is known about their roles in behavior and in neurological and psychiatric disorders. Gofflot et al. now provide a systematic quantitative and anatomical expression atlas of the entire NR gene family in 104 regions of the adult mouse brain at cellular resolution. The data are organized in an interactive database called MousePat. Using the MousePat resource, NR expression patterns can be clustered into anatomical and regulatory networks that indicate the role of NRs in specialized brain functions.
 

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Research Highlights
Technology: A new tool for analysing structural variation | PDF (268 KB)

p822 | doi:10.1038/nrg2230
Cancer genetics: Networks uncover new cancer susceptibility suspect | PDF (138 KB)

p823 | doi:10.1038/nrg2229
In brief
Complex traits | Quantitative genetics | Evolution | Genomics | PDF (117 KB)

p823 | doi:10.1038/nrg2265
Association studies: Dog genes mapped at a SNP | PDF (300 KB)

p824 | doi:10.1038/nrg2233
Development: Mutual collaboration | PDF (185 KB)

p824 | doi:10.1038/nrg2234
In brief
Chromatin | Behavioural genetics | Stem cells | Gene regulation | PDF (116 KB)

p824 | doi:10.1038/nrg2266
Chromatin: Remodellers are more than just muscle | PDF (364 KB)

p825 | doi:10.1038/nrg2231
Genetic screens: Epistasis on the double | PDF (661 KB)

p826 | doi:10.1038/nrg2221
Genomics: HapMap Phase II unveiled | PDF (323 KB)

p826 | doi:10.1038/nrg2235
Gene regulation: The many paths to coexpression | PDF (361 KB)

p827 | doi:10.1038/nrg2228
Ethics watch
Carrier testing in minors: conflicting views | PDF (207 KB)

p828 | doi:10.1038/nrg2222
Top of page
Progress
Histone lysine demethylases: emerging roles in development, physiology and disease

Yang Shi

p829 | doi:10.1038/nrg2218

Functions of histone lysine demethylases in a range of developmental and physiological processes are rapidly being uncovered, as are the roles of these enzymes in disease. Histone demethylases also provide a promising new route towards the therapeutic targeting of epigenetic regulators.

* Abstract
* Full Text
* PDF (335 KB)

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Reviews
Genetic links between diet and lifespan: shared mechanisms from yeast to humans

Nicholas A. Bishop & Leonard Guarente

p835 | doi:10.1038/nrg2188

Recent studies in yeast, invertebrates and mammals have begun to solve the puzzle of how dietary restriction results in increased longevity. An increased knowledge of the underlying pathways promises to provide new directions for treating ageing-related diseases in humans.

* Abstract
* Full Text
* PDF (963 KB)

Which evolutionary processes influence natural genetic variation for phenotypic traits?

Thomas Mitchell-Olds, John H. Willis & David B. Goldstein

p845 | doi:10.1038/nrg2207

A combination of ecological, population genetic and molecular studies has stimulated progress in understanding the forces that shape natural phenotypic variation. Technical advances that allow fitness differences to be linked to individual polymorphisms now promise rapid progress in this field.

* Abstract
* Full Text
* PDF (1,492 KB)

Recent and ongoing selection in the human genome

Rasmus Nielsen, Ines Hellmann, Melissa Hubisz, Carlos Bustamante & Andrew G. Clark

p857 | doi:10.1038/nrg2187

Identifying regions of the human genome that have been subject to selection is key to understanding our evolution, and provides insights into the genetic basis of disease. However, important caveats require consideration when interpreting the results of attempts to identify selected regions.

* Abstract
* Full Text
* PDF (780 KB)

From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

Beverly S. Emanuel & Sulagna C. Saitta

p869 | doi:10.1038/nrg2136

Advances in technology and improved genome annotation have greatly clarified the role of genome architecture in the aetiology of many well-known and newly described clinical disorders. The authors focus on a group of genomic disorders mediated by segmental duplications to illustrate recent advances in their dissection and diagnosis.

* Abstract
* Full Text
* PDF (1,056 KB)

Specialization and evolution of endogenous small RNA pathways

Elisabeth J. Chapman & James C. Carrington

p884 | doi:10.1038/nrg2179

Eukaryotes have evolved small RNA-guided regulatory networks to control RNA transcripts, chromatin, repeated genomic sequences and invasive agents, such as viruses. Spatiotemporal regulation of the transcriptome through these pathways has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.

* Abstract
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Perspective
Timeline
Opportunities for women in early genetics

Marsha L. Richmond

p897 | doi:10.1038/nrg2200

Although the early years of genetics have been well described by historians, it is only now being realized that this was one of the earliest emerging disciplines in twentieth-century biology to benefit from the contributions of women. Many, however, became 'silent scientists' — publishing no paper beyond their dissertation.

* Abstract
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Correspondence
Correspondence: Semes for analysis of evolution: de Duve's peroxisomes and Meyer's hydrogenases in the sulphurous Proterozoic eon

Lynn Margulis, Michael Chapman & Michael F. Dolan

| doi:10.1038/nrg2071-c1

* Full Text
* PDF (1,197 KB)

Correspondence: Mutation rate variation in eukaryotes: evolutionary implications of site-specific mechanisms

D. G. King & Y. Kashi

| doi:10.1038/nrg2158-c1

* Full Text
* PDF (138 KB)

Correspondence: Reply to: Mutation rate variation in eukaryotes: evolutionary implications of site-specific mechanisms

Charles F. Baer, Michael M. Miyamoto & Dee R. Denver

| doi:10.1038/nrg2158-c2
http://www.nature.com/nrg/journal/v8/n11/index.html#rv
 

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Molecular Therapy

Volume 15, No 11
November 2007
ISSN: 1525-0016
EISSN: 1525-0024


FEATURED ARTICLES
ORIGINAL ARTICLE
"Zinc fingering" ocular antiangiogenic therapy
ORIGINAL ARTICLE
Enriching cardiomyocytes from hESCs
ORIGINAL ARTICLE
RNAi for hand, foot and mouth disease
ORIGINAL ARTICLE
Therapeutic applications of microRNAs
ORIGINAL ARTICLE
Hydrodynamic gene delivery
Current issue table of contents
Advance online publication in full
NEWS

Stem cells can be genetically manipulated to select for and enrich their specialization into heart muscle cells according to a study published in Molecular Therapy. Read the press release and article, which is one of the first to document the successful selection of one kind of cell in hESCs.

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Perfect placement. Molecular Therapy encourages authors to submit figures and artwork for the journal's cover - a prime position to gain great exposure for your research. Gene or stem cell-related images are especially of interest. For more information on image requirements, download the cover specifications sheet.

Read some of the top cited articles in Molecular Therapy free!

Progress towards in vivo use of siRNAs

Robust Systemic Transduction with AAV9 Vectors in Mice: Efficient Global Cardiac Gene Transfer Superior to That of AAV8

Adeno-associated Virus Serotypes: Vector Toolkit for Human Gene Therapy

A two-stage poly(ethylenimine)-mediated cytotoxicity: implications for gene transfer/therapy

Regulatable Gene Expression Systems for Gene Therapy Applications: Progress and Future Challenges
 

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Environmental signal integration by a modular AND gate

Christopher Anderson1,2, Christopher A Voigt1 & Adam P Arkin2

1. Department of Pharmaceutical Chemistry, QB3: California Institute for Quantitative Biological Research, The University of California San Francisco, San Francisco, CA, USA
2. Department of Bioengineering, University of California, Howard Hughes Medical Institute, QB3: California Institute for Quantitative Biological Research, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

Correspondence to: Christopher A Voigt1 Department of Pharmaceutical Chemistry, The University of California—San Francisco, Box 2540, Room 408C, 1700 4th Street, San Francisco, CA 94158-2330, USA. Tel.: +1 41 55027050; Fax: +1 41 55024690; Email: cavoigt@picasso.ucsf.edu

Received 12 March 2007; Accepted 6 July 2007; Published online 14 August 2007

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission.
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Abstract

Microorganisms use genetic circuits to integrate environmental information. We have constructed a synthetic AND gate in the bacterium Escherichia coli that integrates information from two promoters as inputs and activates a promoter output only when both input promoters are transcriptionally active. The integration occurs via an interaction between an mRNA and tRNA. The first promoter controls the transcription of a T7 RNA polymerase gene with two internal amber stop codons blocking translation. The second promoter controls the amber suppressor tRNA supD. When both components are transcribed, T7 RNA polymerase is synthesized and this in turn activates a T7 promoter. Because inputs and outputs are promoters, the design is modular; that is, it can be reconnected to integrate different input signals and the output can be used to drive different cellular responses. We demonstrate this modularity by wiring the gate to integrate natural promoters (responding to Mg2+ and AI-1) and using it to implement a phenotypic output (invasion of mammalian cells). A mathematical model of the transfer function is derived and parameterized using experimental data.
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Introduction

Genetically programming cells require sensors to receive information, circuits to process the inputs, and actuators to link the circuit output to a cellular response (Andrianantoandro et al, 2006; Chin, 2006; Voigt, 2006; Tan et al, 2007). In this paradigm, sensing, signal integration, and actuation are encoded by distinct 'devices' comprised of genes and regulatory elements (Knight and Sussman, 1997; Endy, 2005). These devices communicate with one another through changes in gene expression and activity. For example, when a sensor is stimulated, this may lead to the activation of a promoter, which then acts as the input to a circuit. There has been a large effort to create and characterize different classes of devices and to make this information publicly available in the Registry of Standard Biological Parts (parts.mit.edu).

We have constructed a device that functions as an AND gate that can integrate two input signals and control a cellular response. An AND gate is a logical operation that integrates multiple input signals. The output of an AND gate is only ON when all of the inputs are ON. If any of the outputs are OFF, then the output is OFF. An AND gate forms the core of electronic computing and is a critical device to create different genetic programs. It is particularly useful to integrate signals from multiple sensors to identify an environment with high specificity.

Bacteria use a variety of mechanisms to sense their environment, including two-component systems, transcription factors, and small RNA molecules (Hoch and Silhavy, 1995). In some cases, an environment is defined by a single signal, such as the presence or absence of a small molecule (e.g., the lac, trp, and fur operons; Setty et al, 2003). In other cases, it is a complex array of signals that are integrated by the bacterium to identify an environment. Integrating multiple signals can increase the sensing specificity. Even signals that are too general to identify a specific environment (e.g., pH, temperature, and osmolarity) can achieve higher specificity together. A similar problem arises when programming cells to identify an environment that is not naturally encountered, and for which there is not a single dominant signal. In this case, genetic logic gates are required to integrate multiple signals to achieve sensing specificity.

Different logic gates have been built using biological components such as transcription factor genes and regulatory elements (Weiss et al, 1999; Guet et al, 2002; Kramer et al, 2004) or protein–protein interactions (Dueber et al, 2003). To date, the architecture of these circuits relies on the specific identity of a particular set of inputs and a particular output. In these examples, changing the identities of the inputs and outputs is not simple. In contrast, a circuit is modular if it can be rapidly connected to different inputs and used to drive different outputs. Modularity facilitates the incorporation of a circuit into different genetic programs.

We have designed and constructed a modular genetic AND gate whose inputs and outputs are promoters (Figure 1). Only when both of the input promoters are active is the output promoter turned on. The architecture of the AND gate involves two parts, both of which are required to express T7 RNA polymerase. The first part is the T7 RNA polymerase gene, which has been modified to contain two amber stop codons that block translation. The second part is the nonsense suppressor tRNA supD, which enables the translation of polymerase. When both of these parts are transcribed from the input promoters, polymerase is expressed and this activates an output T7 promoter.
Figure 1
Figure 1 : Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com

A schematic representation of the genetic AND gate is shown. Two promoters are the inputs into the gate. The first promoter is linked to the transcription of the amber suppressor tRNA supD. The second promoter drives the transcription of T7 RNA polymerase. The polymerase gene has been modified to contain two amber stop codons (T7ptag). These stop codons are translated as serine when supD is also transcribed. Polymerase is expressed only when both SupD and T7ptag mRNA are present. To characterize the transfer function of the AND gate, two input promoters are used that respond to the small molecules salicylate and arabinose. In addition, the output is connected to the expression of fast-degrading green fluorescent protein.
Full figure and legend (80K)Figures & Tables index

Using two inducible systems as inputs (promoters that respond to arabinose and salicylate) and connecting the output to the expression of green fluorescent protein (gfp), we demonstrate that this circuit behaves as a near-digital AND gate. These data are used to parameterize a simple model of the steady-state input–output response (transfer function) of the circuit. This formalization will facilitate the integration of this circuit into larger genetic systems. To demonstrate the circuit is modular, two constructs are made that switch the input promoters and connect the output to a different response. First, new inputs are added that respond to the quorum signal AI-1 (luxR) and magnesium limitation (phoPQ). Second, the output is switched to the invasin gene, which enables the bacteria to invade mammalian cells. In both cases, the circuit behaves as an AND gate.
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Results
Circuit design and construction

A two-input AND gate activates an output only when both inputs are on. If either or both of the inputs are off, then the output is off. Ideally, the circuit should be designed to be modular, such that the inputs and outputs can be rapidly rewired. In transcription-based systems, it is convenient that the connections between devices be promoters (Basu et al, 2004, 2005; Endy, 2005). For example, if a two-component system turns a promoter on, then this promoter can be used as the input into the next device. Similarly, if the output is a promoter, then this can either express a gene that produces a cellular phenotype or act as an input into the next device.

Our AND gate design uses two promoters as inputs and turns on an output promoter. Transcription occurs from the output promoter only when both input promoters are active. The circuit integrates the inputs via a translational interaction (Figure 1). The first input promoter drives the transcription of mRNA encoding T7 RNA polymerase that by itself cannot be translated due to the presence of amber stop codons. The second input promoter drives the transcription of an amber suppressor, which allows the activator to be expressed and activate an output promoter.

The suppression is based on the TAG amber stop codon and the SupD amber suppressor tRNA derived from Escherichia coli tRNA2Ser (Hoffman and Wilhelm, 1970). In wild-type bacteria, the TAG codon is decoded by release factor 1 resulting in translation termination. In the presence of SupD, TAG codons are decoded as serine, and translation resumes to generate the full-length protein. Because there are only 326 TAG codons in E. coli (Blattner et al, 1997), suppressed expression can be as efficient as 50% with no loss of viability (Anderson et al, 2002). We verified that the T7 RNA polymerase and supD parts do not affect the growth rate or morphology when expressed in E. coli (Supplementary information).

T7 RNA polymerase was chosen to be the activator in the circuit, although in principle any transcriptional regulator could be used in this design. The T7 gene was modified to contain amber codons at positions 8 and 14 (T7ptag). This causes premature translational termination, resulting in a non-functional polypeptide. This combination of mutations afforded the lowest basal T7 RNA polymerase activity and the highest gain in activity when coexpressed with an amber suppressor (Santoro et al, 2002). When both the polymerase and supD genes are expressed, full-length polymerase is synthesized, and the output T7 promoter becomes activated.

To characterize the circuit dynamics, two promoters that can be induced with small molecules were used as inputs (Figure 1, plasmid details in Supplementary information). The supD gene was placed under the control of a salicylate-activated promoter (Psal) (input 1). The T7ptag gene was placed under the control of an arabinose-inducible promoter (PBAD) (input 2). To monitor activation, a fast folding green fluorescent protein containing a degradation tag (GFPmut3_LAA), was placed under the control of the T7 promoter.

The first construct contained a strong ribosome binding site (rbs) (Table I) and did not function as an AND gate. The circuit was always inducible by arabinose, independent of the concentration of salicylate (not shown). Intuitively, this could result if the basal expression of T7ptag was high, where a sufficient amount of activator was produced even in the absence of arabinose. In other words, the range of the activity of the input promoter did not match the range required for the proper behavior of the circuit. This problem has been observed before in genetic circuit design (Yokobayashi et al, 2002). A successful approach to matching the range of the input to a downstream circuit has been to mutagenize the rbs, either using rational substitutions or random mutagenesis (Yokobayashi et al, 2002; Feng et al, 2004; Anderson et al, 2006).
Table 1: Sequenced ribosome binding sites
Table 1 - Sequenced ribosome binding sites
Full tableFigures & Tables index

To tune the range of the PBAD input, we designed a saturation mutagenic library of three positions in the rbs and the first base of the start codon (Table I). This library of 128 theoretical variants was plated on media containing arabinose and salicylate, and 50% of the colonies were visibly fluorescent green. Of these, 48 green colonies were subsequently grown in liquid media with no inducer, only salicylate, or both inducers and assayed by fluorimetry. Of the 48 assayed variants 44 showed at least five-fold gain in fluorescence when both inducers were added compared to values obtained when only one or no inducer was added (Supplementary information). Therefore, most variants displayed AND-gate behavior. Two variants, B9 and F11, were chosen for further characterization. The B9 clone has a weaker rbs and behaves as a functional AND gate. The F11 clone has a weaker rbs than the initial sequence, but it produces a similar salicylate-independent response.

The B9 clone was used to further characterize the function of the AND gate circuit. The output of the circuit was measured by growing cells to mid-log phase in different combinations of the two inducers (Materials and methods). The output of the circuit was measured using fluorimetry (Figure 2). The transitions between the on and off states were very steep, thus producing a near-digital AND gate. Flow cytometry was used to measure the population heterogeneity (Figure 2B and Supplementary information). There was no detectable expression in the absence of either inducer and a 1000-fold induction when both inducers are present.
Figure 2
Figure 2 : Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com

Integration of two inducible promoters by the AND gate. (A) The fluorescence was measured for 64 combinations of inducer in a fluorimeter. The data are shown for (left to right) 0, 3.2 times 10-7, 1.3 times 10-6, 5.2 times 10-6, 2.1 times 10-5, 8.3 times 10-5, 3.3 times 10-4, and 1.3 times 10-3 M arabinose, and (bottom to top) 0, 1.5 times 10-7, 6.1 times 10-7, 2.4 times 10-6, 9.8 times 10-6, 3.9 times 10-5, 1.6 times 10-4, and 6.2 times 10-4 M salicylate. (B) The fluorescence was measured in individual cells using a flow cytometer to determine the population level behavior. The entire population of cells is turned on in the presence of both arabinose and salicylate (1.3 times 10-3 and 6.2 times 10-4 M, respectively). When either inducer is not added, the entire population is turned off. There is a 1000-fold induction between the ON and OFF states. The data for this figure were obtained using plasmids pAC-SalSer914, pBACr-AraT7940, and pBR939b (Supplementary information).
Full figure and legend (168K)Figures & Tables index

Transfer function model

The transfer function of a genetic circuit describes the steady-state response as a function of the activity of the input promoters. For a logic gate, this is a two-dimensional function, where two inputs are being integrated into a single output. An analytical form for the transfer function was derived on the basis of biochemical interaction underlying the circuit architecture and a simple model of translation control (Gilchrist and Wagner, 2006). The model relates the normalized output of the AND gate (G/Gmax) to the individual transfer functions of the two input promoters, I1 and I2.

The transfer function was derived in order to understand how the range of the input promoters affects the function of the circuits. To characterize the circuit, two promoters are used that can be induced by small molecules (salicylate and arabinose). However, to generalize the model, I1 and I2 should be the activity of the PBAD and Psal promoters and not dependent on the concentrations of the small molecules. The activity of these promoters can be measured independently by fusing gfp to the promoter and measuring the output in response to the small-molecule inducer, thus producing a one-dimensional function (Figure 3). The individual responses of the two promoters are then used to parameterize the transfer function.
Figure 3
Figure 3 : Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com

The individual transfer functions for the input promoters are shown. The transfer functions were measured by fusing the promoter to gfp and measuring the fluorescence as a function of the concentration of small molecule inducer (salicylate or arabinose). The transfer functions were used to parameterize the AND gate model. The left panel shows the activation of Psal in response to salicylate. This promoter is leaky even in the complete absence of inducer. The right panel shows the transfer functions for the PBAD parent rbs (triangle), F11 (red filled square), and B9 (blue circle) clones (Table I). The average and standard deviation of four fluorimetry experiments are shown (the error is often smaller than the size of the data point). The data shown in this figure were obtained using plasmids pBACr899 (Psal), pBAC872s (PBAD, parent rbs), pBAC978 (PBAD, F11 rbs), pBAC987 (PBAD, B9 rbs) (Supplementary information).
Full figure and legend (73K)Figures & Tables index

The full derivation of the transfer function is described in the Supplementary information. The form of transfer function relating fluorescence measurements is as follows:
Environmental signal integration by a modular AND gate

where Gmax is the maximum fluorescence observed for the output. Once a and b are calculated, these parameters could be used in conjunction with any two input promoters, provided that their one-dimensional transfer function was determined under the same standard growth conditions and plasmids.

Equation (1) was parameterized using the full set of experimental data for the B9 clone when both inducers were systematically varied (Figure 2A). To calculate the one-dimensional transfer functions for I1 and I2, the gene for a fast-degrading green fluorescent protein was fused to the salicylate and arabinose promoters (Supplementary information). For the salicylate promoter, a strong rbs was used as a standard measure of promoter activity (Table I). For the arabinose reporters, the original, B9, and F11 rbss were inserted upstream of GFP. The fusions were cloned into a plasmid and the fluorescence was measured as a function of inducer concentration (Figure 3). For each pair of salicylate and arabinose concentrations, the one-dimensional fluorescence data were used to obtain I1 and I2, respectively. The two-dimensional data were used to obtain the value of G/Gmax. Fitting these data to equation (1) yielded the following: a=50plusminus20 and b=3000plusminus1000 (Figure 4; Supplementary Figure S1).
Figure 4
Figure 4 : Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com

The AND gate model was parameterized using fluorescence data. The fit to the AND gate transfer function is shown for the B9 clone. Each point represents one experimental data point from the two-dimensional array of inducer combinations (Figure 2). This was compared to the value of G/Gmax calculated using equation (1) and using the values of I1 and I2 from the one-dimensional data (Figure 3). The fit was performed using a non-linear regression algorithm to yield a=50 and b=3000. The Pearson correlation coefficient for the fit is 0.971. The full fit to all of the data is shown in the Supplementary information.
Full figure and legend (15K)Figures & Tables index

The parameterized transfer function captures the behavior of the circuit when input promoters with different transfer functions are connected to the AND gate (Figure 5). When the model is extrapolated outside of the B9 data used for parameterization, it can be seen that different ranges of I2 lead to different responses. In particular, a stronger rbs (as for the original and F11 clones) extends the upper limit of the range. This leads to a loss of the AND gate function, as now the circuit is inducible independent of I1. Note that for any range of I1, it is possible to generate a functional gate by altering the strength of the rbs of I2. This suggests that it is better that leaky promoters (such as Psal) be used as I1, as this can be compensated for by adjusting the rbs of I2. Here, we have relied on random mutagenesis and screening to identify functional rbss. Our ultimate goal is to use the transfer function and lists of standardized functional rbss (e.g., Registry of Standard Biology Parts entries BBa_J61100-39) to predict the rbs required to make the circuit functional for two input promoters.
Figure 5
Figure 5 : Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com

The activity range of the input promoters affects the function of the AND gate circuit. In top panel, the experimental fluorescence of the B9 and F11 gates is shown as a function of I1 and I2. In the bottom panel, the theoretical transfer function (bottom) is calculated using equation (1) and the fit values for the parameters a and b. The white boxes show the ranges for the wild type as well as the F11 and B9 mutants, which have progressively weaker rbss. These boxes are drawn on the basis of range of the one-dimensional transfer functions (Figure 3). It is only the B9 clone that behaves like an AND gate, requiring the maximal activation of both promoters before the output is turned on. In contrast, the F11 clone always shows some activity at high levels of I2, independent of I1.
Full figure and legend (123K)Figures & Tables index

Circuit modularity

The AND gate is designed to be modular, where the inputs and outputs can be changed by swapping promoters and directing mutagenesis to the rbs. Using this device, any two environmental signals can be connected to the AND gate, as long as they lead to the activation of a promoter. Similarly, the T7 promoter can be used to drive a cellular response or act as the input to another downstream circuit.

To demonstrate the modularity of the circuit, two constructs containing different inputs and outputs were designed and analyzed. First, the inputs are swapped for two natural promoters (quorum sensing and Mg2+ responsive). Next, the output is swapped from gfp to the invasin gene, which enables the bacteria to invade mammalian cells. Both of these circuits demonstrated AND-gate behavior, thus demonstrating the modularity of the circuit and the capability to integrate natural inputs and control cellular behavior as an output.

To replace the inputs, PBAD and Psal were replaced with PmgrB and Plux, which respond to magnesium limitation and the AI-1 quorum signal, respectively (Supplementary Figure S7). Two-component systems are a ubiquitous sensing motif in bacteria, consisting of a membrane-bound sensor and a cytoplasmic response regulator (Hoch and Silhavy, 1995). When stimulated by an environmental signal, the sensor phosphorylates the response regulator, which can then modulate gene expression. The E. coli PhoPQ two-component system responds to the external magnesium concentration. The PhoQ regulator activates the mgrB promoter in the absence of exogenous magnesium (Kato et al, 1999; Minagawa et al, 2003). Quorum sensing systems are used by bacteria to communicate (Bassler and Losick, 2006). These systems have been used extensively as communication devices in synthetic genetic systems to program cells to form patterns (Basu et al, 2005), regulate their density (You et al, 2004), and kill malignant cells in response to bacterial density (Anderson et al, 2006). The lux promoter and luxR gene, derived from the Vibrio fischeri quorum sensing circuit, is induced in response to exogenous N-3-oxohexanoyl-L-homoserine lactone (AI-1) (Sitnikov et al, 1995).

The inputs were connected to the circuit one at a time. First, the mgrB promoter was placed in front of the T7ptag gene with the B9 rbs. The circuit function was then assayed using the salicylate input to drive supD. This construct did not generate an AND-gate as cells showed no fluorescence when induced with salicylate. Presumably, this is because insufficient transcript was produced from PmgrB. As before, this problem was overcome by retuning the rbs. A clone was identified with a stronger rbs (Table I) that yielded a functional AND-gate. Next, Plux and the luxR gene were used to transcribe the supD gene. The circuit shows 15-fold fluorescence over background when fully induced but undetectable fluorescence in the presence of Mg2+ or the absence of AI-1 (Figure 6).
Figure 6
Figure 6 : Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com

The modularity of the AND gate was demonstrated by swapping the inputs and output of the circuit. (A) The inputs of the circuit were exchanged with the lux and mgrB promoters. The lux promoter responds to the quorum signal input AI-1 and the mgrB promoter responds to the absence of exogenous magnesium via the PhoPQ two-component system. Only when both promoters are active (in the presence of AI-1 and under magnesium limitation) is the output on. The white bar shows the background fluorescence of E. coli DH10B cells with no plasmids. The plasmids used to obtain these data are pBACr-Mgr940, pSupDLuxR, and pBR939b (Supplementary information). (B) Replacing the output gfp gene with the inv gene results in the invasion of mammalian cells only when both input promoters are on. The invasiveness of the bacteria is equivalent to the expression of inv from a constitutive promoter (white bar). The stars indicate no invasion being detected. In both panels, the error bars show the standard deviation of four replicates. The plasmids used to obtain these data are pSalSer914 and pBACr-Mgr951 (Supplementary information).
Full figure and legend (145K)Figures & Tables index

We next examined whether the output of the AND gate could control a cellular behavior. The expression of the invasin gene (inv) of Yersinia pseudotuberculosis in E. coli confers the ability to invade mammalian cells expressing beta1-integrin (Isberg et al, 1987). We have previously shown that singular environmentally-responsive promoters controlling inv confer environment-dependent invasion (Anderson et al, 2006). Here, the inv gene is substituted for gfp and the AND gate is tested using the salicylate and Mg2+ inputs.

In a previous study, we created an rbs variant of inv that conferred arabinose-dependent invasion under a PBAD promoter (Anderson et al, 2006). This construct was placed under the control of the T7 promoter and combined with the AND gate plasmids that have PmgrB and Psal as inputs. After being grown in different combinations of the inputs, the bacteria were assayed for invasion of HeLa cells (Materials and methods). Bacteria grown in the presence of Mg2+ or the absence of salicylate show no detectable invasion (Figure 6B). The bacteria only invade when both of the input promoters are on. These experiments demonstrate the ability of a modular AND gate to integrate multiple environmental signals and respond with cellular behavior.
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Discussion

We have constructed a modular AND gate based on the amber suppression of T7 RNA polymerase. Only when two input promoters are active is an output turned on. Because the inputs and outputs of this gate are transcriptional signals, they can be easily replaced. This modularity is demonstrated by swapping the inputs and outputs of the circuit while preserving the AND-gate behavior. In this paradigm, changes in transcription become a common currency allowing the modular integration of individual devices (Weiss et al, 1999; Endy, 2005).

The modular nature of this type of transcriptional logic gate will facilitate its use in a variety of engineering applications. In particular, AND logic would be useful in obtaining gene expression in a specific microenvironment. A set of promoters—identified rationally or with a microarray—could be used as inputs to the AND gate. Rather than directly detecting the presence of a new environment with a single engineered promoter or sensing system, independent promoters sense different aspects of the environment. The AND gate activates only when all conditions are present to induce cellular responses. Often microenvironments are defined by multiple nonspecific signals such as oxygen, pH, cell density, lactate, and glucose. It is only when several of these inputs are integrated that specificity can be achieved.

A two-dimensional transfer function of a simple mathematical form captures the input–output behavior of the AND gate. This model could be used to predict the genetic changes required to connect two inputs to the circuit to produce a functional AND gate. To be able to use the model, the inputs have to be characterized using the plasmid and fluorescent reporter system used in this study. In this sense, this work represents a step toward standardization, where circuits are characterized quantitatively to understand their collective function when connected in series. This will be a critical approach in the design of large integrated systems consisting of multiple genetic circuits.

The transfer function we derived relies on a steady-state assumption and is based on a deterministic model. However, the response of the circuit may have dynamic or stochastic aspects that are not predicted from the model. For some applications where the induction of inputs is transient, the dynamics of the circuit could be critical to the successful implementation of the output process. A further obstacle to standardization is that the circuit may show different response characteristics in different environments or stages of growth. For example, this AND gate produces a lower gain at low cell densities (not shown). This change in the output range could impact its connection to a downstream circuit.

The ultimate goal in genetic circuit design is to incorporate them into more complex systems consisting of multiple circuits, sensors, and actuators. Unlike electronic circuits, where the spatial wiring of a circuit determines the flow of information through the circuit, intracellular circuits prevent cross-communication through specificity of biochemical interactions. Once a part—such as T7 or SupD—is used, it cannot be used in any of the other devices. Therefore, the use of the T7 RNA polymerase-based gate makes this valuable gene unavailable for protein overexpression within the same system. An advantage of our design is that any particular transcriptional activator, including engineered sequence-specific transcription factors (Mandell and Barbas, 2006), could be used in place of the polymerase gene. Similarly, the use of amber suppression precludes its use in other systems. For example, translational recoding with unnatural amino acids using amber suppression could not coexist with this logic gate (Wang et al, 2006). Other translational regulators that could be used in this gate include nonsense, missense, and frameshift suppressors, or riboregulators (Anderson et al, 2002; Isaacs et al, 2004).

Pushing the boundary of genetic engineering will require a toolbox of genetic circuits that perform prescribed functions and are designed to be incorporated into larger systems. Toward this end, we have described the construction and analysis of a genetic AND gate. We have demonstrated that this gate is modular, so that it can be connected to different promoter-based inputs and used to drive different outputs. Further, in a step toward standardization, we developed a model that could be empirically parameterized, and used to predict how new promoters will connect to the gate. Circuits like this will find broad application in genetic engineering of systems in which multiple transcriptional signals must be combined to produce a specific cellular response.
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Materials and methods
Strains and growth conditions

All manipulations were performed in E. coli strain MC1061, DH10B, or EC100D™ pir-116 (Epicentre, Madison, WI) growing in 2YT liquid media or LB agar plates supplemented with antibiotics at 25 mug/ml at 37°C. HeLa cells were obtained from the UCSF Cell Culture Facility (San Francisco, CA) and grown in DMEM media supplemented with 10% FCS and 1% streptomycin/penicillin solution. DNA-modifying enzymes were purchased from New England Biolabs. Oligonucleotides were synthesized by Sigma-Genosys (The Woodlands, TX) and used unpurified. PCR was performed with the Roche High-Fidelity PCR kit. Plasmid pLC113 containing the salicylate promoter was a gift from Sandy Parkinson (Ames et al, 2002). Plasmid pAC-SupD and the double amber mutant of T7 RNA polymerase were described previously (Anderson et al, 2002; Santoro et al, 2002). N-3-oxohexanoyl-L-homoserine lactone, L-arabinose, and sodium salicylate were from Sigma.
Plasmid design

Sequences of the plasmids constructed for this study are available through the Registry of Standard Biological Parts (http://parts.mit.edu). Reporter plasmid pBR939B is a pBR322 derivative containing the pMB1 origin of replication, an ampicillin resistance gene, and a GFPmut3_LAA gene under the control of a T7 promoter and a rrnB terminator. Plasmid pAC-SalSer914 is a pACYC184 derivative containing the p15A origin of replication, a chloramphenicol resistance gene, and the supD gene under the control of a salicylate operon and an rrnB terminator. To construct pAC-SalSer914, the salicylate operon was PCR-amplified from plasmid pLC113 with oligonucleotides ca899F and ca899R and inserted into the NotI and BamHI sites of plasmid pAC581 (Anderson et al, 2006) to obtain plasmid pAC899. Subsequently, the supD gene was PCR-amplified from plasmid pAC-SupD with oligonucleotides ca914F and ca914R and inserted into the BamHI and EcoRI sites of plasmid pAC899. T7 RNA polymerase-expressing plasmids were constructed in plasmid pBAC872s (Anderson et al, 2006) containing the F plasmid origin of replication and par genes, an R6K origin of replication, a kanamycin resistance gene, and a BamHI/EcoRI cassette flanked by an arabinose promoter and a TrrnB terminator. In strain EC100D™ pir-116, the R6K origin confers high copy number. In strain MC1061, pBAC872s derivatives are single-copy plasmids. Arabinose-inducible GFP reporter plasmids pBAC987 and pBAC978 containing the B9 and F11-derived rbss were constructed from plasmid pBAC872s. The GFP cassette present in pBAC872s was PCR-amplified with oligonucleotides ca978F or ca987F and ca606R and inserted into the BamHI and EcoRI sites of pBAC872s. The GFP sequence contains a degradation tag that confers a half-life of 40 min (Miller et al, 2000).

To construct Plasmid pSupDLuxR, a variant of pAC581 (pAC-SupDb) was first constructed with BamHI and EcoRI sites upstream of the supD gene. The entire lux operon was PCR-amplified with oligonucleotides ca742F and ca721R from plasmid pAC-LuxGfp (Anderson et al, 2006) and inserted into the BamHI and EcoRI sites of pAC-SupDb to obtain plasmid pSupDLux. The luxI gene in pSupDLux was then excised by inverse PCR with oligonucleotides ca752F and ca747R and recircularization with BglII to obtain pSupDLuxR.

Plasmid pBACr-Mgr940 was constructed from plasmid pBAC874t, a variant of pBAC872s with a Ptet promoter (Anderson et al, 2006). The mgrB promoter was PCR-amplified from E. coli strain MG1655 genomic DNA with oligonucleotides ca901F and ca901R and inserted into the NotI and BamHI sites of pBAC874t to obtain plasmid pBACr-Mgr901. Subsequently, T7ptag variants were inserted into the BamHI and EcoRI sites of pBACr-Mgr901.

Plasmid pBACr-Mgr951 was constructed from plasmids pBACr-Mgr940 and pBACr-Inv939. Plasmid pBACr-Inv939 is a pBAC874t derivative containing a T7-GFP cassette derived from pBR939b within the NotI and BamHI sites upstream of the BamHI/EcoRI cassette from plasmid pBACr-AraInv (Anderson et al, 2006) containing the rbs and the invasin gene. The T7-GFP-Invasin fragment of pBACr-Inv939 was PCR-amplified with oligonucleotides ca279 and ca951R and inserted into the NotI site of pBACr-Mgr940 to yield plasmid pBACr-Mgr951.
Saturation mutagenesis and library screening

To construct the T7 RNA polymerase rbs library, the T7 RNA polymerase gene with two amber stop codons and a short 5' linker sequence was PCR-amplified with oligonucleotides ca940F and ca564R from plasmid pREP2-HLAA02 (Santoro et al, 2002) and inserted into the BamHI and EcoRI sites of pBAC872s or pBACr-Mgr901 under the control of the arabinose promoter. In this manner, the 5' flanking bases of the rbs and the first base of the start codon were replaced with random sequence. The library of 5'UTR variants was inserted into MC1061 cells harboring pBR939b and pAC-SalSer914 and plated on LB media supplemented with the appropriate antibiotics, 100 mug/ml salicylate and arabinose. Individual green-fluorescing colonies were grown in 500 mul aliquots in a 96-well block in the presence of 100 mug/ml salicylate, 100 mug/ml arabinose, 10 muM N-3-oxohexanoyl-L-homoserine lactone and/or 50 mM MgCl2, or no additive, and then assayed for fluorescence in a Tecan Safire fluorescence plate reader (Tecan). From this screen, individual variants B9, F11, and pBACr-Mgr940 were characterized further. A third variant was sequenced and found to introduce a hairpin occluding the rbs, which may result in aberrant translation (Isaacs et al, 2004). Thus, this variant is not considered further.
Induction experiments

To observe AND gate induction by cytometry, 50 ml cultures of MC1061 cells (salicylate and arabinose gate) or DH10B cells (AHL and no Mg2+ gate) were grown in 2YT media in the presence or absence of inducers and the appropriate antibiotics for 3 h at 37°C to OD600=1 in a baffled flask with aeration. Cytometry analysis was performed with a Becton Dickinson FACSCalibur™ on bacteria diluted in PBS buffer. Counts were gated by side and forward scatter. Data for 30 000 cells were collected for each experiment. Fluorescence was tuned relative to bacteria without a GFP gene centered within the first decade of fluorescence. For fluorimetry measurements, bacteria were grown in 400 mul cultures in 96-well blocks with shaking for 8 h at 37°C to OD600=1. Aliquots of 100 mul each were transferred to 96-well plates and assayed for fluorescence in a Tecan.
Invasion assays

Bacterial cultures were diluted 100-fold in 2YT media, and 50 mul was added to 1 ml of DMEM media in 24-well plates containing a confluent culture of HeLa cells (MOI=5). After 1 h incubation at 37°C, the wells were washed once in DMEM media and then incubated for 1 h with 1 ml of DMEM supplemented with 100 mug/ml gentamicin. Subsequently the wells were washed three times with DMEM, lysed with 1 ml of 1% Triton X-100, and then spread on LB agar plates and grown 24 h. Percent invasion was determined as the ratio of recovered bacteria divided by the number of CFU present in the original diluted culture as determined by titer. Values were averaged over four repetitions of the experiment
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Acknowledgements

We thank Sandy Parkinson for supplying plasmid pLC113. JCA is supported by a Damon Runyon Cancer Research Foundation Postdoctoral Fellowship. APA was supported by the Howard Hughes Medical Institute. CAV was supported by the Sloan Foundation, Pew Fellowship, ONR, Packard Fellowship, NIH EY016546, NIH AI067699, NSF BES-0547637, UC-Discovery, and a Sandler Family Opportunity Award. APA, CAV, and JCA are supported by the SynBERC NSF ERC (www.synberc.org).

The authors declare that they have no competing financial interests.
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Công nghệ sinh học trên người và động vật

Nhà xuất bản GD vừa cho ra mắt quyển" Công nghệ sinh học trên người và động vật" của 2 tác giả.Là Thầy Phan Kim Ngọc và anh Phạm văn Phúc (ĐHKHTN_ĐHQGTPHCM).Mời các bạn quan tâm tìm đọc.(Ảnh bìa sách lấy từ trang vinastemcell.com)
 

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I. Giới thiệu
II. Kĩ thuật chuẩn bị giao tử
III. Kĩ thuật hỗ trợ sự thụ tinh
IV. Cấy truyền phôi
V. Một số kĩ thuật liên quan
Chương 5. Công nghệ tạo dòng vô tính
I. Giới thiệu
II. Một số quá trình sinh học của công nghệ tạo dòng
III. Các kĩ thuật cơ bản trong tạo dòng in vitro
IV. Một số khiếm khuyết ở động vật tạo dòng vô tính
V. Ứng dụng của tạo dòng vô tính động vật
VI. Vấn đề tạo dòng vô tính ở người
Chương 6. Tế bào gốc
I. Giới thiệu
II. Tế bào gốc phôi (embryonic stem cell – ES)
III. Tế bào gốc trưởng thành (aldult stem cell – AS)
Chương 7. Động vật biến đổi gen
I. Giới thiệu
II. Phương pháp biến đổi gen ở động vật
III. Định hướng gen chuyển (gene – targeting)
IV. Ứng dụng động vật biến đổi gen trong y học
V. Sử dụng động vật biến đổi gen cho các mục đích khác
Chương 8. Công nghệ sinh học trong chăn nuôi
I. Giới thiệu
II.Công nghệ sinh học trong chăn nuôi gia súc và gia cầm
III. Công nghệ sinh học trong nuôi trồng thủy sản
IV. Công nghệ sinh học trong chăn nuôi và vấn đề bảo tồn giống vật nuôi
Chương 9. Chẩn đoán phân tử
I. Giới thiệu
II. Một số kĩ thuật chẩn đoán bệnh
III. Ứng dụng các kĩ thuật chẩn đoán
Chương 10. Liệu pháp gen
I. Giới thiệu
II. Vector dùng trong liệu pháp gen
III. Sự tồn tại gen liệu pháp trong tế bào
IV. Nhắm mục tiêu gen (gene targeting)
V. Ứng dụng
Chương 11. Công nghệ sinh học dược phẩm
I. Dược phẩm – Sinh dược phẩm
II. Công nghệ sản xuất sinh dược phẩm
III. Công nghệ thu nhận sản phẩm sinh dược phẩm
IV. Phát triển một sinh dược phẩm mới
V. Một số kĩ thuật mới trong nghiên cứu sinh dược phẩm
VI. Thực phẩm chức năng
Chương 12. Vật liệu Y – Sinh học
I. Giới thiệu
II. Tính chất của vật liệu sinh học
III. Miễn dịch cấy ghép vật liệu sinh học
IV. Một số vật liệu dùng trong y học
V. Vật liệu tự nhiên
VI. Ứng dụng của vật liệu sinh học trong y học
VII. Công nghệ nano và vật liệu sinh học nano
VIII. Khuôn vật liệu cố định tế bào và enzyme
IX. Tương lai vật liệu sinh học
Chương 13. Ngân hàng và thị trường tế bào, mô động vật
I. Ngân hàng
II. Hàng hóa và thị trường
III. Quyền sở hữu trí tuệ về công nghệ sinh học
IV. Công nghệ sinh học với nền kinh tế tri thức
Chương 14. Đạo lí sinh học
I. Khái niệm đạo lí và đạo lí sinh học
II. Sử dụng động vật
III. Đạo lí sinh học trong công nghệ hỗ trợ sinh sản
IV. Lựa chọn và chuyển đổi giới tính
V. Đạo lí trong chẩn đoán phân tử và liệu pháp gen
VI. Tạo dòng vô tính người và động vật
VII. Sử dụng thông tin di truyền và sự lạm dụng
VIII. Tế bào gốc và đạo lí sinh học
IX. Vấn đề động vật biến đổi gen
X. Cái chết tự nguyện và việc hiến xác
XI. Vũ khí sinh học
XII. Công nghệ gen và tuyên ngôn UNESCO
XIII. Đạo lí sinh học và nhà trường
 

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