Showing papers by "James J. Collins published in 2009"

Synthetic gene networks that count.

Abstract: Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy.

Abstract: Antimicrobial drug development is increasingly lagging behind the evolution of antibiotic resistance, and as a result, there is a pressing need for new antibacterial therapies that can be readily designed and implemented. In this work, we engineered bacteriophage to overexpress proteins and attack gene networks that are not directly targeted by antibiotics. We show that suppressing the SOS network in Escherichia coli with engineered bacteriophage enhances killing by quinolones by several orders of magnitude in vitro and significantly increases survival of infected mice in vivo. In addition, we demonstrate that engineered bacteriophage can enhance the killing of antibiotic-resistant bacteria, persister cells, and biofilm cells, reduce the number of antibiotic-resistant bacteria that arise from an antibiotic-treated population, and act as a strong adjuvant for other bactericidal antibiotics (e.g., aminoglycosides and β-lactams). Furthermore, we show that engineering bacteriophage to target non-SOS gene networks and to overexpress multiple factors also can produce effective antibiotic adjuvants. This work establishes a synthetic biology platform for the rapid translation and integration of identified targets into effective antibiotic adjuvants.

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

Abstract: Engineering artificial gene networks from modular components is a major goal of synthetic biology. However, the construction of gene networks with predictable functions remains hampered by a lack of suitable components and the fact that assembled networks often require extensive, iterative retrofitting to work as intended. Here we present an approach that couples libraries of diversified components (synthesized with randomized nonessential sequence) with in silico modeling to guide predictable gene network construction without the need for post hoc tweaking. We demonstrate our approach in Saccharomyces cerevisiae by synthesizing regulatory promoter libraries and using them to construct feed-forward loop networks with different predicted input-output characteristics. We then expand our method to produce a synthetic gene network acting as a predictable timer, modifiable by component choice. We use this network to control the timing of yeast sedimentation, illustrating how the plug-and-play nature of our design can be readily applied to biotechnology.

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium.

Abstract: We have shown that smoking impacts bronchial airway gene expression and that heterogeneity in this response associates with smoking-related disease risk. In this study, we sought to determine whether microRNAs (miRNAs) play a role in regulating the airway gene expression response to smoking. We examined whole-genome miRNA and mRNA expression in bronchial airway epithelium from current and never smokers (n = 20) and found 28 miRNAs to be differentially expressed (P < 0.05) with the majority being down-regulated in smokers. We further identified a number of mRNAs whose expression level is highly inversely correlated with miRNA expression in vivo. Many of these mRNAs contain potential binding sites for the differentially expressed miRNAs in their 3'-untranslated region (UTR) and are themselves affected by smoking. We found that either increasing or decreasing the levels of mir-218 (a miRNA that is strongly affected by smoking) in both primary bronchial epithelial cells and H1299 cells was sufficient to cause a corresponding decrease or increase in the expression of predicted mir-218 mRNA targets, respectively. Further, mir-218 expression is reduced in primary bronchial epithelium exposed to cigarette smoke condensate (CSC), and alteration of mir-218 levels in these cells diminishes the induction of the predicted mir-218 target MAFG in response to CSC. These data indicate that mir-218 levels modulate the airway epithelial gene expression response to cigarette smoke and support a role for miRNAs in regulating host response to environmental toxins.

Next-generation synthetic gene networks

Abstract: Synthetic biology is focused on the rational construction of biological systems based on engineering principles. During the field's first decade of development, significant progress has been made in designing biological parts and assembling them into genetic circuits to achieve basic functionalities. These circuits have been used to construct proof-of-principle systems with promising results in industrial and medical applications. However, advances in synthetic biology have been limited by a lack of interoperable parts, techniques for dynamically probing biological systems and frameworks for the reliable construction and operation of complex, higher-order networks. As these challenges are addressed, synthetic biologists will be able to construct useful next-generation synthetic gene networks with real-world applications in medicine, biotechnology, bioremediation and bioenergy.

Social Reproduction in Classrooms and Schools

Abstract: Social reproduction theory argues that schools are not institutions of equal opportunity but mechanisms for perpetuating social inequalities. This review discusses the emergence and development of social reproduction analyses of education and examines three main perspectives on reproduction: economic, cultural, and linguistic. Reproduction analyses emerged in the 1960s and were largely abandoned by the 1990s; some of the conceptual and political reasons for this turning away are addressed. New approaches stress concepts such as agency, identity, person, and voice over the structural constraints of political economy or code, but results have been mixed. Despite theoretical and methodological advances—including new approaches to multilevel analysis and alertness to temporal processes—the difficult problem remains to understand how social inequality results from the interplay of classrooms, schools, and the wider society.

A network biology approach to aging in yeast

Abstract: In this study, a reverse-engineering strategy was used to infer and analyze the structure and function of an aging and glucose repressed gene regulatory network in the budding yeast Saccharomyces cerevisiae. The method uses transcriptional perturbations to model the functional interactions between genes as a system of first-order ordinary differential equations. The resulting network model correctly identified the known interactions of key regulators in a 10-gene network from the Snf1 signaling pathway, which is required for expression of glucose-repressed genes upon calorie restriction. The majority of interactions predicted by the network model were confirmed using promoter-reporter gene fusions in gene-deletion mutants and chromatin immunoprecipitation experiments, revealing a more complex network architecture than previously appreciated. The reverse-engineered network model also predicted an unexpected role for transcriptional regulation of the SNF1 gene by hexose kinase enzyme/transcriptional repressor Hxk2, Mediator subunit Med8, and transcriptional repressor Mig1. These interactions were validated experimentally and used to design new experiments demonstrating Snf1 and its transcriptional regulators Hxk2 and Mig1 as modulators of chronological lifespan. This work demonstrates the value of using network inference methods to identify and characterize the regulators of complex phenotypes, such as aging.

Globalization and language in contact : scale, migration, and communicative practices

Abstract: Space, scale and accents: constructing migrant identity in Beijing / J.K. Dong & J. Blommaert -- Goffman and globalisation: frame, footing and scale in migration-connected multilingualism / J. Collins & S. Slembrouck -- The spaces of language: the everyday practices of Somali refugee and asylum seeker young people / G. Valentine, D. Sporton & K. Bang Nielsen -- Immigration in Catalonia: marking territory through language / J. Pujolar -- Either and both the changing concept of living space among Polish post-communist migrants to the United Kingdom / A. Galasinska & O. Kozlowska -- Canada meets France: recasting identities of Canadianess and Francit through global economic exchanges / G. Budach -- Changing participation in changing practice: uses of language and literacy among Portuguese migrant women in the UK. / C. Keating -- A relational understanding of language practice: interacting time-spaces in a single ethnographic site / C. B. Vigouroux -- Transnational flows, networks and transcultural capital: reflections on researching migrant networks through linguistic ethnography / U. H. Meinhof -- Just one day like today: the notion of scale and the analysis of space time orientation in narratives of displacement / M. Baynham -- Weighing the scales: recontextualisation as horizontal scaling / C. Kell -- From space to spatialization in narrative studies / A. De Fina.

Mortality rates among workers exposed to dioxins in the manufacture of pentachlorophenol

Abstract: OBJECTIVE: We sought to determine if workers exposed to dioxins in pentachlorophenol (PCP) manufacturing were at increased risk of death from specific causes. METHODS: We examined death rates among 773 workers exposed to chlorinated dioxins during PCP manufacturing from 1937 to 1980 using serum dioxin evaluations to estimate exposures to five dioxins. RESULTS: Deaths from all causes combined, all cancers combined, lung cancer, diabetes, and ischemic heart disease were near expected levels. There were eight deaths from non-Hodgkin lymphoma (standardized mortality ratios = 2.4, 95% CI = 1.0 to 4.8). We observed no trend of increasing risk for any cause of death with increasing dioxin exposure. However, the highest rates of non-Hodgkin lymphoma were found in the highest exposure group (standardized mortality ratios = 4.5, 95% CI = 1.2 to 11.5). CONCLUSIONS: Other than possibly an increased risk of non-Hodgkin lymphoma, we find no other cause of death related to the mixture of the dioxin contaminants found in PCP.

Modular nucleic acid-based circuits for counters, binary operations, memory, and logic

Abstract: We have created novel engineered genetic counter designs and methods of use thereof that utilize DNA recombinases to provide modular systems, termed single invertase memory modules (SIMMs), for encoding memory in cells and cellular systems. Our designs are easily extended to compute to high numbers, by utilizing the >100 known recombinases to create subsequent modules. Flexibility in our engineered genetic counter designs is provided by daisy-chaining individual modular components, i.e., SIMMs together. These modular components of the engineered genetic counters can be combined in other network topologies to create circuits that perform, amongst other things, logic and memory. Our novel engineered genetic counter designs allow for the maintenance of memory and provide the ability to count between discrete states by expressing the recombinases between their cognate recognition sites.

Mortality in employees at a New Zealand agrochemical manufacturing site.

Abstract: Background Previous studies at the Dow AgroSciences (Formerly Ivon Watkins-Dow) plant in New Plymouth, New Zealand, had raised concerns about the cancer risk in a subset of workers at the site with potential exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin. As the plant had been involved in the synthesis and formulation of a wide range of agrochemicals and their feedstocks, we examined the mortality risk for all workers at the site. Aims To quantify the mortality hazards arising from employment at the Dow AgroSciences agrochemical production site in New Plymouth, New Zealand. Methods Workers employed between 1 January 1969 and 1 October 2003 were followed up to the end of 2004. Standardized mortality ratios (SMRs) were calculated using national mortality rates by employment duration, sex, period of hire and latency. Results A total of 1754 employees were followed during the study period and 247 deaths were observed. The all causes and all cancers SMRs were 0.97 (95% CI 0.85–1.10) and 1.01 (95% CI 0.80–1.27), respectively. Mortality due to all causes was higher for short-term workers (SMR 1.23, 95% CI 0.91–1.62) than long-term workers (SMR 0.92, 95% CI 0.80–1.06) and women had lower death rates than men. Analyses by latency and period of hire did not show any patterns consistent with an adverse impact of occupational exposures. Conclusions The mortality experience of workers at the site was similar to the rest of New Zealand.

Engineered bacteriophages as adjuvants for antimicrobial agents and compositions and methods of use thereof

Abstract: The present invention relates to the treatment and prevention of bacteria and bacterial infections. In particular, the present invention relates to engineered bacteriophages used in combination with antimicrobial agents to potentiate the antimicrobial effect and bacterial killing by the antimicrobial agent. The present invention generally relates to methods and compositions comprising engineered bacteriophages and antimicrobial agents for the treatment of bacteria, and more particularly to bacteriophages comprising agents that inhibit antibiotic resistance genes and/or cell survival genes, and/or bacteriophages comprising repressors of SOS response genes or inhibitors of antimicrobial defense genes and/or expressing an agent which increases the sensitivity of bacteria to an antimicrobial agent in combination with at least one antimicrobial agent, and their use thereof.

Weight-of-the-evidence review of acrylonitrile reproductive and developmental toxicity studies.

Abstract: Risk assessment of acrylonitrile (AN) toxicity to humans has focused on potential carcinogenicity and acute toxicity. Epidemiological studies from China reported reproductive and developmental effects in AN workers, including infertility, birth defects, and spontaneous abortions. A weight-of-the-evidence (WoE) evaluation of the AN database assessed study strength, characterized toxicity, and identified no-observed-adverse-effect levels (NOAELs). The epidemiological studies do not demonstrate causality and are not sufficiently robust to be used for risk assessment. Rodent developmental studies showed fetotoxicity and malformations at maternally toxic levels; there was no unique developmental susceptibility. NOAELs for oral and inhalation exposures were 10 mg/kg/day and 12 ppm (6 h/day), respectively. Drinking-water and inhalation reproductive toxicity studies showed no clear effects on reproductive performance or fertility. Maternally toxic concentrations caused decreased pup growth. The drinking-water reproductive NOAEL was 100 ppm (moderate confidence due to study limitations). The inhalation exposure reproductive and neonatal toxicity high confidence NOAEL was 45 ppm (first generation 90 ppm) (6 h/day). The inhalation reproductive toxicity study provides the most robust data for risk assessment. Based on the WoE evaluation, AN is not expected to be a developmental or reproductive toxicant in the absence of significant maternal toxicity.

A network biology approach for identifying targets for combination therapies

Abstract: Described herein is a network biology approach useful for the identification of multiple therapeutic targets, which can be targeted simultaneously using an agent (or a plurality of agents) to modulate cellular phenotypes, or in combination with pharmaceutical compounds to improve drug sensitivity and/or reduce drug doses to maintain efficacy while minimizing side effects. The preferred approach disclosed herein relies on first identifying the mediators of a condition of interest, and second, selecting gene combinations that are in competing/parallel pathways as targets for combination therapy.

In vivo gene sensors

Abstract: Described are methods and compositions for the detection of target genes. The inventors have developed a synthetic nucleic acid sensor-effector gene circuit. In cells without a target gene, the circuit suppresses e.g., effector production, but in the presence of the target gene the suppression is subject to competition, such that the synthetic sensor is de-repressed and permits expression of the effector gene. The methods and compositions described further permit the selective expression of an effector gene in those cells expressing the target gene. In this manner, cells expressing a target gene can be selectively targeted for treatment or elimination. In certain aspects, the methods and compositions described permit the selective expression of an agent such as a therapeutic gene product, in a specifically targeted population of cells in an organism.

Mortality among chemical workers at Texas City plant: 1940-2001.

Abstract: To evaluate the mortality experience of workers at a major chemical manufacturing site and to examine brain and liver cancers excesses reported at this site in previous studies. This study included 9,730 employees at the Texas City location who worked between 1940 and 2001. Standardized mortality ratios and confidence intervals were calculated. There was less than expected deaths due to all cause mortality and no increase in all cancer mortality. Brain tumor mortality, which did exceed expected rates in past years, was at expected levels in recent years. Liver cancer mortality was greater than expected. Brain tumor mortality was either due to chance in the early years or the cause of the brain tumors has been eliminated. Mortality due to liver cancer is higher than expected but only among men hired before 1950.

Journal club. A bioengineer gets schooled by Escherichia coli.

Abstract: The ability to learn from situations and to predict certain outcomes sets us apart from many living things. It prevents many of us from chasing balls into busy streets or placing bottles of ethanol near Bunsen burners. Still, it didn’t stop thousands of US researchers submitting applications for the National Institutes of Health’s Challenge Grants — funded by President Barack Obama’s economic stimulus package — despite an expected success rate little better than one or two per cent. To enjoy the benefits of learning and predictive behaviour, we usually assume that you need a nervous system or at least a neuron. So it was surprising to read that Saeed Tavazoie at Princeton University, New Jersey, and his colleagues have demonstrated that bacteria can learn and exhibit anticipatory behaviour (I. Tagkopoulos et al. Science 320, 1313–1317; 2008). They show computationally and experimentally that Escherichia coli can learn temporal correlations between environmental stimuli — for example, that an increase in temperature is followed by a decrease in oxygen levels — allowing the bacteria to predict and prepare for future environmental changes. The researchers show that this associative learning is accomplished by rewiring of biochemical networks. Strikingly, they also show that, like many of us, E. coli quickly ‘unlearn’ (in fewer than 100 generations) what they had learned in a new situation. Now we know that bacteria can be taught such tricks, it will be interesting to see if we can use novel combinations of environmental stimuli to train microbes to efficiently convert biomass into energy sources, such as hydrogen or butanol. By providing E. coli with such an educational stimulus package, we may be able to boost the global economy. GEOLOGY

Systems biology promises to personalize medicine via network-based biomarkers that predict therapeutic effectiveness. Toward this goal, Chang et al. (2009) recently introduced a systems-based approach to break down oncogenic signaling networks into modules that predict the effectiveness of pathway-specific therapeutics.

Abstract: proteins and are often perturbed in cancer. These networks consist of proteins that modulate the activity of downstream targets through mechanisms such as phosphorylation. Commonly, signaling cascades are conceptualized as linear chains of events. In reality, these pathways are branched with proteins influencing multiple downstream targets and are extremely complex due to a high degree of overlap and crosstalk among pathways. This complexity is critical in defining cancer phenotypes but extremely hard to dissect and analyze. To address this challenge, Chang and colleagues devised a method to dissect signal transduction pathways into individual signaling modules, based on gene expression profiles. The authors first identified a set of genes likely impacted by alterations to a given signaling pathway. These genes were selected using a protein-protein interaction network or gene expression data from experiments in which the pathway of interest was active. Factor analysis was then used in conjunction with a compendium of cancer data (NCI-60) to decompose expression profiles of these genes into a number of underlying signatures, which were taken to represent individual signaling modules in the pathway. Each signature was defined by a set of weighted genes, and the expression levels of these genes were weighted and averaged to create a signature score. These scores were hypothesized to represent the activity of the individual signaling modules. Factor analysis is a statistical technique used to uncover hidden variables within complex data sets, and it has been previously used to study biomolecular