Infrastructure development is central to the processes that abate and produce vulnerabilities in cities. Urban actors, especially those with power and authority, perceive and interpret vulnerability ...and decide when and how to adapt. When city managers use infrastructure to reduce urban risk in the complex, interconnected city system, new fragilities are introduced because of inherent system feedbacks. We trace the interactions between system dynamics and decision-making processes over 700 years of Mexico City’s adaptations to water risks, focusing on the decision cycles of public infrastructure providers (in this case, government authorities). We bring together two lenses in examining this history: robustness-vulnerability trade-offs to explain the evolution of systemic risk dynamics mediated by feedback control, and adaptation pathways to focus on the evolution of decision cycles that motivate significant infrastructure investments. Drawing from historical accounts, archeological evidence, and original research on water, engineering, and cultural history, we examine adaptation pathways of humans settlement, water supply, and flood risk. Mexico City’s history reveals insights that expand the theory of coupled infrastructure and lessons salient to contemporary urban risk management: (1) adapting by spatially externalizing risks can backfire: as cities expand, such risks become endogenous; (2) over time, adaptation pathways initiated to address specific risks may begin to intersect, creating complex trade-offs in risk management; and (3) city authorities are agents of risk production: even in the face of new exogenous risks (climate change), acknowledging and managing risks produced endogenously may prove more adaptive. History demonstrates that the very best solutions today may present critical challenges for tomorrow, and that collectively people have far more agency in and influence over the complex systems we live in than is often acknowledged.
A large outbreak of diarrhea and the hemolytic-uremic syndrome caused by an unusual serotype of Shiga-toxin-producing Escherichia coli (O104:H4) began in Germany in May 2011. As of July 22, a large ...number of cases of diarrhea caused by Shiga-toxin-producing E. coli have been reported--3167 without the hemolytic-uremic syndrome (16 deaths) and 908 with the hemolytic-uremic syndrome (34 deaths)--indicating that this strain is notably more virulent than most of the Shiga-toxin-producing E. coli strains. Preliminary genetic characterization of the outbreak strain suggested that, unlike most of these strains, it should be classified within the enteroaggregative pathotype of E. coli.
We used third-generation, single-molecule, real-time DNA sequencing to determine the complete genome sequence of the German outbreak strain, as well as the genome sequences of seven diarrhea-associated enteroaggregative E. coli serotype O104:H4 strains from Africa and four enteroaggregative E. coli reference strains belonging to other serotypes. Genomewide comparisons were performed with the use of these enteroaggregative E. coli genomes, as well as those of 40 previously sequenced E. coli isolates.
The enteroaggregative E. coli O104:H4 strains are closely related and form a distinct clade among E. coli and enteroaggregative E. coli strains. However, the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors.
Our findings suggest that horizontal genetic exchange allowed for the emergence of the highly virulent Shiga-toxin-producing enteroaggregative E. coli O104:H4 strain that caused the German outbreak. More broadly, these findings highlight the way in which the plasticity of bacterial genomes facilitates the emergence of new pathogens.
Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in ...industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this "core genome" confirmed the diverse history of the ETEC pathovar and provides a finer resolution of the E. coli relationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETEC E. coli genomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.
Background. Enteroaggregative Escherichia coli (EAEC) is a cause of epidemic and sporadic diarrhea, yet its role as an enteric pathogen is not fully understood. Methods. We characterized 121 EAEC ...strains isolated in 2008 as part of a case-control study of moderate to severe acute diarrhea among children 0-59 months of age in Bamako, Mali. We applied multiplex polymerase chain reaction and comparative genome hybridization to identify potential virulence factors among the EAEC strains, coupled with classification and regression tree modeling to reveal combinations of factors most strongly associated with illness. Results. The gene encoding the autotransporter protease SepA, originally described in Shigella species, was most strongly associated with diarrhea among the EAEC strains tested (odds ratio, 5.6 95% confidence interval, 1.92-16.17; P = .0006). In addition, we identified 3 gene combinations correlated with diarrhea: (1) a clonal group positive for sepA and a putative hemolysin; (2) a group harboring the EAST-1 enterotoxin and the flagellar type H33 but no other previously identified EAEC virulence factor; and (3) a group carrying several of the typical EAEC virulence genes. Conclusion. Our data suggest that only a subset of EAEC strains are pathogenic in Mali and suggest that sepA may serve as a valuable marker for the most virulent isolates.
Summary
We describe the development of a high‐density Arabidopsis‘whole genome’ oligonucleotide probe array for expression analysis (the Affymetrix ATH1 GeneChip® probe array) that contains ...approximately 22 750 probe sets. Precedence on the array was given to genes for which either expression evidence or a credible database match existed. The remaining space was filled with ‘hypothetical’ genes. The new ATH1 array represents approximately 23 750 genes of which 60% were detected in RNA from cultured seedlings. Sensitivity of the array, determined using spiking controls, was approximately one transcript per cell. The array demonstrated high technical reproducibility and concordance with real‐time PCR results. Indole‐3 acetic acid (IAA)‐induced changes in gene expression were used for biological validation of the array. A total of 222 genes were significantly upregulated and 103 significantly downregulated by exposure to IAA. Of the genes whose products could be functionally classified, the largest specific classes of upregulated genes were transcriptional regulators and protein kinases, many fewer of which were represented among the downregulated genes. Over one‐third of the auxin‐regulated genes have no known function, although many belong to gene families with members that have previously been shown to be auxin regulated. For the 6714 genes represented both on this and the earlier Arabidopsis Genome (AG) array, both signal intensities and gene expression ratios were very similar. Mapping of the oligonucleotides on the ATH1 array to the latest (version 4.0) annotation showed that over 95% of the probe sets (based on version 2.0 annotation) still fully represented their original target genes.
Summary
Shigella flexneri is a Gram‐negative pathogen that invades the colonic epithelium. While invasion has been thoroughly investigated, it is unknown how Shigella first attaches to the ...epithelium. Previous literature suggests that Shigella utilizes adhesins that are induced by environmental signals, including bile salts, encountered in the small intestine prior to invasion. We hypothesized that bile would induce adherence factors to facilitate attachment to colonic epithelial cells. To test our hypothesis, S. flexneri strain 2457T was subcultured in media containing bile salts, and the ability of the bacteria to adhere to the apical surface of polarized T84 epithelial cells was measured. We observed a significant increase in adherence, which was absent in a virulence plasmid‐cured strain and a type‐III secretion system mutant. Microarray expression analysis indicated that the ospE1/ospE2 genes were induced in the presence of bile, and bile‐induced adherence was lost in a ΔospE1/ΔospE2 mutant. Further studies demonstrated that the OspE1/OspE2 proteins were localized to the bacterial outer membrane following exposure to bile salts. The data presented are the first demonstration that the OspE1/OspE2 proteins promote initial adherence to the intestinal epithelium. The adhesins required for Shigella attachment to the colonic epithelium may serve as ideal targets for vaccine development.
Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced ...for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs), which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants.
We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes.
High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula.
We report the draft genome sequences of the collection referred to as the Escherichia coli DECA collection, which was assembled to contain representative isolates of the 15 most common diarrheagenic ...clones in humans (http://shigatox.net/new/). These genomes represent a valuable resource to the community of researchers who examine these enteric pathogens.
Summary
We have developed two long‐oligonucleotide microarrays for the analysis of genome features in Arabidopsis thaliana, in particular for the high‐throughput identification of transcription ...factor‐binding sites. The first platform contains 190 000 probes representing the 2‐kb regions upstream of all annotated genes at a density of seven probes per promoter. The second platform is divided into three chips, each of over 390 000 features, and represents the entire Arabidopsis genome at a density of one probe per 90 bases.
Protein–DNA complexes resulting from the formaldehyde fixation of leaves of plants 2 h after exposure to 1 mm salicylic acid (SA) were immunoprecipitated using antibodies against the TGA2 transcription factor. After reversal of the cross‐links and amplification, the resulting ChIP sample was hybridized to both platforms. High signal ratios of the ChIP sample versus raw chromatin for clusters of neighboring probes provided evidence for 51 putative binding sites for TGA2, including the only previously confirmed site in the promoter of PR‐1 (At2g14610). Enrichment of several regions was confirmed by quantitative real‐time PCR. Motif search revealed that the palindromic octamer TGACGTCA was found in 55% of the enriched regions. Interestingly, 15 of the putative binding sites for TGA2 lie outside the presumptive promoter regions. The effect of the 2‐h SA treatment on gene expression was measured using Affymetrix ATH1 arrays, and SA‐induced genes were found to be significantly over‐represented among genes neighboring putative TGA2‐binding sites.
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