Periodic stripe patterns are ubiquitous in living organisms, yet the underlying developmental processes are complex and difficult to disentangle. We describe a synthetic genetic circuit that couples cell density and motility. This system enabled programmed Escherichia coli cells to form periodic stripes of high and low cell densities sequentially and autonomously. Theoretical and experimental analyses reveal that the spatial structure arises from a recurrent aggregation process at the front of the continuously expanding cell population. The number of stripes formed could be tuned by modulating the basal expression of a single gene. The results establish motility control as a simple route to establishing recurrent structures without requiring an extrinsic pacemaker.

Two bacterial strains, B-5 T and NO1A, were isolated from the surface water of the Bohai Sea and deep-sea sediment of the east Pacific Ocean, respectively. Both strains were halophilic, aerobic, Gram-negative, non-spore-forming, catalase-and oxidase-positive motile rods. They grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. On the basis of 16S rRNA gene sequence similarity, strains B-5 T and NO1A were shown to belong to the c-Proteobacteria. Highest similarity values were found with Alcanivorax venustensis (95?2 %), Alcanivorax jadensis (94?6 %) and Alcanivorax borkumensis (94?1 %). Principal fatty acids of both strains were C 16 : 0 , C 16 : 1 v7c and C 18 : 1 v7c. The chemotaxonomically characteristic fatty acid C 19 : 0 cyclo v8c was also detected. On the basis of the above, together with results of physiological and biochemical tests, DNA-DNA hybridization, comparisons of 16S-23S internal transcribed spacer sequences and comparisons of the partial deduced amino acid sequence of alkane hydroxylase, both strains were affiliated to the genus Alcanivorax but were differentiated from recognized Alcanivorax species. Therefore, a novel species, Alcanivorax dieselolei sp. nov., represented by strains B-5 T and NO1A is proposed, with the type strain B-5 T (=DSM 16502 T =CGMCC 1.3690 T ).The genus Alcanivorax comprises three recognized species at present. The type species, Alcanivorax borkumensis, was first described in 1998 to accommodate Gram-negative, halophilic, aerobic c-Proteobacteria that use aliphatic hydrocarbons as the sole source of carbon and energy . A second species, Alcanivorax venustensis, was subsequently described and the misclassified species [Fundibacter] jadensis was assigned to Alcanivorax jadensis (Fernández-Martínez et al., 2003). Since 1998, the isolation of Alcanivorax species, or detection of their 16S rRNA gene sequences, from diverse habitats worldwide has been reported increasingly. Thus they are regarded as cosmopolitan bacteria. This group of marine bacteria exclusively uses petroleum oil hydrocarbons as sources of carbon and energy, and has been used for bioremediative interventions in polluted marine and coastal systems. In addition, Alcanivorax species have obvious potential to produce biocatalysts in non-polluting industrial processes and to act as a biosensor for in situ monitoring of aromatic or aliphatic compounds (Golyshin et al., 2003).Strain B-5 T was isolated from oil-contaminated surface water of the Bohai Sea at the Yellow River dock of Shengli oilfield in November 2001; this dock had suffered a long period of crude oil pollution. A second strain, designated NO1A, was retrieved from a deep-sea sediment sample in the east Pacific Ocean. This was collected by a multi-core sampler from Pacific nodule region A station (7 u 139 460 N, 153u 529 190 W, 5027 m water depth), a specific area with polymetallic nodules abundant on the sea bottom, during cruise DY105-11 of DAYANG Number 1 in 2001. The sediment samples were loaded into steri...

Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter's growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed "adder-per-origin" model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.acteria can regulate tightly and coordinate the various events in their cell cycles to accurately duplicate their genomes and to homeostatically regulate their cell sizes. This is a particular challenge under fast growth conditions where cells are undergoing multiple concurrent rounds of DNA replication. Despite much progress, we still have an incomplete understanding of the processes that coordinate DNA replication, cell growth, and cell division. This lack of understanding is manifested, for instance, in discrepancies among various recent studies that propose different models for control of cell division in the bacterium Escherichia coli.One class of models suggests that cell division is triggered by the accumulation of a constant size (e.g., volume, length, or surface area) between birth and division (1-3). Such models are supported by experiments measuring correlations between cell size at birth and cell size at division, which showed that, when averaged over all cells of a given birth size vB , cell size at division vD approximately followswhere the constant v0 sets the average cell size at birth. This is known as the "incremental" or "adder" model, and cells following this behavior are said to exhibit "adder correlations" (1-7). Importantly, these models postulate that cell division is governed by a phenomenological size variable, with no explicit reference to DNA replication. A...

Besides genome editing, CRISPR-Cas12a has recently been used for DNA detection applications with attomolar sensitivity but, to our knowledge, it has not been used for the detection of small molecules. Bacterial allosteric transcription factors (aTFs) have evolved to sense and respond sensitively to a variety of small molecules to benefit bacterial survival. By combining the single-stranded DNA cleavage ability of CRISPR-Cas12a and the competitive binding activities of aTFs for small molecules and double-stranded DNA, here we develop a simple, supersensitive, fast and high-throughput platform for the detection of small molecules, designated CaT-SMelor ( C RISPR-Cas12a- and aT F-mediated s mall m ol e cu l e detect or ). CaT-SMelor is successfully evaluated by detecting nanomolar levels of various small molecules, including uric acid and p -hydroxybenzoic acid among their structurally similar analogues. We also demonstrate that our CaT-SMelor directly measured the uric acid concentration in clinical human blood samples, indicating a great potential of CaT-SMelor in the detection of small molecules.

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Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has recently been established to coordinate activities worldwide.

BackgroundSubstantial efforts have been made to link the gut bacterial community to many complex human diseases. Nevertheless, the gut phages are often neglected.ResultsIn this study, we used multiple bioinformatic methods to catalog gut phages from whole-community metagenomic sequencing data of fecal samples collected from both type II diabetes (T2D) patients (n = 71) and normal Chinese adults (n = 74). The definition of phage operational taxonomic units (pOTUs) and identification of large phage scaffolds (n = 2567, ≥ 10 k) revealed a comprehensive human gut phageome with a substantial number of novel sequences encoding genes that were unrelated to those in known phages. Interestingly, we observed a significant increase in the number of gut phages in the T2D group and, in particular, identified 7 pOTUs specific to T2D. This finding was further validated in an independent dataset of 116 T2D and 109 control samples. Co-occurrence/exclusion analysis of the bacterial genera and pOTUs identified a complex core interaction between bacteria and phages in the human gut ecosystem, suggesting that the significant alterations of the gut phageome cannot be explained simply by co-variation with the altered bacterial hosts.ConclusionsAlterations in the gut bacterial community have been linked to the chronic disease T2D, but the role of gut phages therein is not well understood. This is the first study to identify a T2D-specific gut phageome, indicating the existence of other mechanisms that might govern the gut phageome in T2D patients. These findings suggest the importance of the phageome in T2D risk, which warrants further investigation.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0410-y) contains supplementary material, which is available to authorized users.