Complex Function by Design Using Spatially Pre-Structured Synthetic Microbial Communities: Degradation of Pentachlorophenol in the Presence of Hg(II)

Naturally occurring microbes perform a variety of useful functions, with more complex processes requiring multiple functions performed by communities of multiple microbes. Synthetic biology via genetic engineering may be used to achieve desired multiple functions, e.g. multistep chemical and biological transformations, by adding genes to a single organism, but this is sometimes not possible due to incompatible metabolic requirements or not desirable in certain applications, especially in medical or environmental applications. Achieving multiple functions by mixing microbes that have not evolved to function together may not work due to competition of microbes, or lack of interactions among microbes. In nature, microbial communities are commonly spatially structured. Here, we tested whether spatial structure can be used to create a community of microbes that can perform a function they do not perform individually or when simply mixed. We constructed a core–shell fiber with Sphingobium chlorophenolicum, a pentachlorophenol (PCP) degrader, in the core layer and Ralstonia metallidurans, a mercuric ion (Hg(II)) reducer, in the shell layer as a structured community using microfluidic laminar flow techniques. We applied a mixture of PCP and Hg(II) to either a simple well-mixed culture broth (i.e. the unstructured community) or the spatially structured core–shell fibers. We found that without spatial structure, the community was unable to degrade PCP in the presence of Hg(II) because S. chlorophenolicum is sensitive to Hg(II). In contrast, with spatial structure in a core–shell fiber system, S. chlorophenolicum in a core layer was protected by R. metallidurans deposited in a shell layer, and the community was able to completely remove both PCP and Hg(II) from a mixture. The appropriate size of the core–shell fiber was determined by the Damköhler number—the timescale of removal of Hg(II) was on the same order of the timescale of diffusion of Hg(II) through the outer layer when the shell layer was on the order of B200 mm. Ultimately, with the ease of a child putting together ‘Legos’ to build a complex structure, using this approach one may be able to put together microorganisms to build communities that perform functions in vitro or even in vivo, e.g. as in a ‘‘microbiome on a pill’’

Cultural Practices to Reduce Cd Content in Edible Parts of Staple Crops in Korea

Objectives of this study were to determine the uptake and translocation of Cd in rice plant from soil with applying the water management and soil ameliorators and to investigate the correlations among heavy metal contents in the brown rice, soil pH and chemical species of Cd existing in soil by sequential extracting method with paddy soil contaminated with Cd near abandoned mine. To identify the effect of soil ameliorators on Cd uptake in rice plants, compost and lime were treated. Plants were grown with irrigation water concentrated by 0.01mg kg^ of cadmium in two soil types (sandy loam and clay loam) with treatments of intermittent irrigation and continuous submersion conditions. Compared to intermittent irrigation plots, average Eh value in the continuous submersion plots was low at 136.7mV whereas pH value was high at 0.3. Eh value was decreased in the treatment of soil ameliorator while pH value was increased by 0.2～0.3. Cd content of leaves and brown rice had significantly positive correlation with Eh value in soils while was negatively correlated with soil pH. At the harvest stage, Cd content in the leaves and brown rice was decreased in the continuous submersion plots by 30% relative to the intermittent irrigation plots. In case of soil ameliorator applied plots, Cd content of leaves and brown rice was lower by 35% than that of N, P, K fertilizer plots, respectively. Compared to the soil types, Cd content of leaves and brown rice in sandy loam soil was lower by 64 and 37% than that in clay loam soil, respectively. Order of reduction to Cd uptake was the compost and lime mixture plot>silicate plot>lime plot. However, the effect of Cd uptake reduction by soil ameliorator was decreased in the N, P, K+compost and N, P, K+phosphate plots. Cd uptake reduction by water management and soil ameliorator was more effective in the sandy loam soil than that in the clay loam soil.Special Revie

Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement

This paper illustrates a plug-based microfluidic approach combining the technique of the chemistrode and the principle of stochastic confinement, which can be used to i) starting from a mixture of cells, stochastically isolate single cells into plugs, ii) incubate the plugs to grow clones of the individual cells without competition among different clones, iii) split the plugs into arrays of identical daughter plugs, where each plug contained clones of the original cell, and iv) analyze each array by an independent technique, including cellulase assays, cultivation, cryo-preservation, Gram staining, and Fluorescence In Situ Hybridization (FISH). Functionally, this approach is equivalent to simultaneously assaying the clonal daughter cells by multiple killing and non-killing methods. A new protocol for single-cell FISH, a killing method, was developed to identify isolated cells of Paenibacillus curdlanolyticus in one array of daughter plugs using a 16S rRNA probe, Pc196. At the same time, live copies of P. curdlanolyticus in another array were obtained for cultivation. Among technical advances, this paper reports a chemistrode that enables sampling of nanoliter volumes directly from environmental specimens, such as soil slurries. In addition, a method for analyzing plugs is described: an array of droplets is deposited on the surface, and individual plugs are injected into the droplets of the surface array to induce a reaction and enable microscopy without distortions associated with curvature of plugs. The overall approach is attractive for identifying rare, slow growing microorganisms and would complement current methods to cultivate unculturable microbes from environmental samples

Signet Ring Cell Carcinoma Arising from a Solitary Juvenile Polyp in the Colon

Juvenile polyps are relatively common polyps that affect predominantly young patients and may occur in isolated, multiple, and/or familial forms. They have been considered to be benign lesions without neoplastic potential, but for patients with multiple juvenile polyposis, the cumulative malignant risk is greater than fifty percents. In patients with a solitary polyp, the risks are minimal, and only a few cases of malignant change from a solitary juvenile polyp have been reported. We describe the case of a twenty one year old female with one solitary juvenile polyp, which contained a signet ring cell carcinoma in the mucosal layer

Nano/Microâ Structured Si/C Anodes with High Initial Coulombic Efficiency in Liâ Ion Batteries

One of the major challenges for designing highâ capacity anode materials is to combine both Coulombic efficiency and cycling stability. Herein, nano/microâ structured Si/C composites are designed and synthesized to address this challenge by decreasing the specific surface area and improving the tap density of Si/C materials. An ultrahigh initial Coulombic efficiency of 91.2â % could be achieved due to a proper particle size, low specific surface area, and optimized structure. The nano/microâ structured Si/C anodes exhibit excellent cycling stability with 96.5â % capacity retention after 100 cycles under a current density of 0.2â Aâ gâ 1.An ode to excellence: Nano/microâ structured Si/C materials were designed and synthesized on a large scale. The asâ obtained Si/C anodes exhibit excellent electrochemical properties in terms of specific capacity, Coulombic efficiency, and cycling stability.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137602/1/asia201600067-sup-0001-misc_information.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137602/2/asia201600067.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137602/3/asia201600067_am.pd

Analysis of reports on orphan lung diseases in Korean children

PurposeOrphan lung diseases are defined as lung diseases with a prevalence of 1 or less in 2,000 individuals. Despite an increase in the numbers of patients with such diseases, few studies on Korean children have appeared. To obtain epidemiologic and demographic data on these diseases, we systematically reviewed reports on pediatric orphan lung diseases in Korea over the last 50 years.MethodsWe reviewed 223 articles that have appeared since 1958 on orphan lung diseases in Korean children. These articles described a total of 519 patients aged between 0 and 18 years. We classified patients by year of publication, diagnosis, geographic region, and journal.ResultsOf 519 patients, 401 had congenital cystic lung diseases and 66 had bronchiolitis obliterans. About 80% of patients were described in reports published in three journals, Pediatric Allergy and Respiratory Disease (Korea), the Korean Journal of Pediatrics, and the Korean Journal of Thoracic and Cardiovascular Surgery, in which papers on 157 (30.2%), 138 (26.6%), and 111 (21.4%) patients appeared, respectively. The frequency of publication of case reports has increased since 1990. Of the 519 patients, 401 (77.3%) were from Seoul/Gyeonggi-do and 72 (13.9%) from Busan/Gyeongsangnam-do.ConclusionThe prevalence of pediatric orphan lung disease has increased since 1990, and some provinces of Korea have a higher incidence of these diseases than do others. Studies exploring the incidence of pediatric orphan lung diseases in Korea are needed for effective disease management