The trabecular pattern of bone in radiographs

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Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase

We performed the first field-scale atrazine remediation study in the United States using chemically killed, recombinant organisms. This field study compared biostimulation methods for enhancing atrazine degradation with a novel bioaugmentation protocol using a killed and stabilized whole-cell suspension of recombinant Escherichia coli engineered to overproduce atrazine chlorohyrolase, AtzA. AtzA dechlorinates atrazine, producing non-toxic and non-phytotoxic hydroxyatrazine. Soil contaminated by an accidental spill of atrazine (up to 29 000 p.p.m.) supported significant populations of indigenous microorganisms capable of atrazine catabolism. Laboratory experiments indicated that supplementing soil with carbon inhibited atrazine biodegradation, but inorganic phosphate stimulated atrazine biodegradation. A subsequent field-scale study consisting of nine (0.75m3) treatment plots was designed to test four treatment protocols in triplicate. Control plots contained moistened soil; biostimulation plots received 300 p.p.m. phosphate; bioaugmentation plots received 0.5% (w/w) killed, recombinant E. coli cells encapsulating AtzA; and combination plots received phosphate plus the enzyme-containing cells. After 8 weeks, atrazine levels declined 52% in plots containing killed recombinant E. coli cells, and 77% in combination plots. In contrast, atrazine levels in control and biostimulation plots did not decline significantly. These data indicate that genetically engineered bacteria overexpressing catabolic genes significantly increased degradation in this soil heavily contaminated with atrazine

Minimal resonances in annular non-Euclidean strips

Differential growth processes play a prominent role in shaping leaves and biological tissues. Using both analytical and numerical calculations, we consider the shapes of closed, elastic strips which have been subjected to an inhomogeneous pattern of swelling. The stretching and bending energies of a closed strip are frustrated by compatibility constraints between the curvatures and metric of the strip. To analyze this frustration, we study the class of "conical" closed strips with a prescribed metric tensor on their center line. The resulting strip shapes can be classified according to their number of wrinkles and the prescribed pattern of swelling. We use this class of strips as a variational ansatz to obtain the minimal energy shapes of closed strips and find excellent agreement with the results of a numerical bead-spring model. Within this class of strips, we derive a condition under which a strip can have vanishing mean curvature along the center line.Comment: 14 pages, 13 figures. Published version. Updated references and added 2 figure

Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation

BACKGROUND: Clostridium difficile is an opportunistic human intestinal pathogen, and C. difficile infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, particularly recurrent form of CDI, is through transplantation of fecal microbiota from a healthy donor to the infected patient. In this study we investigated the distal gut microbial communities of three CDI patients before and after fecal microbiota transplantation, and we compared these communities to the composition of the donor’s fecal microbiota. We utilized phylogenetic Microbiota Array, high-throughput Illumina sequencing, and fluorescent in situ hybridization to profile microbiota composition down to the genus and species level resolution. RESULTS: The original patients’ microbiota had low diversity, was dominated by members of Gammaproteobacteria and Bacilli, and had low numbers of Clostridia and Bacteroidia. At the genus level, fecal samples of CDI patients were rich in members of the Lactobacillus, Streptococcus, and Enterobacter genera. In comparison, the donor community was dominated by Clostridia and had significantly higher diversity and evenness. The patients’ distal gut communities were completely transformed within 3 days following fecal transplantation, and these communities remained stable in each patient for at least 4 months. Despite compositional differences among recipients’ pre-treatment gut microbiota, the transplanted gut communities were highly similar among recipients post-transplantation, were indistinguishable from that of the donor, and were rich in members of Blautia, Coprococcus, and Faecalibacterium. In each case, the gut microbiota restoration led to a complete patient recovery and symptom alleviation. CONCLUSION: We conclude that C. difficile infection can be successfully treated by fecal microbiota transplantation and that this leads to stable transformation of the distal gut microbial community from the one abundant in aerotolerant species to that dominated by members of the Clostridia

Toolbox approaches using molecular markers and 16S rRNA gene amplicon data sets for identification of fecal pollution in surface water

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small

Lipopeptide surfactin produced by Bacillus amyloliquefaciens KPS46 is required for biocontrol efficacy against Xanthomonas axonopodis pv

ABSTRACT The biological control of root and foliar diseases of soybeans caused by fungi and bacteria (e.g. Xanthomonas axonopodis pv. glycines, Xag) using the plant growth promoting rhizobacterium Bacillus amyloliquefaciens KPS46 has been previously reported. Disease suppression is thought to be due, in part, to the production of secondary metabolites. While a wide variety of these active compounds has been identified, their mode of action and mechanism of disease suppression on soybeans are not fully understood. The study used HPLC to identify secondary metabolites produced by B. amyloliquefaciens KPS46 and tested these compounds for biological control activity against soybean bacterial pustule disease caused by Xag. HPLC analyses indicated that a lipopeptide surfactin was present in KPS46 cell-free culture extracts, with maximum yields of ~550 ± 20.3 mg L -1 . Exogenous application of KPS46-produced surfactin to soybean plants directly that inhibited Xag, reduced disease severity and enhanced plant growth. UV mutagenesis of KPS46 and PCR assays were carried out to assess the role of surfactin production on the biocontrol activity. An independently-generated srfAA mutant of KPS46, strain M6, was unable to produce lipopeptide surfactin. The M6 mutant also was severely affected in its ability to produce extracellular enzymes, including endoglucanase, cellulase, and protease; and had reduced motility on the surface of agar compared to the wild-type strain KPS46. In contrast, the M6 mutant had enhanced production of α-amylase, and faster growth rate in nutrient broth, than did the parental strain. Soybean plant assays using the srfAA mutant and wild-type biocontrol agents against bacterial pustule disease indicated that the mutant strain M6 had significantly less effect on disease reduction compared to the wild-type parental strain. Results of this study suggest that the ability of B. amyloliquefaciens KPS46 to reduce bacterial pustule severity on soybeans is associated with the production of a lipopeptide surfactin encoded by srfAA, and that mutations in this locus also effect extracellular enzyme production

Proceedings of the 2014 A.S.P.E.N. Research Workshop

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141886/1/jpen0167.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141886/2/jpen0167-sup-0001.pd

Soil nitrogen transformations under elevated atmospheric CO2 and O3 during the soybean growing season

We investigated the influence of elevated CO2 and O3 on soil N cycling within the soybean growing season and across soil environments (i.e., rhizosphere and bulk soil) at the Soybean Free Air Concentration Enrichment (SoyFACE) experiment in Illinois, USA. Elevated O3 decreased soil mineral N likely through a reduction in plant material input and increased denitrification, which was evidenced by the greater abundance of the denitrifier gene nosZ. Elevated CO2 did not alter the parameters evaluated and both elevated CO2 and O3 showed no interactive effects on nitrifier and denitrifier abundance, nor on total and mineral N concentrations. These results indicate that elevated CO2 may have limited effects on N transformations in soybean agroecosystems. However, elevated O3 can lead to a decrease in soil N availability in both bulk and rhizosphere soils, and this likely also affects ecosystem productivity by reducing the mineralization rates of plant-derived residues

When should patients with stroke receive thrombolytics?

Thrombolytic therapy should be limited to patients with acute ischemic stroke who meet strict inclusion and exclusion criteria and who can adhere to strict treatment protocol. Patients treated under these conditions have improved combined mortality and disability outcomes at 1 year when treated with recombinant tissue plasminogen activator (rtPA) (number needed to treat [NNT]=18; 95% confidence interval [CI], 11-56) (strength of recommendation [SOR]: B, meta-analysis of randomized controlled trials with significant heterogeneity)