The tunicamycin derivative TunR2 exhibits potent antibiotic properties with low toxicity in an in vivo Mycobacterium marinum-zebrafish TB infection model.

Tunicamycins (TUN) are well-defined, Streptomyces-derived natural products that inhibit protein N-glycosylation in eukaryotes, and by a conserved mechanism also block bacterial cell wall biosynthesis. TUN inhibits the polyprenylphosphate-N-acetyl-hexosamine-1-phospho-transferases (PNPT), an essential family of enzymes found in both bacteria and eukaryotes. We have previously published the development of chemically modified TUN, called TunR1 and TunR2, that have considerably reduced activity on eukaryotes but that retain the potent antibacterial properties. A mechanism for this reduced toxicity has also been reported. TunR1 and TunR2 have been tested against mammalian cell lines in culture and against live insect cells but, until now, no in vivo evaluation has been undertaken for vertebrates. In the current work, TUN, TunR1, and TunR2 are investigated for their relative toxicity and antimycobacterial activity in zebrafish using a well-established Mycobacterium marinum (M. marinum) infection system, a model for studying human Mycobacterium tuberculosis infections. We also report the relative ability to activate the unfolded protein response (UPR), the known mechanism for the eukaryotic toxicity observed with TUN treatment. Importantly, TunR1 and TunR2 retained their antimicrobial properties, as evidenced by a reduction in M. marinum bacterial burden, compared to DMSO-treated zebrafish. In summary, findings from this study highlight the characteristics of recently developed TUN derivatives, mainly TunR2, and its potential for use as a novel anti-bacterial agent for veterinary and potential medical purposes.

Precursor-Directed Biosynthesis and Biological Testing of omega-Alicyclic- and neo-Branched Tunicamycin N-Acyl Variants.

Tunicamycins (TUNs) are Streptomyces-derived natural products, widely used to block protein N-glycosylation in eukaryotes or cell wall biosynthesis in bacteria. Modified or synthetic TUN analogues that uncouple these activities have considerable potential as novel mode-of-action antibacterial agents. Chemically modified TUNs reported previously with attenuated activity on yeast have pinpointed eukaryotic-specific chemophores in the uridyl group and the N-acyl chain length and terminal branching pattern. A small molecule screen of fatty acid biosynthetic primers identified several novel alicyclic- and neo-branched TUN N-acyl variants, with primer incorporation at the terminal omega-acyl position. TUNs with unique 5- and 6-carbon ω-cycloalkane and ω-cycloalkene acyl chains are produced under fermentation and in yields comparable with the native TUN. The purification, structural assignments, and the comparable antimicrobial properties of 15 of these compounds are reported, greatly extending the structural diversity of this class of compounds for potential medicinal and agricultural applications.

Branched Chain Lipid Metabolism As a Determinant of the N-Acyl Variation of Streptomyces Natural Products.

Branched-chain fatty acids (BCFA) are encountered in Gram-positive bacteria, but less so in other organisms. The bacterial BCFA in membranes are typically saturated, with both odd- and even-numbered carbon chain lengths, and with methyl branches at either the ω-1 (iso) or ω-2 (anteiso) positions. The acylation with BCFA also contributes to the structural diversity of microbial natural products and potentially modulates biological activity. For the tunicamycin (TUN) family of natural products, the toxicity toward eukaryotes is highly dependent upon N-acylation with trans-2,3-unsaturated BCFA. The loss of the 2,3-unsaturation gives modified TUN with reduced eukaryotic toxicity but crucially with retention of the synergistic enhancement of the ß-lactam group of antibiotics. Here, we infer from genomics, mass spectrometry, and deuterium labeling that the trans-2,3-unsaturated TUN variants and the saturated cellular lipids found in TUN-producing Streptomyces are derived from the same pool of BCFA metabolites. Moreover, non-natural primers of BCFA metabolism are selectively incorporated into the cellular lipids of TUN-producing Streptomyces and concomitantly produce structurally novel neo-branched TUN N-acyl variants.

Exploring the Active Site of the Antibacterial Target MraY by Modified Tunicamycins.

The alarming growth of antibiotic resistance that is currently ongoing is a serious threat to human health. One of the most promising novel antibiotic targets is MraY (phospho-MurNAc-pentapeptide-transferase), an essential enzyme in bacterial cell wall synthesis. Through recent advances in biochemical research, there is now structural information available for MraY, and for its human homologue GPT (GlcNAc-1-P-transferase), that opens up exciting possibilities for structure-based drug design. The antibiotic compound tunicamycin is a natural product inhibitor of MraY that is also toxic to eukaryotes through its binding to GPT. In this work, we have used tunicamycin and modified versions of tunicamycin as tool compounds to explore the active site of MraY and to gain further insight into what determines inhibitor potency. We have investigated tunicamycin variants where the following motifs have been modified: the length and branching of the tunicamycin fatty acyl chain, the saturation of the fatty acyl chain, the 6″-hydroxyl group of the GlcNAc ring, and the ring structure of the uracil motif. The compounds are analyzed in terms of how potently they bind to MraY, inhibit the activity of the enzyme, and affect the protein thermal stability. Finally, we rationalize these results in the context of the protein structures of MraY and GPT.

Rhodium-catalyzed reductive modification of pyrimidine nucleosides, nucleotide phosphates, and sugar nucleotides.

Nucleosides and nucleotides are a group of small molecule effectors and substrates which include sugar nucleotides, purine and pyrimidine-based nucleotide phosphates, and diverse nucleotide antibiotics. We previously reported that hydrogenation of the nucleotide antibiotic tunicamycin leads to products with reduced toxicity on eukaryotic cells. We now report the hydrogenation of diverse sugar nucleosides, nucleotide phosphates, and pyrimidine nucleotides. UDP-sugars and other uridyl and thymidinyl nucleosides are quantitatively reduced to the corresponding 5,6-dihydro-nucleosides. Cytidyl pyrimidines are reduced, but the major products are the corresponding 5,6-dihydrouridyl nucleosides resulting from a deamination of the cytosine ring.

Synergistic enhancement of beta-lactam antibiotics by modified tunicamycin analogs TunR1 and TunR2.

The ß-lactams are the most widely used group of antibiotics in human health and agriculture, but this is under threat due to the persistent rise of pathogenic resistance. Several compounds, including tunicamycin (TUN), can enhance the antibacterial activity of the ß-lactams to the extent of overcoming resistance, but the mammalian toxicity of TUN has precluded its use in this role. Selective hydrogenation of TUN produces modified compounds (TunR1 and TunR2), which retain the enhancement of ß-lactams while having much lower mammalian toxicity. Here we show that TunR1 and TunR2 enhance the antibacterial activity of multiple ß-lactam family members, including penems, cephems, and third-generation penicillins, to a similar extent as does the native TUN. Eleven of the ß-lactams tested were enhanced from 2 to >256-fold against Bacillus subtilis, with comparable results against a penicillin G-resistant strain. The most significant enhancements were obtained with third-generation aminothiazolidyl cephems, including cefotaxime, ceftazidime, and cefquinome. These results support the potential of low toxicity tunicamycin analogs (TunR1 and TunR2) as clinically valid, synergistic enhancers for a broad group of ß-lactam antibiotics.

Physical and chemical properties of pyrolyzed biosolids for utilization in sand-based turfgrass rootzones.

Biosolids are several forms of treated sewage sludge that are intended for use as soil conditioners for horticultural, agricultural and industrial crops. The objectives of this research were to determine the chemical and physical properties of biosolids pyrolyzed at several different temperatures, and their effect on perennial ryegrass seed germination and growth. Biosolids were thermally treated in an oxygen-free (nitrogen atmosphere) retort oven at 300, 400, 500, 700 and 900 °C. As pyrolysis temperatures increased, bulk densities, total surface areas, micropore surface areas, % minerals and pH values of the pyrolyzed biosolids increased, while carbon percentage decreased compared to untreated biosolids. Fourier-transform infrared spectroscopy analysis showed decreased surface functionality as pyrolysis temperature increased. Perennial ryegrass (Lolium perenne L. 'Nui') plants were grown in mixtures of 10% (v/v) biosolids or 10% (v/v) of the various pyrolyzed biosolids and 90% coarse sand. Ryegrass plants grown in the biosolids and the 300 °C pyrolyzed biosolids mixture had the greatest shoot heights of any of the treatments after 4 weeks of growth. These results indicate that pyrolyzing biosolids at 300 °C would produce material with excellent potential as a long-term peat replacement for water and nutrient retention in sand-based rootzones.

Selective catalytic hydrogenation of the N-acyl and uridyl double bonds in the tunicamycin family of protein N-glycosylation inhibitors.

Tunicamycin is a Streptomyces-derived inhibitor of eukaryotic protein N-glycosylation and bacterial cell wall biosynthesis, and is a potent and general toxin by these biological mechanisms. The antibacterial activity is dependent in part upon a π-π stacking interaction between the tunicamycin uridyl group and a specific Phe residue within MraY, a tunicamycin-binding protein in bacteria. We have previously shown that reducing the tunicamycin uridyl group to 5,6-dihydrouridyl (DHU) significantly lowers its eukaryotic toxicity, potentially by disrupting the π-stacking with the active site Phe. The present report compares the catalytic hydrogenation of tunicamycin and uridine with various precious metal catalysts, and describe optimum conditions for the selective production of N-acyl reduced tunicamycin or for tunicamycins reduced in both the N-acyl and uridyl double bonds. At room temperature, Pd-based catalysts are selective for the N-acyl reduction, whereas Rh-based catalysts favor the double reduction to provide access to fully reduced tunicamycin. The reduced DHU is highly base-sensitive, leading to amide ring opening under mild alkaline conditions.

A one-pot synthesis of 1,6,9,13-tetraoxadispiro(4.2.4.2)tetradecane by hydrodeoxygenation of xylose using a palladium catalyst.

In an effort to expand the number of biobased chemicals available from sugars, xylose has been converted to 1,6,9,13-tetraoxadispiro(4.2.4.2)tetradecane in a one-pot reaction using palladium supported on silica-alumina as the catalyst. The title compound is produced in 35-40% yield under 7 MPa H2 pressure at 733 K using 3-10 wt%Pd on silica-alumina catalyst. It is isolated using a combination of liquid-liquid extractions and flash chromatography. This dimer can be converted to its monomer, 2-hydroxy-(2-hydroxymethyl)tetrahydrofuran, which ring opens under acid conditions to 1,5-dihydroxy-2-pentanone. This diol can then be esterified with vinylacetate in phosphate buffer to produce 1,5-bis(acetyloxy)-2-pentanone which is an inhibitor of mammalian 11ß-hydroxysteroid dehydrogenase 1. (1)H and (13)C nmr spectra of each of these species are reported. The single crystal X-ray structure of the title compound is also reported. These data were collected in a temperature range of 100 K-273 K and show a solid state phase change from triclinic to monoclinic between 175 K and 220 K without a conformational change.

Introduction and comparison of new EBSD post-processing methodologies.

Electron Backscatter Diffraction (EBSD) provides a useful means for characterizing microstructure. However, it can be difficult to obtain index-able diffraction patterns from some samples. This can lead to noisy maps reconstructed from the scan data. Various post-processing methodologies have been developed to improve the scan data generally based on correlating non-indexed or mis-indexed points with the orientations obtained at neighboring points in the scan grid. Two new approaches are introduced (1) a re-scanning approach using local pattern averaging and (2) using the multiple solutions obtained by the triplet indexing method. These methodologies are applied to samples with noise introduced into the patterns artificially and by the operational settings of the EBSD camera. They are also applied to a heavily deformed and a fine-grained sample. In all cases, both techniques provide an improvement in the resulting scan data, the local pattern averaging providing the most improvement of the two. However, the local pattern averaging is most helpful when the noise in the patterns is due to the camera operating conditions as opposed to inherent challenges in the sample itself. A byproduct of this study was insight into the validity of various indexing success rate metrics. A metric based given by the fraction of points with CI values greater than some tolerance value (0.1 in this case) was confirmed to provide an accurate assessment of the indexing success rate.

Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates.

Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-products. We irradiated Y. lipolytica NRRL YB-567 with UV-C to enhance ammonia (for fertilizer) and lipid (for biodiesel) production on low-cost protein and carbohydrate substrates. The resulting strains were screened for ammonia and oil production using color intensity of indicators on plate assays. Seven mutant strains were selected (based on ammonia assay) and further evaluated for growth rate, ammonia and oil production, soluble protein content, and morphology when grown on liver infusion medium (without sugars), and for growth on various substrates. Strains were identified among these mutants that had a faster doubling time, produced higher maximum ammonia levels (enzyme assay) and more oil (Sudan Black assay), and had higher maximum soluble protein levels (Bradford assay) than wild type. When grown on plates with substrates of interest, all mutant strains showed similar results aerobically to wild-type strain. The mutant strain with the highest oil production and the fastest doubling time was evaluated on coffee waste medium. On this medium, the strain produced 0.12 g/L ammonia and 0.20 g/L 2-phenylethanol, a valuable fragrance/flavoring, in addition to acylglycerols (oil) containing predominantly C16 and C18 residues. These mutant strains will be investigated further for potential application in commercial biodiesel production.

A Dictionary Approach to Electron Backscatter Diffraction Indexing.

We propose a framework for indexing of grain and subgrain structures in electron backscatter diffraction patterns of polycrystalline materials. We discretize the domain of a dynamical forward model onto a dense grid of orientations, producing a dictionary of patterns. For each measured pattern, we identify the most similar patterns in the dictionary, and identify boundaries, detect anomalies, and index crystal orientations. The statistical distribution of these closest matches is used in an unsupervised binary decision tree (DT) classifier to identify grain boundaries and anomalous regions. The DT classifies a pattern as an anomaly if it has an abnormally low similarity to any pattern in the dictionary. It classifies a pixel as being near a grain boundary if the highly ranked patterns in the dictionary differ significantly over the pixel's neighborhood. Indexing is accomplished by computing the mean orientation of the closest matches to each pattern. The mean orientation is estimated using a maximum likelihood approach that models the orientation distribution as a mixture of Von Mises-Fisher distributions over the quaternionic three sphere. The proposed dictionary matching approach permits segmentation, anomaly detection, and indexing to be performed in a unified manner with the additional benefit of uncertainty quantification.

Co-pyrolysis of swine manure with agricultural plastic waste: laboratory-scale study.

Manure-derived biochar is the solid product resulting from pyrolysis of animal manures. It has considerable potential both to improve soil quality with high levels of nutrients and to reduce contaminants in water and soil. However, the combustible gas produced from manure pyrolysis generally does not provide enough energy to sustain the pyrolysis process. Supplementing this process may be achieved with spent agricultural plastic films; these feedstocks have large amounts of available energy. Plastic films are often used in soil fumigation. They are usually disposed in landfills, which is wasteful, expensive, and environmentally unsustainable. The objective of this work was to investigate both the energetics of co-pyrolyzing swine solids with spent plastic mulch films (SPM) and the characteristics of its gas, liquid, and solid byproducts. The heating value of the product gas from co-pyrolysis was found to be much higher than that of natural gas; furthermore, the gas had no detectable toxic fumigants. Energetically, sustaining pyrolysis of the swine solids through the energy of the product gas could be achieved by co-pyrolyzing dewatered swine solids (25%m/m) with just 10% SPM. If more than 10% SPM is used, the co-pyrolysis would generate surplus energy which could be used for power generation. Biochars produced from co-pyrolyzing SPM and swine solid were similar to swine solid alone based on the surface area and the (1)H NMR spectra. The results of this study demonstrated the potential of using pyrolysis technology to manage two prominent agricultural waste streams (SPM and swine solids) while producing value-added biochar and a power source that could be used for local farm operations.

Determination of fusaric acid in maize using molecularly imprinted SPE clean-up.

A new LC method to detect fusaric acid (FA) in maize is reported based on a molecularly imprinted SPE clean-up using mimic-templated molecularly imprinted polymers. Picolinic acid was used as a toxin analog for imprinting polymers during a thermolytic synthesis. Both acidic and basic functional monomers were predicted to have favorable binding interactions by MP2 ab initio calculations. Imprinted polymers synthesized with methacrylic acid or 2-dimethylaminoethyl methacrylate exhibited imprinting effects in SPE analysis. FA levels were determined using RP ion-pairing chromatography with diode-array UV detection and tetrabutylammonium hydrogen sulfate in the mobile phase. A method was developed to detect FA in maize using molecularly imprinted SPE analysis within the range of 1-100 µg/g with recoveries between 83.9 and 92.1%.

A model based iterative reconstruction algorithm for high angle annular dark field-scanning transmission electron microscope (HAADF-STEM) tomography.

High angle annular dark field (HAADF)-scanning transmission electron microscope (STEM) data is increasingly being used in the physical sciences to research materials in 3D because it reduces the effects of Bragg diffraction seen in bright field TEM data. Typically, tomographic reconstructions are performed by directly applying either filtered back projection (FBP) or the simultaneous iterative reconstruction technique (SIRT) to the data. Since HAADF-STEM tomography is a limited angle tomography modality with low signal to noise ratio, these methods can result in significant artifacts in the reconstructed volume. In this paper, we develop a model based iterative reconstruction algorithm for HAADF-STEM tomography. We combine a model for image formation in HAADF-STEM tomography along with a prior model to formulate the tomographic reconstruction as a maximum a posteriori probability (MAP) estimation problem. Our formulation also accounts for certain missing measurements by treating them as nuisance parameters in the MAP estimation framework. We adapt the iterative coordinate descent algorithm to develop an efficient method to minimize the corresponding MAP cost function. Reconstructions of simulated as well as experimental data sets show results that are superior to FBP and SIRT reconstructions, significantly suppressing artifacts and enhancing contrast.

Sorption of ochratoxin A from aqueous solutions using ß-cyclodextrin-polyurethane polymer.

The ability of a cyclodextrin-polyurethane polymer to remove ochratoxin A from aqueous solutions was examined by batch rebinding assays. The results from the aqueous binding studies were fit to two parameter models to gain insight into the interaction of ochratoxin A with the nanosponge material. The ochratoxin A sorption data fit well to the heterogeneous Freundlich isotherm model. The polymer was less effective at binding ochratoxin A in high pH buffer (9.5) under conditions where ochratoxin A exists predominantly in the dianionic state. Batch rebinding assays in red wine indicate the polymer is able to remove significant levels of ochratoxin A from spiked solutions between 1-10 µg·L(-1). These results suggest cyclodextrin nanosponge materials are suitable to reduce levels of ochratoxin A from spiked aqueous solutions and red wine samples.

Removal of patulin from aqueous solutions by propylthiol functionalized SBA-15.

Propylthiol functionalized SBA-15 silica was investigated to detoxify aqueous solutions contaminated with the regulated mycotoxin patulin. Micelle templated silicas with a specific pore size were synthetically modified to possess propylthiol groups, a functional group known to form Michael reaction products with the conjugated double bond system of patulin. BET surface area analysis indicated the propylthiol functionalized SBA-15 possesses channels with the pore size of 5.4 nm and a surface area of 345 m(2)g(-1). Elemental analysis indicates the silicon/sulfur ratio to be 10:1, inferring one propylthiol substituent for every ten silica residues. The propylthiol modified SBA-15 was effective at significantly reducing high levels of patulin from aqueous solutions (pH 7.0) in batch sorption assays at room temperature. The material was less effective at lower pH; however heating low pH solutions and apple juice to 60 °C in the presence of propylthiol functionalized SBA-15 significantly reduced the levels of patulin in contaminated samples. Composite molecular models developed by semi-empirical PM3 and empirical force field methods support patulin permeation through the mesoporous channels of propylthiol functionalized SBA-15. Density functional study at the B3LYP/6-31G(d,p) level predicts the proposed patulin adducts formed by reaction with the thiol residues exhibit less electrophilic properties than patulin. It is demonstrated the use of propylthiol functionalized SBA-15 is a viable approach to reduce patulin levels in aqueous solutions, including contaminated apple juice.

A mathematical framework for separating the direct and bystander components of cellular radiation response.

UNLABELLED: A mathematical model for fractional tumor cell survival was developed incorporating components of cell killing due to direct radiation interactions and bystander signals resulting from non-local dose deposition. MATERIAL AND METHODS: Three possible mechanisms for signal production were tested by fitting predictions to available experimental results for tumor cells (non-small cell lung cancer NCI-H460 and melanoma MM576) exposed to gradient x-ray fields. The parameter fitting allowed estimation of the contribution of bystander signaling to cell death (20-50% for all models). Separation of the two components of cell killing allowed determination of the α and ß parameters of the linear-quadratic model both with and without the presence of bystander signaling. RESULTS AND DISCUSSION: For both cell lines, cell death from bystander signaling and direct radiation interactions were comparable. For NCI-H460 cells, the values for α and ß were 0.18 Gy⁻¹ and 0.10 Gy⁻² respectively when direct and bystander effects were combined, and 0.053 Gy⁻¹ and 0.061 Gy⁻² respectively when the signaling component was removed. For MM576, the corresponding respective values were 0.09 Gy⁻¹ and 0.011 Gy⁻² for the combined response, and 0.014 Gy⁻¹ and 0.002 Gy⁻² for the isolated direct radiation response. The bystander component in cell death was found to be significant and should not be ignored. Further experimental evidence is required to determine how these results translate to the in vivo situation where tumor control probability (TCP) models that currently assume cellular independence may need to be revised.

Seasonal changes in sleep duration in African American and African college students living in Washington, D.C.

Duration of nocturnal melatonin secretion, a marker of "biological night" that relates to sleep duration, is longer in winter than in summer in patients with seasonal affective disorder (SAD), but not in healthy controls. In this study of African and African American college students, we hypothesized that students who met criteria for winter SAD or subsyndromal SAD (S-SAD) would report sleeping longer in winter than in summer. In addition, based on our previous observation that Africans report more "problems" with change in seasons than African Americans, we expected that the seasonal changes in sleep duration would be greater in African students than in African American students. Based on Seasonal Pattern Assessment Questionnaire (SPAQ) responses, African American and African college students in Washington, D.C. (N = 575) were grouped into a winter SAD/S-SAD group or a no winter diagnosis group, and winter and summer sleep length were determined. We conducted a 2 (season) x 2 (sex) x 2 (ethnicity) x 2 (winter diagnosis group) ANCOVA on reported sleep duration, controlling for age. Contrary to our hypothesis, we found that African and African American students with winter SAD/S-SAD report sleeping longer in the summer than in the winter. No differences in seasonality of sleep were found between African and African American students. Students with winter SAD or S-SAD may need to sacrifice sleep duration in the winter, when their academic functioning/efficiency may be impaired by syndromal or subsyndromal depression, in order to meet seasonally increased academic demands.

Mood sensitivity to seasonal changes in African college students living in the greater Washington D.C. metropolitan area.

The purpose of this study was to estimate the degree of seasonality and prevalence of winter- and summer-type seasonal affective disorder (SAD) in African immigrant college students in comparison with African American peers. A convenience sample of 246 African immigrants and 599 African Americans studying in Washington, D.C. completed the Seasonal Pattern Assessment Questionnaire (SPAQ), which was used to calculate a global seasonality score (GSS) and to estimate the prevalence of winter- and summer-type SAD. Degree of seasonality was related to a complex interaction between having general awareness of SAD, ethnicity, and gender. A greater percentage of African students reported experiencing a problem with seasonal changes relative to African American students, and had summer SAD, but the groups did not differ on GSS and winter SAD. African students reported more difficulties with seasonal changes than their African American peers, which could represent a manifestation of incomplete acclimatization to a higher latitude and temperate climate. As Africans also had a greater rate of summer SAD, this argues against acclimatization to heat.