Development and investigation of an apparatus for standard preparation of environmental samples

xi, 83 leaves : ill. ; 28 cm.Includes abstract and appendices.Includes bibliographical references (leaves 72-75).An apparatus for preparing particulate matter (PM) standards has been developed. Investigation and characterization of the test sample standard reference material (SRM) coal fly ash (CFA) 1633b standards prepared using this apparatus were carried out using a combination of instrumental analysis techniques. These include solution nebulization inductively coupled plasma mass spectrometry (SN-ICP-MS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), and scanning electron microscopy energy dispersive X-ray spectroscopy (SEM-EDS). The results showed that homogeneous PM standards could be prepared that have potential for use in environmental monitoring of industrial emissions

Ultra-compact silicon nitride grating coupler for microscopy systems

Grating couplers have been widely used for coupling light between photonic chips and optical fibers. For various quantum-optics and bio-optics experiments, on the other hand, there is a need to achieve good light coupling between photonic chips and microscopy systems. Here, we propose an ultra-compact silicon nitride (SiN) grating coupler optimized for coupling light from a waveguide to a microscopy system. The grating coupler is about 4 by 2 mu m(2) in size and a 116 nm 1 dB bandwidth can be achieved theoretically. An optimized fabrication process was developed to realize suspended SiN waveguides integrated with these couplers on top of a highly reflective bottom mirror. Experimental results show that up to 53% (2.76 dB loss) of the power of the TE mode can be coupled from a suspended SiN waveguide to a microscopy system with a numerical aperture (NA) = 0.65. Simulations show this efficiency can increase up to 75% (1.25 dB loss) for NA = 0.95

Product Search Algorithm Based on Improved Ant Colony Optimization in a Distributed Network

The crowd intelligence-based e-commerce transaction network (CIeTN) is a distributed and unstructured network structure. Smart individuals, such as buyers, sellers, and third-party organizations, can store information in local nodes and connect and share information via moments. The purpose of this study is to design a product search algorithm on the basis of ant colony optimization (ACO) to achieve an efficient and accurate search for the product demand of a node in the network. We introduce the improved ideas of maximum and minimum ants to design a set of heuristic search algorithms on the basis of ACO. To reduce search blindness, additional relevant heuristic factors are selected to define the heuristic calculation equation. The pheromone update mechanism integrating into the product matching factor and forwarding probability is used to design the network search rules among nodes in the search algorithm. Finally, the search algorithm is facilitated by Java language programming and PeerSim software. Experimental results show that the algorithm has significant advantages over the flooding method and the random walk method in terms of search success rate, search time, product matching, search network consumption, and scalability. The search algorithm introduces the idea of improving the maximum and minimum ant colony system and proposes new ideas in the design of heuristic factors in the heuristic equation and the pheromone update strategy. The search algorithm can search for product information effectively

Cloning, reassembling and integration of the entire nikkomycin biosynthetic gene cluster into Streptomyces ansochromogenes lead to an improved nikkomycin production

<p>Abstract</p> <p>Background</p> <p>Nikkomycins are a group of peptidyl nucleoside antibiotics produced by <it>Streptomyces ansochromogenes</it>. They are competitive inhibitors of chitin synthase and show potent fungicidal, insecticidal, and acaricidal activities. Nikkomycin X and Z are the main components produced by <it>S. ansochromogenes</it>. Generation of a high-producing strain is crucial to scale up nikkomycins production for further clinical trials.</p> <p>Results</p> <p>To increase the yields of nikkomycins, an additional copy of nikkomycin biosynthetic gene cluster (35 kb) was introduced into nikkomycin producing strain, <it>S. ansochromogenes </it>7100. The gene cluster was first reassembled into an integrative plasmid by Red/ET technology combining with classic cloning methods and then the resulting plasmid(pNIK)was introduced into <it>S. ansochromogenes </it>by conjugal transfer. Introduction of pNIK led to enhanced production of nikkomycins (880 mg L^-1, 4 -fold nikkomycin X and 210 mg L^-1, 1.8-fold nikkomycin Z) in the resulting exconjugants comparing with the parent strain (220 mg L^-1nikkomycin X and 120 mg L^-1nikkomycin Z). The exconjugants are genetically stable in the absence of antibiotic resistance selection pressure.</p> <p>Conclusion</p> <p>A high nikkomycins producing strain (1100 mg L^-1nikkomycins) was obtained by introduction of an extra nikkomycin biosynthetic gene cluster into the genome of <it>S. ansochromogenes</it>. The strategies presented here could be applicable to other bacteria to improve the yields of secondary metabolites.</p

Selectively improving nikkomycin Z production by blocking the imidazolone biosynthetic pathway of nikkomycin X and uracil feeding in Streptomyces ansochromogenes

<p>Abstract</p> <p>Background</p> <p>Nikkomycins are a group of peptidyl nucleoside antibiotics and act as potent inhibitors of chitin synthases in fungi and insects. Nikkomycin X and Z are the main components produced by <it>Streptomyces ansochromogenes</it>. Of them, nikkomycin Z is a promising antifungal agent with clinical significance. Since highly structural similarities between nikkomycin Z and X, separation of nikkomycin Z from the culture medium of <it>S. ansochromogenes </it>is difficult. Thus, generating a nikkomycin Z selectively producing strain is vital to scale up the nikkomycin Z yields for clinical trials.</p> <p>Results</p> <p>A nikkomycin Z producing strain (sanPDM) was constructed by blocking the imidazolone biosynthetic pathway of nikkomycin X via genetic manipulation and yielded 300 mg/L nikkomycin Z and abolished the nikkomycin X production. To further increase the yield of nikkomycin Z, the effects of different precursors on its production were investigated. Precursors of nucleoside moiety (uracil or uridine) had a stimulatory effect on nikkomycin Z production while precursors of peptidyl moiety (L-lysine and L-glutamate) had no effect. sanPDM produced the maximum yields of nikkomycin Z (800 mg/L) in the presence of uracil at the concentration of 2 g/L and it was approximately 2.6-fold higher than that of the parent strain.</p> <p>Conclusion</p> <p>A high nikkomycin Z selectively producing was obtained by genetic manipulation combined with precursors feeding. The strategy presented here might be applicable in other bacteria to selectively produce targeted antibiotics.</p

SabR enhances nikkomycin production via regulating the transcriptional level of sanG, a pathway-specific regulatory gene in Streptomyces ansochromogenes

<p>Abstract</p> <p>Background</p> <p><it>sabR </it>is a pleiotropic regulatory gene which has been shown to positively regulate the nikkomycin biosynthesis and negatively affect the sporulation of <it>Streptomyces ansochromogenes</it>. In this study, we investigate the mechanism of SabR on modulating nikkomycin production in <it>Streptomyces ansochromogenes</it>.</p> <p>Results</p> <p>The transcription start point of <it>sabR </it>was determined by high-resolution S1 nuclease mapping and localized at the nucleotide T at position 37 bp upstream of the potential <it>sabR </it>translation start codon (GTG). Disruption of <it>sabR </it>enhanced its own transcription, but retarded the nikkomycin production. Over-expression of <it>sabR </it>enhanced nikkomycin biosynthesis in <it>Streptomyces ansochromogenes</it>. EMSA analysis showed that SabR bound to the upstream region of <it>sanG</it>, but it did not bind to the upstream region of its encoding gene (<it>sabR</it>), <it>sanF </it>and the intergenic region between <it>sanN </it>and <it>sanO</it>. DNase 1 footprinting assays showed that the SabR-binding site upstream of <it>sanG </it>was 5'-CTTTAAGTCACCTGGCTCATTCGCGTTCGCCCAGCT-3' which was designated as SARE. Deletion of SARE resulted in the delay of nikkomycin production that was similar to that of <it>sabR </it>disruption mutant.</p> <p>Conclusions</p> <p>These results indicated that SabR modulated nikkomycin biosynthesis as an enhancer via interaction with the promoter region of <it>sanG</it>, and expanded our understanding about regulatory cascade in nikkomycin biosynthesis.</p

Characterization of EndoTT, a novel single-stranded DNA-specific endonuclease from Thermoanaerobacter tengcongensis

EndoTT encoded by tte0829 of Thermoanaerobacter tengcongensis binds and cleaves single-stranded (ss) and damaged double-stranded (ds) DNA in vitro as well as binding dsDNA. In the presence of a low concentration of NaCl, EndoTT cleaved ss regions of damaged dsDNA efficiently but did not cleave DNA that was entirely ss or ds. At high concentrations of NaCl or MgCl2 or ATP, there was also specific cleavage of ssDNA. This suggested a preference for ss/ds junctions to stimulate cleavage of the DNA substrates. EndoTT has six specific sites (a–f) in the oriC region (1–70 nt) of T. tengcongensis. Substitutions of nucleotides around site c prevented cleavage by EndoTT of both sites c and d, implying that the cleavage specificity may depend on both the nucleotide sequence and the secondary structure of the ssDNA. A C-terminal sub-fragment of EndoTT (residues 107–216) had both endonucleolytic and DNA-binding activity, whereas an N-terminal sub-fragment (residues 1–110) displayed only ssDNA-binding activity. Site-directed mutations showed that G170, R172 and G177 are required for the endonuclease activity of EndoTT, but not for DNA-binding, whereas D171, R178 and G189 are partially required for the DNA-binding activity