2,526 research outputs found

    Geochemical characterization of organic matter in Victoria Harbour sediments, Hong Kong.

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    The organic carbon-to-nitrogen ratio demonstrated fluctuations in the sources of organic matter throughout the Holocene unit of MBH 54/2. High fluxes in the carbon-to-nitrogen ratio may reflect strong storms, where excess terrigenous plant material is transported into the area. Sediment intervals impacted by sewage waste had isotopic compositions (i.e., delta 13Corg and delta15N) consistent with those reported in the literature for sewage in coastal environments.Sources of organic matter could be differentiated using free lipids, which consisted of sterols, n-alcohols, fatty acids, and n-alkanes. Environmental conditions in Kowloon Bay were inferred to be anoxic based on the relative abundance of stanols-to-sterols. Sewage contaminated sediments were confirmed by the presence of fecal sterols. Periods of improved environmental conditions were noted by the occurrence of sterols common to aquatic organisms. Bound lipids appear to retain lipid profiles descriptive of bacterial communities in the sediments. More in-depth comparisons to lipid profiles of bacterial strains might allow bacterial remnants in sediments to be identified, allowing us to better speculate on their role in the remineralization of organic matter in Recent sediments.Victoria Harbour is located between Kowloon and Hong Kong Island in the southeastern prodelta region of the Pearl River system. Since the mid-1900s, the population in Hong Kong has grown rapidly, coastal areas surrounding Victoria Harbour have been reclaimed, and excess raw sewage has been disposed into the Harbour. Release of methane from harbour sediments during dredging activities instigated interest in studying the sources of methane trapped in Victoria Harbour sediments. Core MBH 54/2, from a heavily polluted area in Victoria Harbour's Kowloon Bay, was selected for this study. However, no methane was detected in sediments from this core. The project was redefined, using a detailed organic geochemical characterization approach to determine the sources of organic matter, evaluate changes in environmental conditions, and to ascertain whether remnants of bacterial lipids might be present to enhance our understanding of processes contributing to methane generation. Bulk properties (e.g., %Corg, %N, delta 13Corg, and delta15N), lipid composition and profiles were applied to delineate changes in organic matter sources deposited in the Kowloon Bay area during the late Quaternary

    Holography in commercially available photoetchable glasses

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    Volume holographic gratings are recorded and retrieved in two commercially available glasses: Schott Foturan and Hoya PEG3. These materials are photoetchable, which describes their major application, but they also allow storage of volume holograms without any chemical etching. The samples are illuminated with ultraviolet light at a wavelength of 325 nm and thermally processed to achieve a maximum diffraction efficiency of approximately 9% for a 1-mm-thick sample. The two glasses show similar behavior; the diffraction efficiencies in Foturan tend to be slightly larger, whereas PEG3 tends to have weaker light scattering

    Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine.

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    The intestinal microbiota are integral to understanding the relationships between nutrition and health. Therefore, fecal sampling and processing protocols for metagenomic surveys should be sufficiently robust, accurate, and reliable to identify the microorganisms present. We investigated the use of different fecal preparation methods on the bacterial community structures identified in human stools. Complete stools were collected from six healthy individuals and processed according to the following methods: (i) randomly sampled fresh stool, (ii) fresh stool homogenized in a blender for 2 min, (iii) randomly sampled frozen stool, and (iv) frozen stool homogenized in a blender for 2 min, or (v) homogenized in a pneumatic mixer for either 10, 20, or 30 min. High-throughput DNA sequencing of the 16S rRNA V4 regions of bacterial community DNA extracted from the stools showed that the fecal microbiota remained distinct between individuals, independent of processing method. Moreover, the different stool preparation approaches did not alter intra-individual bacterial diversity. Distinctions were found at the level of individual taxa, however. Stools that were frozen and then homogenized tended to have higher proportions of Faecalibacterium, Streptococcus, and Bifidobacterium and decreased quantities of Oscillospira, Bacteroides, and Parabacteroides compared to stools that were collected in small quantities and not mixed prior to DNA extraction. These findings indicate that certain taxa are at particular risk for under or over sampling due to protocol differences. Importantly, homogenization by any method significantly reduced the intra-individual variation in bacteria detected per stool. Our results confirm the robustness of fecal homogenization for microbial analyses and underscore the value of collecting and mixing large stool sample quantities in human nutrition intervention studies

    Comparison of the DNA Association Kinetics of the Lacy Repressor Tetramet, Its Dimeric Mutant LacI(Adi), and the Native Dimeric Gal Repressor

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    The rates of association of the tetrameric Lacy repressor (LacI), dimeric LacI(adi) (a deletion mutant of LacI), and the native dimeric Gal repressor (GalR) to DNA restriction fragments containing a single specific site were investigated using a quench-flow DNase I \u27foot-printing\u27 technique. The dimeric proteins, LacI(adi) and GalR, and tetrameric LacI possess one and two DNA binding sites, respectively. The nanomolar protein concentrations used in these studies ensured that the state of oligomerization of each protein was predominantly either dimeric or tetrameric, respectively. The bimolecular association rate constants (k(a)) determined for the LacI tetramer exceed those of the dimeric proteins. The values of k(a) obtained for LacI, LacI(adi), and GalR display different dependences on [KCl]. For LacI(adi) and GalR, they diminish as [KCl] increases from 25 mM to 200 mM, approaching rates predicted for three-dimensional diffusion. In contrast, the k(a) values determined for the tetrameric LacI remain constant up to 300 mM [KCl], the highest salt concentration that could be investigated by quench- flow footprinting. The enhanced rate of association of the tetramer relative to the dimeric proteins can be modeled by enhanced \u27sliding\u27 (Berg, O. G., Winter, R. B., and von Hippel, P. H. (1981) Biochemistry 20, 6929-6948) of the LacI tetramer relative to the LaeI(adi) dimer or a combination of enhanced sliding and the superimposition of \u27direct transfer\u27 mediated by the bidentate DNA interactions of the tetramer

    Native cellular architecture of Treponema denticola revealed by cryo-electron tomography

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    Using cryo-electron tomography, we are developing a refined description of native cellular structures in the pathogenic spirochete Treponema denticola. Tightly organized bundles of periplasmic flagella were readily observed in intact plunge-frozen cells. The periplasmic space was measured in both wild-type and aflagellate strains, and found to widen by less than the diameter of flagella when the latter are present. This suggests that a structural change occurs in the peptidoglycan layer to accommodate the presence of the flagella. In dividing cells, the flagellar filaments were found to bridge the cytoplasmic cylinder constriction site. Cytoplasmic filaments, adjacent to the inner membrane, run parallel to the tightly organized flagellar filaments. The cytoplasmic filaments may be anchored by a narrow plate-like structure. The tapering of the cell ends was conserved between cells, with a patella-shaped structure observed in the periplasm at the tip of each cytoplasmic cylinder. Several incompletely characterized structures have been observed in the periplasm between dividing cells, including a cable-like structure linking two cytoplasmic cylinders and complex foil-shaped structures
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