The direct-methods procedure for single isomorphous replacement (SIR) data Hauptman (1982). Acta Cryst. A38, 289-294, as modified by Fortier, Moore & Fraser Acta Cryst. (1985), A41, 571-577 has been ...implemented and tested with a large number of known structures. It was found that the modified procedure greatly reduces the bias toward 'unresolved' SIR invariant values associated with estimates of 0 or pi, but does not remove it entirely. If the heavy atoms are not in a centrosymmetric array the centroid of the distribution of invariant estimates is not centered on true protein values, but is biased toward conventional SIR values by up to 15 degrees, thus errors in the estimates are not random but systematic. When the heavy atoms are in a centrosymmetric array (or single heavy-atom site in space group P21), the distribution of estimates is often sharply bimodal, with peaks centered at both true invariant values and pure 'unresolved' SIR values. Simple procedures are given which can be applied in both situations to reduce significantly the bias with no overall loss of accuracy. An additional correction factor is then described which can be used to remove nearly all of the bias, and improve the accuracy as well. The result is that errors in the corrected invariant estimates are small in magnitude, but are now also random instead of systematic. Since the number of estimates greatly exceeds the number of phases, the remaining random errors should have little impact in phasing processes.
An approach to the underwater robot trajectory control system synthesis is considered. The nonlinear control algorithms and their adaptive modifications are derived.< >
Bacteria play a crucial role in the uptake, transformation and release of organic matter and organic matter itself can play a role in structuring in-situ microbial communities. Most naturally ...abundant bacteria cannot be cultured, emphasizing the need for new approaches for their identification, quantification and for the determination of bacterial contribution to organic matter cycling and formation. This study used bacterial regrowth experiments to determine the response of Arctic bacterial communities to various organic matter substrates. Experiments consisted of carbon enrichments with diverse Arctic organic matter sources including ice algae, ice entrained debris and terrestrial peat as well as unamended controls. The phylogenetic response of the bacterial community to the organic matter enrichments was monitored by following changes in ribosomal RNA (rDNA) among different members of the bacterial community by length heterogeneity-polymerase chain reaction (LH-PCR). Samples for lipid analysis were collected to examine the relationship between lipids synthesized, bacterial community structure and the impact of differing sources of organic matter on the distribution of both. Results on bacterial community composition suggest that the community structure shifted in all of the treatments over time. rDNAs putatively identified as Alpha- and Gammaproteobacteria contributed approximately equally to the bacterial community of spring Arctic waters used for incubations. Unamended controls shifted over time towards rDNAs putatively identified as Bacteroidetes or Gammaproteobacteria. Community composition was similar in the peat, algal and ice rafted debris additions. Peat enrichments with extended incubation times (23 days total) were dominated by Alphaproteobacteria, mostly members of the Roseobacter clade. The distribution of fatty acids (GC and GC-MS) and intact polar lipids (LC-MS)was compared with rDNA to ascertain whether shifts in bacterial community structure were reflected in lipid synthesis. Fatty acid distribution overlapped among the treatments, with the general trend of 16:1delta9 and 16:0n dominant. Phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) were observed by LC-MS as the only phospholipids produced, with 16:1 and 16:0 the most common side chains observed. No shift in the composition of either fatty acids or IPLs was detected among the incubations amended with organic matter, indicating that phylogenetically diverse bacteria synthesize similar cell membrane lipids on natural organic matter substrates.
Understanding how specific groups of bacteria contribute to and regulate biogeochemical reservoirs is dependent on the ability to recognize their presence in the environment and those factors which ...alter their community structure. We used a series of enrichment experiments to examine the impact of dissolved organic matter (DOM) from different sources on bacterial community structure in the Delaware estuary and Chesapeake Bay systems. Amendments of protein and glucose were used investigate the impact of DOM availability on bacterial abundance, growth and lipid markers in the absence of grazers. Detailed molecular level lipid analysis was compared with fluorescence in situ hybridization (FISH) to link changes in the heterotrophic bacterial community with their chemical signature as seen in lipids. Over the 48 hour incubation times, growth on natural DOM from sites ranging from freshwater to lower Bay showed significant changes in bacterial growth and abundance in protein amended incubations compared to controls. Dramatic changes were observed in bacterial derived fatty acids among all sites by 48 hours, with a four-fold increase in a suite of specific odd chain and branched fatty acids when protein was added. FISH analysis of bacterial community structure shows that the shift in lipid composition is due to an increased abundance of Cytophaga- Flavobacteria and to a lesser extent, the alpha- proteobacteria. These results are consisted with results of separate Micro-FISH experiments which suggest that Cytophaga- Flavobacteria dominate protein use whereas alpha-proteobacteria use free amino acids. By linking geochemical signatures of actively growing bacteria with phylogenetic analysis, this work provides a path to determine which bacteria are active consumers of DOM as well as follow their contribution to organic carbon pool in the water column and sediments.
Dissolved organic matter (DOM) is ubiquitous and plays critical roles in nutrient cycling, aquatic food webs and numerous other biogeochemical processes. Furthermore, various factors control the ...quality and quantity of DOM, including land use, soil composition, in situ production, microbial uptake and assimilation and hydrology. As a component of DOM, dissolved organic carbon (DOC) has been recently identified as a drinking water constituent of concern due to its propensity to form EPA-regulated carcinogenic compounds when disinfected for drinking water purposes. Therefore, understanding the sources, cycling and modification of DOC across various landscapes is of direct relevance to a wide range of studies. The Willow Slough watershed is located in the Central Valley of California (U.S.A.) and is characterized by both diverse geomorphology as well as land use. The watershed drains approximately 425 km2 and is bordered by Cache and Putah Creeks to the north and south. The study area in the watershed includes the eastern portion of the foothills of the inner Coast Range and the alluvial plain and encompasses diverse land uses, including orchards, viticulture, dairy, pasture and natural grasslands. The Willow Slough watershed represents a unique opportunity to examine DOC dynamics through multiple land uses and hydrologic flow paths that are common throughout California. Preliminary data show that DOC concentrations at the watershed mouth peak during winter storms and also increase gradually throughout the summer months during the agricultural irrigation season. The increasing DOC concentrations during the summer months may result from agricultural runoff and/or primary production in channel. In addition, initial results using the chromophoric DOM (CDOM) absorption coefficient and spectral slope parameters indicate seasonal differences in the composition of the DOM. Spectral slopes decreased during both the summer irrigation season and winter storms relative to winter base flow, consistent with an increase in terrestrial signature. Biomolecular markers such as lignin phenols provide diagnostic source information on DOM as they are derived uniquely from vascular plants. Lignin can be used to differentiate angiosperm and gymnosperm tissues, but more importantly for this study, carbon-normalized yields can help to constrain the proportions of the increasing DOC during irrigation that come from vascular plants versus in situ production. In addition to supplying useful source information, dissolved lignin phenols undergo rapid photodegradation when exposed to adequate solar radiation, and this process is 'imprinted'through increases in the acidic components of lignin and decreases in the syringyl phenols, thus providing insight into DOM cycling in agriculture-dominated watersheds. Data will be presented highlighting the use of a range of analytical and spectrophotometric measurements including lignin phenols, 13C of DOC and CDOM in the Willow Slough watershed for investigating sources and dynamics of DOM throughout the watershed.
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