Quantitative structure–activity relationship (QSAR) analysis of aromatic effector specificity in NtrC-like transcriptional activators from aromatic oxidizing bacteria

A quantitative structure–activity relationship (QSAR) approach was taken to provide mechanistic insights into the interaction between the chemical structure of inducing compounds and the transcriptional activation of aromatic monooxygenase operons among the XylR/DmpR subclass of bacterial NtrC-like transcriptional regulators. Compared to XylR and DmpR, a broader spectrum of effector compounds was observed for the TbuT system from Ralstonia pickettii PKO1. The results of QSAR analysis for TbuT suggested that a steric effect, rather than hydrophobic or electronic effects, may be the predominant factor in determining aromatic effector specificity, and the active site of the regulator may positively interact not only with the methyl moiety but also with the most electron-rich aryl side of an aromatic effector.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74885/1/S0378-1097_03_00400-2.pd

Gap Analysis Based Decision Support Methodology to Improve Level of Service of Water Services

One of water utility’s managerial challenges is to make a balance in between two distinctive managerial goals, cost-effective provision of water service and improving customer satisfaction of water service. As management priorities of the water utility perspective do not reconcile from the customer’s perspective, this gap challenges the sustainable provision of water service. In this study, the new methodology based on a gap analysis was proposed to improve the Overall Level of Service (O-LOS) of water service. Two new indexes (Gap Index [GI] and the Efficiency Index [EI]) were developed to improve the O-LOS and minimize the gap between the customers and the service providers. The methodology proposed in this study is effective in supporting the water utility decisions on budget allocation to make a balance in between the customers’ demand and the service providers’ needs

Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria

Subsurface bacteria commonly exist in a starvation state with only periodic exposure to utilizable sources of carbon and energy. In this study, the effect of carbon starvation on aerobic toluene degradation was quantitatively evaluated with a selection of bacteria representing all the known toluene oxygenase enzyme pathways. For all the investigated strains, the rate of toluene biodegradation decreased exponentially with starvation time. First-order deactivation rate constants for TMO-expressing bacteria were approximately an order of magnitude greater than those for other oxygenase-expressing bacteria. When growth conditions (the type of growth substrate and the type and concentration of toluene oxygenase inducer) were varied in the cultures prior to the deactivation experiments, the rate of deactivation was not significantly affected, suggesting that the rate of deactivation is independent of previous substrate/inducer conditions. Because TMO-expressing bacteria are known to efficiently detoxify TCE in subsurface environments, these findings have significant implications for in situ TCE bioremediation, specifically for environments experiencing variable growth-substrate exposure conditions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45353/1/10532_2005_Article_9014.pd

Influence of substrate exposure history on biodegradation in porous media by <italic>Ralstonia pickettii</italic> PKO1.

An experimental study was undertaken with Ralstonia pickettii PKO1 to explore the stability and induction of biodegradation in a TCE (trichloroethylene)-degrading toluene monooxygenase bacterium in response to (i) varying lengths of carbon starvation period and (ii) varying levels of organic contaminant exposure. Preculturing at high TCE concentrations (above 110 mg/l) resulted in a surviving population that tolerated TCE degradation-dependent toxicity under growing conditions. Further examination of the effect of TCE preexposure indicated that solvent stress (rather than toxic TCE degradation intermediates) was the likely dominant factor in cell selection. In a column experiment designed to examine the influence of fluctuating toluene concentrations on aerobic degradation, toluene deprivation resulted in the decline of biodegradative activity (deactivation) in attached-growth cells. A lag-phase was observed prior to subsequent reactivation, leading to a delayed response of column degradation. The traditional Michaelis-Menten-type biodegradation equation, based upon suspended-batch-measured-biodegradation kinetic parameters for toluene-grown PKO1 cells, could not predict the observed column degradation behavior because it could not incorporate deactivation and lag. Subsequent batch experiments further revealed that the deactivation observed in the toluene-deprived environments could be attributed to carbon starvation rather than a lack of inducer. The experiments also indicated that the lengths of lag and transient phases for the subsequent induction of T3MO activity depended upon (i) the length of the previous carbon starvation period and (ii) the concentration level of the inducer. In contrast, the steady-state biodegradation rate was not affected by the length of the previous carbon starvation period, but only by inducer concentration. Additional experiments were conducted to examine the effect of oxygen limitation on toluene degradation. These revealed that toluene could not induce toluene degradation in attached-growth and suspended-growth cells when deprived of oxygen. Based upon these batch and column experimental observations, a quantitative framework (mathematical model/correlations), refining the traditional Michaelis-Menten model, was proposed to better describe the kinetics of induction of biodegradation under fluctuating substrate/inducer concentration conditions, representative of natural attenuation or in situ bioremediation scenarios.Ph.D.Applied SciencesBiological SciencesEnvironmental engineeringEnvironmental scienceHealth and Environmental SciencesMicrobiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/130355/2/3042151.pd

What we can see from very small size sample of metagenomic sequences

Abstract Background Since the analysis of a large number of metagenomic sequences costs heavy computing resources and takes long time, we examined a selected small part of metagenomic sequences as “sample”s of the entire full sequences, both for a mock community and for 10 different existing metagenomics case studies. A mock community with 10 bacterial strains was prepared, and their mixed genome were sequenced by Hiseq. The hits of BLAST search for reference genome of each strain were counted. Each of 176 different small parts selected from these sequences were also searched by BLAST and their hits were also counted, in order to compare them to the original search results from the full sequences. We also prepared small parts of sequences which were selected from 10 publicly downloadable research data of MG-RAST service, and analyzed these samples with MG-RAST. Results Both the BLAST search tests of the mock community and the results from the publicly downloadable researches of MG-RAST show that sampling an extremely small part from sequence data is useful to estimate brief taxonomic information of the original metagenomic sequences. For 9 cases out of 10, the most annotated classes from the MG-RAST analyses of the selected partial sample sequences are the same as the ones from the originals. Conclusions When a researcher wants to estimate brief information of a metagenome’s taxonomic distribution with less computing resources and within shorter time, the researcher can analyze a selected small part of metagenomic sequences. With this approach, we can also build a strategy to monitor metagenome samples of wider geographic area, more frequently

Variable Phenotypes of Epilepsy, Intellectual Disability, and Schizophrenia Caused by 12p13.33–p13.32 Terminal Microdeletion in a Korean Family: A Case Report and Literature Review

A simultaneous analysis of nucleotide changes and copy number variations (CNVs) based on exome sequencing data was demonstrated as a potential new first-tier diagnosis strategy for rare neuropsychiatric disorders. In this report, using depth-of-coverage analysis from exome sequencing data, we described variable phenotypes of epilepsy, intellectual disability (ID), and schizophrenia caused by 12p13.33–p13.32 terminal microdeletion in a Korean family. We hypothesized that CACNA1C and KDM5A genes of the six candidate genes located in this region were the best candidates for explaining epilepsy, ID, and schizophrenia and may be responsible for clinical features reported in cases with monosomy of the 12p13.33 subtelomeric region. On the background of microdeletion syndrome, which was described in clinical cases with mild, moderate, and severe neurodevelopmental manifestations as well as impairments, the clinician may determine whether the patient will end up with a more severe or milder end-phenotype, which in turn determines disease prognosis. In our case, the 12p13.33–p13.32 terminal microdeletion may explain the variable expressivity in the same family. However, further comprehensive studies with larger cohorts focusing on careful phenotyping across the lifespan are required to clearly elucidate the possible contribution of genetic modifiers and the environmental influence on the expressivity of 12p13.33 microdeletion and associated characteristics

Automatic Actuation of the Anti-Freezing System Using SMA Coil Springs

Studies have been actively conducted on systems that prevent the breakage of water pipes from freezing in winter. Shape memory alloy (SMA) coil springs have been used as the key components of actuators that can operate automatically by detecting the real-time outside temperature changes, but research on its use as an actuator that can operate at sub-zero temperatures is insufficient. This study proposes the anti-freezing system using Ni-44.08Ti-1.46Co (wt.%) SMA coil springs that operate near sub-zero temperatures to prevent the freezing accident of water pipes. After fabricating the SMA coil springs, the test for performance evaluation of the springs applied static load conditions was conducted on the specific outside temperature. To examine the operation of anti-freezing systems applied the SMA coil spring as an actuator, the water discharge test (WDT) was also conducted along with the computational fluid simulation. The results of water discharge measurement obtained by WDT, simulations, and theoretical equations applied to the fluid resupply system constructed were compared with each other to verify the reliability. Consequently, it was confirmed that water discharge can be automatically controlled in real time according to temperature changes of SMA coil springs in the anti-freezing system