Microcosm study reveals the microbial and environmental effects on tributyltin degradation in an estuarine sediment.

Tributyltin (TBT) is one of the most harmful contaminants ever released into the aquatic environment. Despite being banned, it is still present at many locations throughout the world. Its degradation in sediment mainly occurs through microbial biodegradation, a process that remains unclear. This study therefore aimed at better understanding TBT biodegradation in estuarine sediment and the microbial community associated with it. Microcosm experiments were set up, embracing a range of environmental control parameters. Major community shifts were recorded, mainly attributed to the change in oxygen status. The highest percentage of degradation (36,8%) occurred at 4 °C in anaerobic conditions. These results are encouraging for the in-situ bioremediation of TBT contaminated muddy sediment in temperate ports worldwide. However, with TBT able to persist in the coastal environment for decades when undisturbed in anoxic sediment, further research is needed to fully understand the mechanisms that triggered this biodegradation observed in the microcosms.

iChip increases the success of cultivation of TBT-resistant and TBT-degrading bacteria from estuarine sediment.

Standard methods of microbial cultivation only enable the isolation of a fraction of the total environmental bacteria. Numerous techniques have been developed to increase the success of isolation and cultivation in the laboratory, some of which derive from diffusion chambers. In a diffusion chamber, environmental bacteria in agar medium are put back in the environment to grow as close to their natural conditions as possible, only separated from the environment by semi-permeable membranes. In this study, the iChip, a device that possesses hundreds of mini diffusion chambers, was used to isolate tributyltin (TBT) resistant and degrading bacteria. IChip was shown to be efficient at increasing the number of cultivable bacteria compared to standard methods. TBT-resistant strains belonging to Oceanisphaera sp., Pseudomonas sp., Bacillus sp. and Shewanella sp. were identified from Liverpool Dock sediment. Among the isolates in the present study, only members of Pseudomonas sp. were able to use TBT as a sole carbon source. It is the first time that members of the genus Oceanisphaera have been shown to be TBT-resistant. Although iChip has been used in the search for molecules of biomedical interest here we demonstrate its promising application in bioremediation.

Combining sediment management and bioremediation in muddy ports and harbours: A review.

This paper reviews two important sources of innovation linked to the maritime environment and more importantly to ports: the potential coupling of sediment management and (bio)remediation. The detrimental effects of dredging are briefly considered, but the focus here is on a sustainable alternative method of managing the problem of siltation. This technique consists of fluidizing the sediment in situ, lowering the shear strength to maintain a navigable under-keel draught. Preliminary investigations show that through this mixing, aeration occurs, which results in a positive remediation effect as well. An overview of port contamination, remediation, and the recent research on aerobic (bio)degradation of port contaminants is made in order to show the potential for such innovative sediment management to reduce dredging need and remediate contaminated mud in ports. This review also highlights the lack of full-scale field applications for such potential remediation techniques, that remain largely confined to the laboratory scale.

Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children.

The atypical antipsychotic risperidone (RSP) is often associated with weight gain and cardiometabolic side effects. The mechanisms for these adverse events are poorly understood and, undoubtedly, multifactorial in etiology. In light of growing evidence implicating the gut microbiome in the host's energy regulation and in xenobiotic metabolism, we hypothesized that RSP treatment would be associated with changes in the gut microbiome in children and adolescents. Thus, the impact of chronic (>12 months) and short-term use of RSP on the gut microbiome of pediatric psychiatrically ill male participants was examined in a cross-sectional and prospective (up to 10 months) design, respectively. Chronic treatment with RSP was associated with an increase in body mass index (BMI) and a significantly lower ratio of Bacteroidetes:Firmicutes as compared with antipsychotic-naïve psychiatric controls (ratio=0.15 vs 1.24, respectively; P<0.05). Furthermore, a longitudinal observation, beginning shortly after onset of RSP treatment, revealed a gradual decrease in the Bacteroidetes:Firmicutes ratio over the ensuing months of treatment, in association with BMI gain. Lastly, metagenomic analyses were performed based on extrapolation from 16S ribosomal RNA data using the software package, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Those data indicate that gut microbiota dominating the RSP-treated participants are enriched for pathways that have been implicated in weight gain, such as short-chain fatty acid production.

Toward a comprehensive view of the skills involved in word reading in Grades 4, 6, and 8.

Research to date has proposed four main variables involved in reading development: phonological awareness, naming speed, orthographic knowledge, and morphological awareness. Although each of these variables has been examined in the context of one or two of the other variables, this study examines all four factors together to assess their unique contribution to reading. A sample of children in Grades 4, 6, and 8 (ages 10, 12, and 14 years) completed a battery of tests that included at least one measure of each of the four variables and two measures of reading accuracy. Phonological awareness, orthographic knowledge, and morphological awareness each contributed uniquely to real word and pseudoword reading beyond the other variables, whereas naming speed did not survive these stringent controls. The results support the sustained importance of these three skills in reading by older readers.

CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis.

Chemotaxis by Bacillus subtilis requires the inter-acting chemotaxis proteins CheC and CheD. In this study, we show that CheD is absolutely required for a behavioural response to proline mediated by McpC but is not required for the response to asparagine mediated by McpB. We also show that CheC is not required for the excitation response to asparagine stimulation but is required for adaptation while asparagine remains complexed with the McpB chemoreceptor. CheC displayed an interaction with the histidine kinase CheA as well as with McpB in the yeast two-hybrid assay, suggesting that the mechanism by which CheC affects adaptation may result from an interaction with the receptor-CheA complex. Furthermore, CheC was found to be related to the family of flagellar switch proteins comprising FliM and FliY but is not present in many proteobacterial genomes in which CheD homologues exist. The distinct physiological roles for CheC and CheD during B. subtilis chemotaxis and the observation that CheD is present in bacterial genomes that lack CheC indicate that these proteins can function independently and may define unique pathways during chemotactic signal transduction. We speculate that CheC interacts with flagellar switch components and dissociates upon CheY-P binding and subsequently interacts with the receptor complex to facilitate adaptation.

CheB is required for behavioural responses to negative stimuli during chemotaxis in Bacillus subtilis.

The methyl-accepting chemotaxis protein, McpB, is the sole receptor mediating asparagine chemotaxis in Bacillus subtilis. In this study, we show that wild-type B. subtilis cells contain approximately 2,000 copies of McpB per cell, that these receptors are localized polarly, and that titration of only a few receptors is sufficient to generate a detectable behavioural response. In contrast to the wild type, a cheB mutant was incapable of tumbling in response to decreasing concentrations of asparagine, but the cheB mutant was able to accumulate to low concentrations of asparagine in the capillary assay, as observed previously in response to azetidine-2-carboxylate. Furthermore, net demethylation of McpB is logarithmically dependent on asparagine concentration, with half-maximal demethylation of McpB occurring when only 3% of the receptors are titrated. Because the corresponding methanol production is exponentially dependent on attractant concentration, net methylation changes and increased turnover of methyl groups must occur on McpB at high concentrations of asparagine. Together, the data support the hypothesis that methylation changes occur on asparagine-bound McpB to enhance the dynamic range of the receptor complex and to enable the cell to respond to a negative stimulus, such as removal of asparagine.

Does PBL Matter? Relations Between Instructional Context, Learning Strategies, and Learning Outcomes.

Purpose: To compare learning strategies used in Problem based learning (PBL) and lectures, and the relations between learning strategies and learning outcomes to determine how different learning strategies associated with PBL and lectures contribute to aspects of clinical competence. Design: The 52-item learning strategies questionnaire was given to preclinical medical students during lecture and PBL sessions in first and third year from 1994 to 1998. Response patterns were compared across the two contexts and factor structures investigated. Regression analyses examined relations between learning strategies and outcomes. Main Outcome Measures/Results: Comparison of responses on the 326 complete pairs of lecture and PBL questionnaires indicated differences at the 0.05 level on 44 of the 52 items. The mean differences were greater than 0.5 (on a 5 point scale) at the 0.001 level for 20 items. Of these, five strategies were used more often in PBL and 15 in lectures. Comparisons of learning strategy use across years showed significant changes with time in both instructional contexts. Principal component analysis revealed a stable factor structure with 4 factors distinctly associated with PBL and 4 factors with the lecture learning context. The remaining 6 factors were mixed and independent of context. Exploratory regression analysis revealed that learning outcomes in examinations were influenced by learning strategies. Multiple choice performance was positively predicted by learning associated with lecture class notes and negatively by group work, whereas the OSCE (objective structured clinical exam) performance was positively predicted by class participation in PBL, self-directed note making and lecture class notes. Conclusion: We have developed a learning strategies questionnaire that shows that students' learning strategies are influenced by instructional context, and patterns of learning strategy use change over time. There is tentative evidence that the students' learning strategies influence learning outcomes.

CheY-dependent methylation of the asparagine receptor, McpB, during chemotaxis in Bacillus subtilis.

For the Gram-positive organism Bacillus subtilis, chemotaxis to the attractant asparagine is mediated by the chemoreceptor McpB. In this study, we show that rapid net demethylation of B. subtilis McpB results in the immediate production of methanol, presumably due to the action of CheB. We also show that net demethylation of McpB occurs upon both addition and removal of asparagine. After each demethylation event, McpB is remethylated to nearly prestimulus levels. Both remethylation events are attributable to CheR using S-adenosylmethionine as a substrate. Therefore, no methyl transfer to an intermediate carrier need be postulated to occur during chemotaxis in B. subtilis as was previously suggested. Furthermore, we show that the remethylation of asparagine-bound McpB requires the response regulator, CheY-P, suggesting that CheY-P acts in a feedback mechanism to facilitate adaptation to positive stimuli during chemotaxis in B. subtilis. This hypothesis is supported by two observations: a cheRBCD mutant is capable of transient excitation and subsequent oscillations that bring the flagellar rotational bias below the prestimulus value in the tethered cell assay, and the cheRBCD mutant is capable of swarming in a Tryptone swarm plate.

Methanol production during chemotaxis to amino acids in Bacillus subtilis.

The 20 common amino acids act as attractants during chemotaxis by the Gram-positive organism Bacillus subtilis. In this study, we report that all amino acids induce B. subtilis to produce methanol both upon addition and removal of the chemoeffector. Asparagine-induced methanol production is specific to the McpB receptor and aspartate-induced methanol production correlates with receptor occupancy. These findings suggest that addition and removal of all amino acids cause demethylation of specific receptors which results in methanol production. We also demonstrate that certain attractants cause greater production of methanol after multiple stimulations. CheC and CheD, while affecting the levels of receptor methylation, are not absolutely required for either methylation or demethylation. In contrast, CheY is necessary for methanol formation upon removal of attractant but not upon addition of attractant. We conclude that methanol formation due to negative stimuli indicates the existence of a unique adaptational mechanism in B. subtilis involving the response regulator, CheY.

Chemotactic methylation and behavior in Bacillus subtilis: role of two unique proteins, CheC and CheD.

We characterized mutants in two novel genes of Bacillus subtilis, cheC and cheD. Mutants in CheC had a high smooth swimming bias and exhibited poor adaptation to positive stimuli. Analysis of tethered cells revealed two distinct subpopulations which differ in their prestimulus bias and extent of adaptation. The receptors, the methyl-accepting chemotaxis proteins (MCPs), of this mutant strain were overmethylated, as a result of an increase in CheR activity. We speculate that CheC helps to control tumbling frequency by regulating CheR, perhaps by a feedback mechanism through the MCPs. In contrast, a cheD mutant exhibited very tumbly behavior, and many of the MCPs were unmethylated. It seems that some B. subtilis MCPs require the presence of CheD for CheR to methylate them, a unique feature of B. subtilis chemotaxis. It is hypothesized that CheD is part of a complex that facilitates methylation of some of the MCPs, and dissociation of CheD from this complex affects CheA activity and may help bring about adaptation.

Cognitive patterns of children with dyslexia: a comparison between groups with high and average nonverbal intelligence.

We tested the hypothesis that children with dyslexia identified by word decoding deficit will be poor in specific cognitive processes that require successive processing and rapid articulation, irrespective of their high or average nonverbal IQ. Children with dyslexia and normally achieving children between 9 years and 11 years of age were divided into four groups comprising average-IQ and high-IQ children with dyslexia and normal readers. All children were administered measures of planning, attention-arousal, simultaneous and successive processes, phonemic segmentation, and nonverbal IQ. Results confirmed the hypothesis: The cognitive tasks that differentiated children with dyslexia from nondyslexic children irrespective of IQ were the successive tasks, as well as two tasks of attention that required articulation and/or phonological coding. Tasks that demanded both phonological coding and articulation correctly classified children with dyslexia and nondyslexic children up to 80%. The importance of remedial training appropriate for alleviating the cognitive and word decoding deficits is discussed.

Chemotactic methylesterase promotes adaptation to high concentrations of attractant in Bacillus subtilis.

The Bacillus subtilis gene encoding CheB (cheBB), the chemotactic methylesterase, has been sequenced. The 39-kDa protein which resulted from the expression of cheBB, using a T7 expression system was consistent with the predicted open reading frame. CheBB shares 39.5% identity with Escherichia coli CheBE and can complement a cheBE null mutant. CheBB is required for removal of methyl groups from the receptors upon attractant stimulus and appears to play an important role in adaptation to the addition of attractants, whereas CheBE plays an important role in adaptation to the addition of repellents. Unlike the cheBE and cheRE mutants of E. coli, which show extreme flagellar rotational biases, the unstimulated cheBB mutant showed a normal (wild type) bias. Upon addition of attractant, the cheBB null mutant showed a counter-clockwise bias that was higher than for wild type and demonstrated only partial adaptation. In the capillary assay for the attractant azetidine-2-carboxylic acid, the mutant gave a wild type response at low concentrations but a very reduced response at high concentrations. We conclude that B. subtilis has an effective methylation-independent adaptation system but must utilize the methylation system for adaptation to high concentrations of attractant.

Novel methyl transfer during chemotaxis in Bacillus subtilis.

If Bacillus subtilis is incubated in radioactive methionine in the absence of protein synthesis, the methyl-accepting chemotaxis proteins (MCPs) become radioactively methylated. If the bacteria are further incubated in excess nonradioactive methionine ("cold-chased") and then given the attractant aspartate, the MCPs lose about half of their radioactivity due to turnover, in which lower specific activity methyl groups from S-adenosylmethionine (AdoMet) replace higher specific activity ones. Due to the cold-chase, the specific activity of the AdoMet pool is reduced at least 2-fold. If, later, the attractant is removed, higher specific activity methyl groups return to the MCPs. Thus, there must exist an unidentified methyl carrier that can "reversibly" receive methyl groups from the MCPs. In a similar experiment, labeled cells were transferred to a flow cell and exposed to addition and removal of attractant and of repellent. All four kinds of stimuli were found to cause methanol production. Bacteria with maximally labeled MCPs were exposed to many cycles of addition and removal of attractant; the maximum amount of radioactive methanol was evolved on the third, not the first, cycle. This result suggests that there is a precursor-product relationship between methyl groups on the MCPs and on the unidentified carrier, which might be the direct source of methanol. However, since no methanol was produced when a methyltransferase mutant, whose MCPs were unmethylated, was exposed to addition and removal of attractant or repellent, the methanol must ultimately derive from methylated MCPs.

Complementation and characterization of chemotaxis mutants of Bacillus subtilis.

A set of chemotaxis mutants of Bacillus subtilis was complemented by using SP beta c2 transducing bacteriophage either containing cloned segments of DNA or derived from abnormal excision of SP beta c2 dl2::Tn917 inserted into the chemotaxis region. Representative mutants were characterized in capillary assays for chemotaxis toward four amino acids and mannitol and in tethered-cell experiments for addition and removal of two attractants and two repellents. Twenty complementation groups were identified, in addition to the cheR previously characterized. All were found to be defective in chemotaxis toward all chemoeffectors. They were assigned the names cheA through cheU. The large number of general chemotaxis genes in B. subtilis, in contrast to the six in Escherichia coli, suggests fundamental differences in the mechanism of chemotaxis in the two species.

Cognitive processes, school achievement, and comprehension of ambiguous sentences.

Previous research has identified three distinct forms of linguistic ambiguity: lexical, surface structural, and deep structural. Cummins and Das (1978) studied these forms of ambiguity in the context of Das, Kirby and Jarman's (1979) model of simultaneous and successive processing, and demonstrated that comprehension of lexical ambiguity depended upon simultaneous processing, while that of surface and deep structural ambiguity depended upon successive processing. The present study investigated the relationship between these cognitive and linguistic processes in a group of older children. The subjects' level of English achievement was also considered. The results showed that comprehension of all three forms of ambiguity was strongly related to level of English achievement, though deep structure ambiguities best descriminated the English achievement groups. Results also showed that perception of all types of ambiguity was related to both simultaneous and successive processing. Subjects with high successive processing scores had an additional advantage in perceiving deep structure ambiguities. These results suggest the need for an elaboration of the Cummins and Das cognitive process model of linguistic processes, demonstrating that a variety of task variables can alter the cognitive processes required in performance of linguistic tasks.