Additional file 1: of Parameter identifiability-based optimal observation remedy for biological networks

Theoretical justifications for identifiability gain computation. (PDF 217 kb

Additional file 1: of Structural identifiability of cyclic graphical models of biological networks with latent variables

Identifiability Preservation by Matrix Reduction. This file contains the theoretical justification for the proposed identifiability matrix reduction operations. (PDF 92 kb

Additional file 2: of Structural identifiability of cyclic graphical models of biological networks with latent variables

Proof of Theorem 1. This file includes the details of theoretical derivation of Theorem 1. (PDF 62 kb

Image_1_Alterations of cerebellar white matter integrity and associations with cognitive impairments in schizophrenia.TIF

“Cognitive dysmetria” theory of schizophrenia (SZ) has highlighted that the cerebellum plays a critical role in understanding the pathogenesis and cognitive impairment in SZ. Despite some studies have reported the structural disruption of the cerebellum in SZ using whole brain approach, specific focus on the voxel-wise changes of cerebellar WM microstructure and its associations with cognition impairments in SZ were less investigated. To further explore the voxel-wise structural disruption of the cerebellum in SZ, the present study comprehensively examined volume and diffusion features of cerebellar white matter in SZ at the voxel level (42 SZ vs. 52 controls) and correlated the observed alterations with the cognitive impairments measured by MATRICS Consensus Cognitive Battery. Combing voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) methods, we found, compared to healthy controls (HCs), SZ patients did not show significant alteration in voxel-level cerebellar white matter (WM) volume and tract-wise and skeletonized DTI features. In voxel-wise DTI features of cerebellar peduncles, compared to HCs, SZ patients showed decreased fractional anisotropy and increased radial diffusivity mainly located in left middle cerebellar peduncles (MCP) and inferior cerebellar peduncles (ICP). Interestingly, these alterations were correlated with overall composite and different cognitive domain (including processing speed, working memory, and attention vigilance) in HCs but not in SZ patients. The present findings suggested that the voxel-wise WM integrity analysis might be a more sensitive way to investigate the cerebellar structural abnormalities in SZ patients. Correlation results suggested that inferior and MCP may be a crucial neurobiological substrate of cognition impairments in SZ, thus adding the evidence for taking the cerebellum as a novel therapeutic target for cognitive impairments in SZ patients.</p

Partnership of Arthrobacter and Pimelobacter in Aerobic Degradation of Sulfadiazine Revealed by Metagenomics Analysis and Isolation

In this study, metagenomic analyses were combined with cultivation-based techniques as a nested approach to identify functionally significant bacteria for sulfadiazine biodegradation within enrichment communities. The metagenomic investigations indicated that our previously isolated sulfadiazine degrader, Arthrobacter sp. D2, and another Pimelobacter bacterium concomitantly occurred as most abundant members in the community of an enrichment culture that performed complete sulfadiazine mineralization for over two years. Responses of the enriched populations to sole carbon source alternation further suggested the ability of this Pimelobacter member to grow on 2-amino­pyrimidine, the most prominent intermediate metabolite of sulfadiazine. Taking advantage of this propensity, additional cultivation procedures have enabled the successful isolation of Pimelobacter sp. LG209, whose genomic sequences exactly matched that of the dominant Pimelobacter bacterium in the sulfadiazine enrichment culture. Integration of metagenomic investigations with the physiological characteristics of the isolates conclusively demonstrated that the sulfadiazine mineralization in a long-running enrichment culture was prominently mediated by primary sulfadiazine-degrading specialist strain Arthrobacter sp. D2 in association with the 2-amino­pyrimidine-degrading partner strain Pimelobacter sp. LG209. Here, we provided the first mechanistic insight into microbial interactions in steady sulfadiazine mineralization processes, which will help develop appropriate bioremediation strategies for sulfadiazine-contaminated hotspot sites

Bacterial Community Dynamics and Taxa-Time Relationships within Two Activated Sludge Bioreactors

<div><p>Background</p><p>Biological activated sludge process must be functionally stable to continuously remove contaminants while relying upon the activity of complex microbial communities. However the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community dynamic is the taxa-time relationship (TTR). Although the TTR of animal and plant species has been well documented, knowledge is still lacking in regard to TTR of microbial communities in activated sludge bioreactors.</p><p>Aims</p><p>1) To characterize the temporal dynamics of bacterial taxa in activated sludge from two bioreactors of different scale and investigate factors affecting such dynamics; 2) to evaluate the TTRs of activated sludge microbial communities in two bioreactors of different scale.</p><p>Methods</p><p>Temporal variation of bacterial taxa in activated sludge collected from a full- and lab-scale activated sludge bioreactor was monitored over a one-year period using pyrosequencing of 16S rRNA genes. TTR was employed to quantify the bacterial taxa shifts based on the power law equation <i>S = cT^w</i>.</p><p>Results</p><p>The power law exponent <i>w</i> for the full-scale bioreactor was 0.43 (<i>R²</i> = 0.970), which is lower than that of the lab-scale bioreactor (<i>w</i> = 0.55, <i>R²</i> = 0.971). The exponents for the dominant phyla were generally higher than that of the rare phyla. Canonical correspondence analysis (CCA) result showed that the bacterial community variance was significantly associated with water temperature, influent (biochemical oxygen demand) BOD, bioreactor scale and dissolved oxygen (DO). Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 20.3% of the variance of bacterial communities independently, followed by operational parameters (19.9%) and bioreactor scale (3.6%).</p><p>Conclusions</p><p>Results of this study suggest bacterial community dynamics were likely driven partly by wastewater and operational parameters and provide evidence that the TTR may be a fundamental ecological pattern in macro- and microbial systems.</p></div

Impacts of Multiwalled Carbon Nanotubes on Nutrient Removal from Wastewater and Bacterial Community Structure in Activated Sludge

<div><p>Background</p><p>The increasing use of multiwalled carbon nanotubes (MWCNTs) will inevitably lead to the exposure of wastewater treatment facilities. However, knowledge of the impacts of MWCNTs on wastewater nutrient removal and bacterial community structure in the activated sludge process is sparse.</p><p>Aims</p><p>To investigate the effects of MWCNTs on wastewater nutrient removal, and bacterial community structure in activated sludge.</p><p>Methods</p><p>Three triplicate sequencing batch reactors (SBR) were exposed to wastewater which contained 0, 1, and 20 mg/L MWCNTs. MiSeq sequencing was used to investigate the bacterial community structures in activated sludge samples which were exposed to different concentrations of MWCNTs.</p><p>Results</p><p>Exposure to 1 and 20 mg/L MWCNTs had no acute (1 day) impact on nutrient removal from wastewater. After long-term (180 days) exposure to 1 mg/L MWCNTs, the average total nitrogen (TN) removal efficiency was not significantly affected. TN removal efficiency decreased from 84.0% to 71.9% after long-term effects of 20 mg/L MWCNTs. After long-term exposure to 1 and 20 mg/L MWCNTs, the total phosphorus removal efficiencies decreased from 96.8% to 52.3% and from 98.2% to 34.0% respectively. Further study revealed that long-term exposure to 20 mg/L MWCNTs inhibited activities of ammonia monooxygenase and nitrite oxidoreductase. Long-term exposure to 1 and 20 mg/L MWCNTs both inhibited activities of exopolyphosphatase and polyphosphate kinase. MiSeq sequencing data indicated that 20 mg/L MWCNTs significantly decreased the diversity of bacterial community in activated sludge. Long-term exposure to 1 and 20 mg/L MWCNTs differentially decreased the abundance of nitrifying bacteria, especially ammonia-oxidizing bacteria. The abundance of PAOs was decreased after long-term exposure to 20 mg/L MWCNTs. The abundance of glycogen accumulating organisms (GAOs) was increased after long-term exposure to 1 mg/L MWCNTs.</p><p>Conclusion</p><p>MWCNTs have adverse effects on biological wastewater nutrient removal, and altered the diversity and structure of bacterial community in activated sludge.</p></div

Ordination of nonmetric multidimentional scaling based on OTUs (3% cutoff) identified from a full- (a) and lab-scale (b) bioreactors.

<p>Sample numbers: 1- May 2010, 2- June 2010, 3-July 2010, 4- August 2010, 5-September 2010, 6- October 2010, 7-November 2010, 8-December 2010, 9-January 2011, 10- February 2011, 11-March 2011, 12-April 2011.</p

Canonical correspondence analysis (CCA) of pyrosequencing data and measurable variables in a full- and lab-scale bioreactors.

<p>Arrows indicate the direction and magnitude of measurable variables associated with bacterial community structures. Circles and triangles represent different bacterial community structures from the full- and lab-scale bioreactor, respectively. Samples are named with “F” (Full-scale bioreactor) or “L” (Lab-scale bioreactor) and numbers. Sample numbers: 1- May 2010, 2- June 2010, 3-July 2010, 4- August 2010, 5-September 2010, 6- October 2010, 7-November 2010, 8-December 2010, 9-January 2011, 10- February 2011, 11-March 2011, 12-April 2011.</p

Characterization of the Chemical Composition of Polyisobutylene-Based Oil-Soluble Dispersants by Fluorescence

A novel methodology based on fluorescence quenching measurements is introduced to determine quantitatively the amine content of polyisobutylene succinimide (PIBSI) dispersants used as engine oil-additives. To this end, a series of five PIBSI dispersants were prepared by reacting 2 mol equiv of polyisobutylene succinic anhydride (PIBSA) with 1 mol equiv of hexamethylenediamine (HMDA), diethylenetriamine, triethylenetetramine, tetraethylenepentamine, and pentaethylenehexamine to yield the corresponding <i>b</i>-PIBSI dispersants. After having demonstrated that the presence of hydrogen bonds between the polyamine linker and the succinimide carbonyls of the dispersants prevents the quantitative analysis of the ¹H NMR and FTIR spectra of the dispersants to determine their chemical composition, alternative procedures based on gel permeation chromatography (GPC) and fluorescence quenching were implemented to estimate the amine content of the <i>b</i>-PIBSI dispersants. Taking advantage of the doubling in size that occurs when 2 mol of PIBSA are reacted with 1 mol of HMDA, a combination of GPC and FTIR was employed to follow how the chemical composition and molecular weight distribution of the polymers produced evolved with the reaction of PIBSA and HMDA mixed at different molar ratios. These experiments provided the PIBSA-to-HMDA molar ratio yielding the largest <i>b</i>-PIBSI dispersants and this molar ratio was then selected to prepare the four other dispersants. Having prepared five <i>b</i>-PIBSI dispersants with well-defined secondary amine content, the fluorescence of the succinimide groups was found to decrease with increasing number of secondary amines present in the polyamine linker. This result suggests that fluorescence quenching provides a valid method to determine the chemical composition of <i>b</i>-PIBSI dispersants which is otherwise difficult to characterize by standard ¹H NMR and FTIR spectroscopies