NETWORKS, BIOLOGY AND SYSTEMS ENGINEERING: A CASE STUDY IN INFLAMMATION

Biological systems can be modeled as networks of interacting components across multiple scales. A central problem in computational systems biology is to identify those critical components and the rules that define their interactions and give rise to the emergent behavior of a host response. In this paper we will discuss two fundamental problems related to the construction of transcription factor networks and the identification of networks of functional modules describing disease progression. We focus on inflammation as a key physiological response of clinical and translational importance.

Validation of new ultrasound parameters for quantifying pelvic floor muscle contraction

OBJECTIVE

To determine the reliability and validity of new ultrasound parameters, measured in the polar coordinate system, for quantifying pelvic floor muscle action.

METHODS

This was a prospective study, from January 2005 to December 2007, in 209 women with urodynamic stress incontinence, to validate new ultrasound parameters for quantifying pelvic floor muscle contraction. The examination of each patient included intravaginal digital palpation of voluntary pelvic floor muscle contractility and an ultrasound assessment of the positions of the bladder neck and anorectal junction at rest and during pelvic floor muscle contraction. The position of the bladder neck was expressed by bladder neck angle and bladder neck distance from the lower border of the pubic symphysis, and the position of the anorectal junction was expressed by the levator hiatal angle and sagittal hiatal diameter. The vector lengths of the motion of the bladder neck and anorectal junction during pelvic floor muscle contraction were calculated from the positions at rest and during pelvic floor muscle contraction by mathematical formulae.

RESULTS

There was good inter- and intraobserver reliability of measurement of ultrasound parameters on stored volumes. During pelvic floor muscle contraction, elevated bladder neck distance and shortened sagittal hiatal diameter were valid parameters representing stronger pelvic floor muscle contractility, with shortened sagittal hiatal diameter having the best correlation (r = - 0.348, P < 0.001).

CONCLUSION

The methods used in this study appear to be reliable for quantifying pelvic floor muscle action. The bladder neck distance with respect to the lower border of the pubic symphysis and the sagittal hiatal diameter were both valid parameters reflecting PFM contractility.

4,4′-(Propane-1,3-diyl)dipiperidinium sulfate monohydrate

In the title compound, C₁₃H₂₈N₂²⁺·SO₄²⁻·H₂O, extensive hydrogen-bonding inter­actions between the protonated 4,4′-(propane-1,3-di­yl)dipiperidinium ions, the sulfate anions and the water mol­ecules lead to a three-dimensional pillared and layered structure with the 4,4′-(propane-1,3-di­yl)­dipiperidinium ions acting as the pillars.

1,4-Diazo-niabicyclo-[2.2.2]octane terephthalate

In the title compound, C₆H₁₄N²⁺·C₈H₄O₄²⁻, the protonated 1,4-diazo­niabicyclo­[2.2.2]octane cations and the deprotonated terephthalate anions are alternately linked by N—H⋯O hydrogen bonds into chains.

Comparative genomics and phylogenetic analysis of S. dysenteriae subgroup

Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading frames, ORFs) of E. coli K12 strain MG1655 and specific ORFs of S. dysenteriae A1 strain Sd51197. The CGH results indicated the genomes of the serotypes contain 2654 conserved ORFs originating from E. coli. However, 219 intrinsic genes of E. coli including those prophage genes, molecular chaperones, synthesis of specific O antigen and so on were absent. Moreover, some specific genes such as type II secretion system associated components, iron transport related genes and some others as well were acquired through horizontal transfer. According to phylogenic trees based on genetic composition, it was demonstrated that A1, A2, A8, A10 were distinct from the other S. dysenteriae serotypes. Our results in this report may provide new insights into the physiological process, pathogenicity and evolution of S. dysenteriae.

Self-assembly of alpha-MnO2 nanorods into spheres: synthesis and electrochemical properties

The alpha-MnO2 spherical assemblies were prepared via a facile hydrothermal approach in the presence of sodium dodecyl sulfate (SDS). The assembled nanostructures were composed of the MnO2 nanorods with 150-200 nm in width and several micrometers in length. The products were characterized by SEM, TEM and XRD. The electrochemical characterization was carried out by cyclic voltammetry, which indicated that the alpha-MnO2 spherical assemblies were of an excellent electrode material for supercapacitor.

Quantification of selected aroma-active compounds in strawberries by headspace solid-phase microextraction gas chromatography and correlation with sensory descriptive analysis

Selected aroma-active compounds in strawberries were quantified using headspace solid-phase microextraction and gas chromatography. Ten strawberry cultivars grown in California and Oregon were studied. The standard curves were built in a synthetic matrix and quantification was achieved using multiple internal standards. Odor activity values (OAVs) of the aroma compounds were calculated to understand their contribution to the overall aroma. Although the concentrations of the aroma compounds varied depending on the cultivars, in general, ethyl butanoate, mesifurane, ethyl hexanoate, ethyl 3-methylbutanoate, hexyl acetate, and gamma-dodecalactone had the highest OAVs. Descriptive sensory analysis was performed by a trained panel of 10 members. A PCA plot was built to understand the aroma contribution of principal components. The chemical results were compared with sensory data. The OAV of esters correlated well with the floral, pineapple, and banana notes. The green notes did not correlate with the concentration or OAVs of aldehydes or C6 alcohols. It is assumed that the higher amounts of green, sulfur, musty, and waxy notes in some cultivars were due to the lack of fruity notes.

Extracting global system dynamics of corticosteroid genomic effects in rat liver

One of the challenges in constructing biological models involves resolving meaningful data patterns from which the mathematical models will be generated. For models that describe the change of mRNA in response to drug administration, questions exist whether the correct genes have been selected given the myriad transcriptional effects that may occur. Oftentimes, different algorithms will select or cluster different groups of genes from the same data set. A new approach was developed that focuses on identifying the underlying global dynamics of the system instead of selecting individual genes. The procedure was applied to microarray genomic data obtained from rat liver after a large single dose of methylprednisolone in 52 adrenalectomized rats. Twelve clusters of at least 30 genes each were selected, reflecting the major changes over time. This method along with isolating the underlying dynamics of the system also extracts and clusters the genes that make up this global dynamic for further analysis as to the contributions of specific mechanisms affected by the drug.

Analysis of time-series gene expression data: methods, challenges, and opportunities

Monitoring the change in expression patterns over time provides the distinct possibility of unraveling the mechanistic drivers characterizing cellular responses. Gene arrays measuring the level of mRNA expression of thousands of genes simultaneously provide a method of high-throughput data collection necessary for obtaining the scope of data required for understanding the complexities of living organisms. Unraveling the coherent complex structures of transcriptional dynamics is the goal of a large family of computational methods aiming at upgrading the information content of time-course gene expression data. In this review, we summarize the qualitative characteristics of these approaches, discuss the main challenges that this type of complex data present, and, finally, explore the opportunities in the context of developing mechanistic models of cellular response.

A novel non-overlapping bi-clustering algorithm for network generation using living cell array data

MOTIVATION

The living cell array quantifies the contribution of activated transcription factors upon the expression levels of their target genes. The direct manipulation of the regulatory mechanisms offers enormous possibilities for deciphering the machinery that activates and controls gene expression. We propose a novel bi-clustering algorithm for generating non-overlapping clusters of reporter genes and conditions and demonstrate how this information can be interpreted in order to assist in the construction of transcription factor interaction networks.

Molecular characterization of serogroup C Neisseria meningitidis isolated in China

An increase in the number of serogroup C meningococcal disease cases occurred in China from September 2003 to January 2006 as a result of several successive outbreaks. In addition, the proportion of serogroup C Neisseria meningitidis isolates from sporadic cases and carriers has also increased. In this study, 113 serogroup C meningococcal isolates were characterized by multilocus sequence typing (MLST) and PorA typing. These isolates comprised those from outbreak cases and their close contacts, the national carriage survey conducted during the same period and some historical isolates from 1966–2002. Twenty MLST sequence types (STs) and 21 PorA variable region (VR) types were identified in the collection. The ST-4821 complex, a newly identified lineage, was the most prevalent lineage (95/113). These data also showed a high level of diversification of serogroup C isolates, as indicated by the number of variants of the ST-4821 clone and the VR types present. There were ten PorA VR types among the ST-4821 isolates, and certain VR types (P1.7-2,14, P1.12-1,16-8) were associated with isolates from outbreak cases. The results of this study allow us to draw a profile of the molecular characteristics of serogroup C strains in China. These data are helpful for monitoring the spread of virulent strains and will provide valuable information for the prevention of bacterial meningitis in China.

Advances of MUC1 as a target for breast cancer immunotherapy

MUC1 is a potential target in breast cancer immunotherapy as MUC1 is overexpressed in breast cancer, and is absent or expressed in low level in normal mammary gland. In addition, MUC1 is mostly aberrantly underglycosylated in cancer and the antigens on the cancer surface are different from normal cell. Therefore targeting MUC1 for cancer immunotherapy can exploit the difference between cancer and normal cells, and eliminating the cancerous cells while leaving the normal mammary cells unharmed. This review will focus on the recent advance of MUC1 breast cancer immunotherapy currently being investigated.

Characterization of serogroup C meningococci isolated from 14 provinces of China during 1966-2005 using comparative genomic hybridization

Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide. In China, serogroup A strains were responsible for over 95% of the cases, while serogroup C strains were only recovered from a few sporadic cases. However, a sudden increase in the number of cases due to serogroup C strains occurred during 2003-2005 in Anhui Province, China. Many cases were found in other provinces at the same time. Multilocus sequence typing (MLST) results indicated that the unique sequence type 4821 clone meningococci, a new hyper-virulent lineage, was responsible for the serogroup C meningitis outbreaks. We have completed the project of sequencing the whole genome of the Chinese N. meningitidis serogroup C representative isolate 053442. We fabricated a whole-genome microarray of N. meningitidis isolate 053442 and analyzed the genome composition differences among 81 serogroup C isolates which were isolated from 14 provinces of China during 1966-2005. The comparative genomic hybridization (CGH) result shows that the genome compositions of nearly all serogroup C isolates are similar to that of 053442. The products of many absent open reading frames (ORFs) are conserved hypothetical proteins. The results will provide a valuable resource from which one can analyze the genome composition and genetic background of serogroup C meningococci in China.

Anti-Cripto Mab inhibit tumour growth and overcome MDR in a human leukaemia MDR cell line by inhibition of Akt and activation of JNK/SAPK and bad death pathways

Doxorubicin (DOX) selection of CCRF-CEM leukaemia cell line resulted in multidrug resistance (MDR) CEM/A7R cell line, which overexpresses MDR, 1 coded P-glycoprotein (Pgp). Here, we report for the first time that oncoprotein Cripto, a founding member of epidermal growth factor-Cripto-FRL, 1-Criptic family is overexpressed in the CEM/A7R cells, and anti-Cripto monoclonal antibodies (Mab) inhibited CEM/A7R cell growth both in vitro and in an established xenograft tumour in severe combined immunodeficiency mice. Cripto Mab synergistically enhanced sensitivity of the MDR cells to Pgp substrates epirubicin (EPI), daunorubicin (DAU) and non-Pgp substrates nucleoside analogue cytosine arabinoside (AraC). In particular, the combination of anti-Cripto Mab at less than 50% of inhibition concentrations with noncytotoxic concentrations of EPI or DAU inhibited more than 90% of CEM/A7R cell growth. Cripto Mab slightly inhibited Pgp expression, and had little effect on Pgp function, indicating that a mechanism independent of Pgp was involved in overcoming MDR. We demonstrated that anti-Cripto Mab-induced CEM/A7R cell apoptosis, which was associated with an enhanced activity of the c-Jun N-terminal kinase/stress-activated protein kinase and inhibition of Akt phosphorylation, resulting in an activation of mitochondrial apoptosis pathway as evidenced by dephosphorylation of Bad at Ser136, Bcl-2 at Ser70 and a cleaved caspase-9.

Image registration in myocardial perfusion MRI

In clinical first-pass myocardial perfusion studies, physiological and patient motions are inevitable. Such motions impair the sensitivity and reliability in assessing myocardial perfusion abnormalities. The current study aims to correct the misregistration of myocardium during first-pass perfusion imaging by using a normalized mutual information approach. Multi-slice registrations were performed in 15 sets of clinical data sets. The proposed registration procedure was found to be fairly robust. With such registration, ROI time courses from normal myocardium and infarcted myocardium were improved, offering potential to quantify myocardial perfusion parameters in a more reliable manner.

catena-Poly[[[cis-aquabis(4-carboxycyclohexane-1-carboxylato-kappa2O,O')cadmium(II)]-mu-4,4'-bipyridine-kappa2N:N] monohydrate]

The title complex, {[Cd(C8H11O4)2(C10H8N2)(H2O)].H2O}(n), consists of linear chains formed through 4,4'-bipyridine ligands linking seven-coordinated Cd(II) ions. Each Cd(II) ion is in a distorted pentagonal-bipyramidal environment, coordinated by one water ligand, two 4-carboxycyclohexane-1-carboxylate ligands and one bridging 4,4'-bipyridine ligand to generate linear chains. The water molecules and the Cd atom on one side, and the 4,4'-bipyridine unit on the other, are bisected by two sets of twofold axes. The carboxylate group of the 4-carboxycyclohexane-1-carboxyl ligand chelates a Cd(II) ion, while the (protonated) carboxyl group forms hydrogen bonds with adjacent chains, resulting in a layered structure. This is the first reported occurrence of a dicarboxycyclohexane ligand exhibiting a non-bridging coordination mode.

The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella

Background

Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all lineages.

Results

For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames (ORFs), with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains.

Conclusion

These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.