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issn:1742-206
1.  Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes 
Molecular bioSystems  2013;9(7):1627-1631.
When selection is strong and mutations are rare, evolution can be thought of as an uphill trajectory in a rugged fitness landscape. In this context the fitness landscape is a directed acyclic graph in which nodes are genotypes and edges lead from lower to higher fitness genotypes that differ by a single mutation. Because the space of genotypes is vastly multi-dimensional, classification of fitness landscapes is challenging. Many proposed summary characteristics of fitness landscapes attempt to quantify biologically relevant and intuitive notions such as roughness or peak accessibility in alternative ways. Here we explore, in different types of landscapes, the behavior of the recently introduced mean path divergence which quantifies the degree of similarity among evolutionary trajectories with the same endpoints. We find that monotonic trajectories in empirical and model fitness landscapes are significantly more constrained, with low median path divergence, than those in purely additive landscapes. By contrast, transcription factor sequence specificity (aptamer binding affinity) landscapes are markedly smoother and allow substantial variability in monotonic paths that can be greater than that in fully additive landscapes. We propose that the smoothness of the specificity landscapes is a consequence of the simple dependence of the transcription factor binding affinity on the aptamer sequence in contrast to the complex sequence-fitness mapping in folding landscapes.
doi:10.1039/c3mb25553k
PMCID: PMC4325993  PMID: 23460358
2.  Rapid Characterization and Engineering of Natural Product Biosynthetic Pathways via DNA Assembler 
Molecular bioSystems  2011;7(4):1056-1059.
We report a synthetic biology strategy for rapid genetic manipulation of natural product biosynthetic pathways. Based on DNA assembler, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the genetic elements required for DNA maintenance and replication in various hosts in a single-step manner through yeast homologous recombination, offering unprecedented flexibility and versatility in pathway manipulations.
doi:10.1039/c0mb00338g
PMCID: PMC4320646  PMID: 21327279
3.  [No title available] 
PMCID: PMC3898201  PMID: 24301521
4.  [No title available] 
PMCID: PMC3947857  PMID: 24327294
5.  Iodotyrosine Deiodinase: A Unique Flavoprotein Present in Organisms of Diverse Phyla 
Molecular bioSystems  2014;10(1):86-92.
Iodide is required for thyroid hormone synthesis in mammals and other vertebrates. The role of both iodide and iodinated tyrosine derivatives is currently unknown in lower organisms, yet the presence of a key enzyme in iodide conservation, iodotyrosine deiodinase (IYD), is suggested by genomic data from a wide range of multicellular organisms as well as some bacteria. A representative set of these genes has now been expressed, and the resulting enzymes all catalyze reductive deiodination of diiodotyrosine with kcat/Km values within a single order of magnitude. This implies a physiological presence of iodotyrosines (or related halotyrosines) and a physiological role for their turnover. At least for Metazoa, IYD should provide a new marker for tracing the evolutionary development of iodinated amino acids as regulatory signals through the tree of life.
doi:10.1039/c3mb70398c
PMCID: PMC3858845  PMID: 24153409
6.  Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks 
Molecular bioSystems  2014;10(1):45-53.
Wnt signalling is a fundamentally important signalling pathway that regulates many aspects of metazoan development and is frequently dysregulated in cancer. Although many of the core components of the Wnt signalling pathway, such as β-catenin, have been extensively studied, the broad systems level responses of the mammalian cell to Wnt signalling are less well understood. In addition, the cell- or tissue-specific protein networks that modulate Wnt signalling in the diverse tissues or developmental stages in which it functions remain to be defined. To address these questions, we undertook a broad survey of the Wnt response in different human cell lines using both interaction and expression proteomics approaches. Our data reveal both similar and divergent responses of pathways and processes in the three cell-lines analyzed as well as a marked attenuation of the response to exogenous Wnt treatment in cells harbouring a stabilizing (activating) mutation of β-catenin. We also identify cell-type specific components of the Wnt signalling network and find that by integrating expression and interaction proteomics data a more complete description of the Wnt interaction network can be achieved. Finally, our results attest to the power of LCMS/MS to reveal novel cellular responses in even relatively well studied biological pathways such as Wnt signalling.
doi:10.1039/c3mb70417c
PMCID: PMC3909504  PMID: 24201312
7.  Binding Structures and Energies of Human Neonatal Fc Receptor with Human Fc and Its Mutants by Molecular Modeling and Dynamics Simulations 
Molecular bioSystems  2013;9(12):10.1039/c3mb70231f.
Homology modeling and molecular dynamics simulations have been carried out to model the detailed structures of human neonatal Fc receptor (FcRn) binding with wild-type Fc of human immunoglobulin G1 (IgG1) and its various mutants. Based on the modeled human FcRn-Fc binding structures, the protein-protein binding interface is composed of three subsites. The first subsite is a hydrophobic core where residue I39 of human Fc can be accommodated very well, and the other two subsites are all composed of critical salt bridges between human FcRn and human Fc. All of the modeled structures and the calculated binding energies are qualitatively consistent with the available experimental data, suggesting that the modeled human FcRn-Fc binding structures are reasonable. The modeled human FcRn-Fc binding structure may be valuable for future rational design of novel mutants of human Fc and Fc-fused therapeutic proteins with a potentially higher binding affinity for human FcRn and, thus, a longer in vivo half-life in human.
doi:10.1039/c3mb70231f
PMCID: PMC3834255  PMID: 24057047
8.  A Fluorogenic Probe for β-Galactosidase Activity Imaging in Living Cells 
Molecular bioSystems  2013;9(12):10.1039/c3mb70269c.
A cell permeable fluorescence turn-on probe, AcGQCy7, was developed to image β-galactosidase activity in living cells. Once internalized by β-galactosidase-expressing cells, the probe was hydrolyzed into a highly fluorescent molecule, and the fluorescent signal was retained in mitochondria for several days. This resulted in a long-lasting and strong β-galactosidase-dependent intracellular fluorescent signal with little background fluorescence in the culture media.
doi:10.1039/c3mb70269c
PMCID: PMC3836597  PMID: 24056749
β-galactosidase; β-galactopyranoside; fluorogenic; cyanine dye; retro-Knoevenagel reaction; thiol
9.  Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer 
Molecular bioSystems  2013;9(12):10.1039/c3mb70172g.
Although high-grade serous ovarian cancer (OVC) is the most lethal gynecologic malignancy in women, little is known about the regulatory mechanisms in the cellular processes that lead to this cancer. Recently, accumulated lines of evidence have shown that the interplay between transcription factors (TFs) and microRNAs (miRNAs) is critical in cellular regulation during tumorigenesis. A comprehensive investigation of TFs and miRNAs, and their target genes, may provide a deeper understanding of the regulatory mechanisms in the pathology of OVC. In this study, we have integrated three complementary algorithms into a framework, aiming to infer the regulation by miRNAs and TFs in conjunction with gene expression profiles. We demonstrated the utility of our framework by inferring 67 OVC-specific regulatory feed-forward loops (FFL) initiated by miRNAs or TFs in high-grade serous OVC. By analyzing these regulatory behaviors, we found that all the 67 FFLs are consistent in their regulatory effects on genes that jointly targeted by miRNAs and TFs. Remarkably, we unveiled an unbalanced distribution of FFLs with different oncogenic effects. In total, 31 of the 67 coherent FFLs were mainly initiated by oncogenes. On the contrary, only 4 of the FFLs were initiated by tumor suppressor genes. These overwhelmingly observed oncogenic genes were further detected in a sub-network with 32 FFLs centered by miRNA let-7b and TF TCF7L1 to regulate cell differentiation. Closer inspection of 32 FFLs revealed that 75% of the miRNAs reportedly play functional roles in cell differentiation, especially when enriched in epithelial–mesenchymal transitions. This study provides a comprehensive pathophysiological overview of recurring coherent circuits in OVC that are co-regulated by miRNAs and TFs. The prevalence of oncogenic coherent FFLs in serous OVC suggests that oncogene-driven regulatory motifs could cooperatively act upon critical cellular process such as cell differentiation in a highly efficient and consistent manner.
doi:10.1039/c3mb70172g
PMCID: PMC3855196  PMID: 24129674
10.  RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal 
Molecular bioSystems  2013;9(12):10.1039/c3mb70114j.
Reactive electrophiles produced during oxidative stress, such as 4-hydroxynonenal (HNE), are increasingly recognized as contributing factors in a variety of degenerative and inflammatory diseases. Here we used the RNA-seq technology to characterize transcriptome responses in RKO cells induced by HNE at subcytotoxic and cytotoxic doses. RNA-seq analysis rediscovered most of the differentially expressed genes reported by microarray studies and also identified novel gene responses. Interestingly, differential expression detection at the coding DNA sequence (CDS) level helped to further improve the consistency between the two technologies, suggesting the utility and importance of the CDS level analysis. RNA-seq data analysis combining gene and CDS levels yielded an informative and comprehensive picture of gradually evolving response networks with increasing HNE doses, from cell protection against oxidative injury at low dose, initiation of cell apoptosis and DNA damage at middle dose and significant deregulation of cellular functions at high dose. These evolving dose-dependent pathway changes, which cannot be observed by the gene level analysis alone, clearly reveal the HNE cytotoxic effect and are supported by IC50 experiments. Additionally, differential expression at the CDS level provides new insights of isoform regulation mechanisms. Taken together, our data demonstrate the power of RNA-Seq to identify subtle transcriptome changes and to characterize effects induced by HNE through the generation of high-resolution data coupled with differential analysis at both gene and CDS levels.
doi:10.1039/c3mb70114j
PMCID: PMC3864034  PMID: 24056865
11.  Identification and Comparative Analysis of Hepatitis C Virus-Host Cell Protein Interactions 
Molecular bioSystems  2013;9(12):3199-3209.
Hepatitis C virus (HCV) alters the global behavior of the host cell to create an environment conducive to its own replication, but much remains unknown about how HCV proteins elicit these changes. Thus, a better understanding of the interface between the virus and host cell is required. Here we report the results of a large-scale yeast two-hybrid screen to identify protein-protein interactions between HCV genotype 2a (strain JFH1) and cellular factors. Our study identified 112 unique interactions between 7 HCV and 94 human proteins, over 40% of which have been linked to HCV infection by other studies. These interactions develop a more complete picture of HCV infection, providing insight into HCV manipulation of pathways, such as lipid and cholesterol metabolism, that were previously linked to HCV infection and implicating novel targets within microtubule-organizing centers, the complement system and cell cycle regulatory machinery. In an effort to understand the relationship between HCV and related viruses, we compared the HCV 2a interactome to those of other HCV genotypes and to the related dengue virus. Greater overlap was observed between HCV and dengue virus targets than between HCV genotypes, demonstrating the value of parallel screening approaches when comparing virus-host cell interactomes. Using siRNAs to inhibit expression of cellular proteins, we found that five of the ten shared targets tested (CUL7, PCM1, RILPL2, RNASET2, and TCF7L2) were required for replication of both HCV and dengue virus. These shared interactions provide insight into common features of the viral life cycles of the family Flaviviridae.
doi:10.1039/c3mb70343f
PMCID: PMC4171131  PMID: 24136289
virus-host cell; dengue; interactome; yeast two-hybrid; microtubule organizing center
12.  Alkynyl-farnesol reporters for detection of protein S-prenylation in cells 
Molecular bioSystems  2010;7(1):67-73.
Protein S-prenylation is a lipid modification that regulates membrane-protein and protein-protein interactions in cell signaling. Though sites of protein S-prenylation can be predicted based upon conserved C-terminal CaaX or CC/CXC motifs, biochemical detection of protein S-prenylation in cells is still challenging. Herein, we report an alkynyl-isoprenol chemical reporter (alk-FOH) as an efficient substrate for prenyltransferases in mammalian cells that enables sensitive detection of S-farnesylated and S-geranylgeranylated proteins using bioorthogonal ligation methods. Fluorescent detection alleviates the need to deplete cellular isoprenoids for biochemical analysis of S-prenylated proteins and enables robust characterization of S-prenylated proteins, such as effectors that are injected into host cells by bacterial pathogens. This alkynyl-prenylation reporter provides a sensitive tool for biochemical analysis and rapid profiling of prenylated proteins in cells.
doi:10.1039/c0mb00183j
PMCID: PMC4231476  PMID: 21107478
13.  An IgE receptor mimetic peptide (PepE) protects mice from IgE mediated anaphylaxis 
Molecular bioSystems  2013;9(11):2853-2859.
Summary
Crosslinking of receptor-bound Immunoglobulin E (IgE) triggers immediate hypersensitivity reactions including anaphylaxis. Blocking the interaction of IgE with its high-affinity receptor, FcεRI, on mast cells and basophils is an attractive strategy for the treatment of allergies. This approach has seen clinical success using the anti-IgE monoclonal antibody, omalizumab. We recently designed and characterized a novel FcεRI–mimetic peptide (PepE) which contains the two key FcεRI α-chain receptor loops known to interact with the ε-heavy chain of IgE, C′–E and B–C, with an optimized linker for joining them. PepE has high specificity and affinity for IgE, blocks IgE binding to FcεRI and prevents IgE induced mediator release from RBL2H3 cells. We have now investigated the biological effects of this peptide in vivo using a line of mice (BALB/c Il4raF709) very sensitive to IgE-mediated systemic anaphylaxis. IgE-deficient (IgE−/−) Il4raF709 mice were passively sensitized with the anti-DNP IgE monoclonal antibody (SPE-7) and subsequently challenged i.v. with DNP-BSA. Mice receiving a single dose of PepE prior to sensitization with SPE-7 IgE, were fully protected from anaphylaxis while vehicle control-treated mice displayed strong reactions with significant core body temperature drops and elevated levels of mouse mast cell protease-1 (mMCP-1) in the serum. However, PepE had no effect on IgE-mediated anaphylaxis if given after IgE administration in IgE−/− mice, suggesting that PepE can block binding of free IgE to FcεRI but cannot compete with the receptor for already bound IgE in vivo. A single dose of PepE treatment did not protect IgE sufficient mice from IgE mediated anaphylaxis. However, a 3-week long course of PepE treatment protected IgE sufficient Il4raF709 mice from body temperature drops and elevation of serum mMCP-1. Our findings establish the potential of this type of structure for blocking IgE binding to mast cells in vivo and suggest that related peptides might have the potential to attenuate clinical allergic reactions.
doi:10.1039/c3mb70286c
PMCID: PMC3820499  PMID: 24056872
14.  Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis 
Molecular bioSystems  2013;9(11):2785-2797.
Effective monitoring of glucose levels is necessary for patients to achieve greater control over their diabetes. However, only about a quarter of subjects with diabetes who requires close serum glucose monitoring, regularly check their serum glucose daily. One of the potential barriers to patient compliance is the blood sampling requirement. Saliva and its protein contents can be altered in subjects with diabetes, possibly due to changes in glycemic control. We propose here that salivary proteomes of subjects with diabetes may be different based on their glycemic control as reflected in A1C levels. A total of 153 subjects with type 1 or 2 diabetes were recruited. Subjects in each type of diabetes were divided into 5 groups based on their A1C levels; <7, 7–8, 8–9, 9–10, >10. To examine the global proteomic changes associated with A1C, the proteomic profiling of pooled saliva samples from each group was created using label-free quantitative proteomics. Similar proteomic analysis for individual subjects (N=4, for each group) were then applied to examine proteins that may be less abundant in pooled samples. Principle component analysis (PCA) and cluster analysis (p<0.01 and p<0.001) were used to define the proteomic differences. We, therefore, defined the salivary proteomic changes associated with A1C changes. This study demonstrates that differences exist between salivary proteomic profiles in subjects with diabetes based on the A1C levels.
doi:10.1039/c3mb70196d
PMCID: PMC3888809  PMID: 24056972
A1C; Diabetes; Mass Spectrometry; Saliva; Proteome
15.  Molecular imaging of Cathepsin E-positive tumors in mice using a novel protease-activatable fluorescent probe† 
Molecular bioSystems  2011;7(12):3207-3213.
The purpose of this study is to demonstrate the ability of imaging Cathepsin E (Cath E) positive tumors in living animals through selective targeting of Cath E proteolytic activity using a sensitive molecular imaging agent. Methods: a peptide-based Cath E imaging probe and a control probe were synthesized for this study. Human Cath E-positive cancer cells (MPanc96-E) were implanted subcutaneously in nude mice. Tumor-bearing mice were examined in vivo with near-infrared fluorescence (NIRF) imaging at various time points after intravenous injection of the Cath E sensing imaging probe. Excised organs and tissues of interest were further imaged ex vivo. Results: upon specific Cath E proteolytic activation, the NIRF signal of the imaging probe a was converted from an optically quenched initial state to a highly fluorescent active state. Imaging probe a was able to highlight the Cath E-positive tumors as early as 24 h post injection. Fluorescent signal in tumor was 3-fold higher than background. The confined specificity of imaging probe a to tumor associated Cath E was verified by using control imaging probe b. Both in vivo and ex vivo imaging results confirmed the superior selectivity and sensitivity of imaging probe a in Cath E imaging. Conclusions: the small animal studies demonstrated the capability of probe a for imaging Cath E-positive tumors. The developed optical probe could be applied in early diagnostic imaging and guiding subsequent surgical procedure.
doi:10.1039/c1mb05215b
PMCID: PMC4207267  PMID: 21935563
16.  Prediction of RNA binding proteins comes of age from low resolution to high resolution† 
Molecular bioSystems  2013;9(10):10.1039/c3mb70167k.
Networks of protein–RNA interactions is likely to be larger than protein–protein and protein–DNA interaction networks because RNA transcripts are encoded tens of times more than proteins (e.g. only 3% of human genome coded for proteins), have diverse function and localization, and are controlled by proteins from birth (transcription) to death (degradation). This massive network is evidenced by several recent experimental discoveries of large numbers of previously unknown RNA-binding proteins (RBPs). Meanwhile, more than 400 non-redundant protein–RNA complex structures (at 25% sequence identity or less) have been deposited into the protein databank. These sequences and structural resources for RBPs provide ample data for the development of computational techniques dedicated to RBP prediction, as experimentally determining RNA-binding functions is time-consuming and expensive. This review compares traditional machine-learning based approaches with emerging template-based methods at several levels of prediction resolution ranging from two-state binding/non-binding prediction, to binding residue prediction and protein–RNA complex structure prediction. The analysis indicates that the two approaches are complementary and their combinations may lead to further improvements.
doi:10.1039/c3mb70167k
PMCID: PMC3870025  PMID: 23872922
17.  Synthesis and Evaluation of Phosphorodithioate-Based Hydrogen Sulfide Donors 
Molecular bioSystems  2013;9(10):2430-2434.
A series of O-aryl- and alkyl-substituted phosphorodithioates were designed and synthesized as hydrogen sulfide (H2S) donors. H2S released capability of these compounds was evaluated by fluorescence methods. O-aryl substituted donors showed slow and sustained H2S release while O-alkylated compounds showed very weak H2S release capability. We also evaluated donors’ protective effects against hydrogen peroxide (H2O2)-induced oxidative damage in myocytes and donors’ toxicity toward B16BL6 mouse melanoma cells.
doi:10.1039/c3mb70145j
PMCID: PMC3789624  PMID: 23917226
18.  Network representations and methods for the analysis of chemical and biochemical pathways 
Molecular bioSystems  2013;9(9):2189-2200.
Systems biologists increasingly use network representations to investigate biochemical pathways and their dynamic behaviours. In this critical review, we discuss four commonly used network representations of chemical and biochemical pathways. We illustrate how some of these representations reduce network complexity but result in the ambiguous representation of biochemical pathways. We also examine the current theoretical approaches available to investigate the dynamic behaviour of chemical and biochemical networks. Finally, we describe how the critical chemical and biochemical pathways responsible for emergent dynamic behaviour can be identified using network mining and functional mapping approaches.
doi:10.1039/c3mb70052f
PMCID: PMC3755892  PMID: 23857078
19.  Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c4mb00354c Click here for additional data file.  
Molecular Biosystems  2014;10(11):2935-2941.
Transcription control insights using blood ChIP sequencing compendium.
Transcription factors play a key role in the development of a disease. ChIP-sequencing has become a preferred technique to investigate genome-wide binding patterns of transcription factors in vivo. Although this technology has led to many important discoveries, the rapidly increasing number of publicly available ChIP-sequencing datasets still remains a largely unexplored resource. Using a compendium of 144 publicly available murine ChIP-sequencing datasets in blood, we show that systematic bioinformatic analysis can unravel diverse aspects of transcription regulation; from genome-wide binding preferences, finding regulatory partners and assembling regulatory complexes, to identifying novel functions of transcription factors and investigating transcription dynamics during development.
doi:10.1039/c4mb00354c
PMCID: PMC4263230  PMID: 25133983
20.  Multivalency Amplifies the Selection and Affinity of Bradykinin-Derived Peptide for Lipid Nanovesicles 
Molecular bioSystems  2013;9(8):2005-2009.
The trimer of a Bradykinin derivative displayed more than five-fold increase in binding affinity for phosphatidylserine-enriched nanovesicles as compared to its monomeric precursor. The nanovesicle selection is directly correlated to multivalency, which amplified the electrostatic attraction. This strategy may lead to novel molecular probes for detecting highly curved membrane bilayers.
doi:10.1039/c3mb70109c
PMCID: PMC3764994  PMID: 23715428
21.  Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?† †Electronic supplementary information (ESI) available: Supplementary files 1–22 and supplementary Fig. 1–3. See DOI: 10.1039/c4mb00290c Click here for additional data file. Click here for additional data file. Click here for additional data file.  
Molecular Biosystems  2014;10(10):2626-2642.
Mutations in short linear motifs impair the functions of intrinsically disordered proteins in cellular signaling/regulation and contribute substantially to human diseases.
Disease mutations are traditionally thought to impair protein functionality by disrupting the folded globular structure of proteins. However, 22% of human disease mutations occur in natively unstructured segments of proteins known as intrinsically disordered regions (IDRs). This therefore implicates defective IDR functionality in various human diseases including cancer. The functionality of IDRs is partly attributable to short linear motifs (SLiMs), but it remains an open question how much defects in SLiMs contribute to human diseases. A proteome-wide comparison of the distribution of missense mutations from disease and non-disease mutation datasets revealed that, in IDRs, disease mutations are more likely to occur within SLiMs than neutral missense mutations. Moreover, compared to neutral missense mutations, disease mutations more frequently impact functionally important residues of SLiMs, cause changes in the physicochemical properties of SLiMs, and disrupt more SLiM-mediated interactions. Analysis of these mutations resulted in a comprehensive list of experimentally validated or predicted SLiMs disrupted in disease. Furthermore, this in-depth analysis suggests that ‘prostate cancer pathway’ is particularly enriched for proteins with disease-related SLiMs. The contribution of mutations in SLiMs to disease may currently appear small when compared to mutations in globular domains. However, our analysis of mutations in predicted SLiMs suggests that this contribution might be more substantial. Therefore, when analysing the functional impact of mutations on proteins, SLiMs in proteins should not be neglected. Our results suggest that an increased focus on SLiMs in the coming decades will improve our understanding of human diseases and aid in the development of targeted treatments.
doi:10.1039/c4mb00290c
PMCID: PMC4306509  PMID: 25057855
22.  Modeling cholesterol metabolism by gene expression profiling in the hippocampus† 
Molecular bioSystems  2011;7(6):1891-1901.
An important part of the challenge of building models of biochemical reactions is determining reaction rate constants that transform substrates into products. We present a method to derive enzymatic kinetic values from mRNA expression levels for modeling biological networks without requiring further tuning. The core metabolic reactions of cholesterol in the brain, particularly in the hippocampus, were simulated. To build the model the baseline mRNA expression levels of genes involved in cholesterol metabolism were obtained from the Allen Mouse Brain Atlas. The model is capable of replicating the trends of relative cholesterol levels in Alzheimer’s and Huntington’s diseases; and reliably simulated SLOS, desmosterolosis, and Dhcr14/Lbr knockout studies. A sensitivity analysis correctly uncovers the Hmgcr, Idi2 and Fdft1 sites that regulate cholesterol homeostasis. Overall, our model and methodology can be used to pinpoint key reactions, which, upon manipulation, may predict altered cholesterol levels and reveal insights into potential drug therapy targets under diseased conditions.
doi:10.1039/c0mb00282h
PMCID: PMC4105148  PMID: 21451815
23.  Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing 
Molecular bioSystems  2012;8(12):3142-3165.
The mode of action of the bacterial ter cluster and TelA genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages has remained enigmatic for almost two decades. Using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of bacteria. Based on contextual information from conserved gene neighborhoods and domain architectures, we show that the ter gene products and TelA lie at the center of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing. Our analysis suggests that the multiple metal-binding and non-binding TerD paralogs and TerC are likely to constitute a membrane-associated complex, which might also include TerB and TerY, and feature several, distinct metal-binding sites. Versions of the TerB domain might also bind small molecule ligands and link the TerD paralog-TerC complex to biosynthetic modules comprised of phosphoribosyltransferases (PRTases), ATP grasp amidoligases, TIM-barrel carbon-carbon lyases, and HAD phosphoesterases, which are predicted to synthesize novel nucleoside-like molecules. One of the PRTases is also likely to interact with RNA by means of its Pelota/Ribosomal protein L7AE-like domain. The von Willebrand factor A domain protein, TerY, is predicted to be part of a distinct phosphorylation switch, coupling a protein kinase and a PP2C phosphatase. We show, based on the evidence from numerous conserved gene neighborhoods and domain architectures, that both the TerB and TelA domains have been linked to diverse lipid-interaction domains, such as two novel PH-like and the Coq4 domains, in different bacteria and are likely to comprise membrane-associated sensory complexes that might additionally contain periplasmic binding-protein-II and OmpA domains. The TerD and TerB domains and the TerY-associated phosphorylation system are also functionally linked to distinct DNA-processing complexes, which contain proteins with SWI2/SNF2 and RecQ-like helicases, multiple AAA+ ATPases, McrC-N-terminal domain proteins, several restriction endonuclease fold DNases, DNA-binding domains and a type-VII/Esx-like system, which is at the center of a predicted DNA transfer apparatus. These DNA-processing modules and associated genes are predicted to be involved in restriction or suicidal action in response to phages and possibly repairing xenobiotic-induced DNA damage. In some eukaryotes, certain components of the ter system appear to have recruited to function in conjunction with the ubiquitin system and calcium-signaling pathways.
doi:10.1039/c2mb25239b
PMCID: PMC4104200  PMID: 23044854
24.  A methodology to infer gene networks from spatial patterns of expression - An application to fluorescence in situ hybridization images 
Molecular bioSystems  2013;9(7):1926-1930.
The proper functional development of a multicellular organism depends on an intricate network of interacting genes that are expressed in accurate temporal and spatial patterns across different tissues. Complex inhibitory and excitatory interactions among genes control the territorial differences that explain specialized cell fates, embryo polarization and tissues architecture in metazoan. Given the nature of the regulatory gene networks, similarity of expression patterns can identify genes and with similar roles. The inference and analysis of the gene interaction networks through complex networks tools can reveal important aspects of the biological system modeled. Here we suggest an image analysis pipeline to quantify co-localization patterns in in situ hybridization images of Drosophila embryos and, based on these patterns, infer gene networks. We analyze the spatial dispersion of the gene expression and show the gene interaction networks for different developmental stages. Our results suggest that the inference of developmental networks based on spatial expression data are biologically relevant and represents a potential tool for the understanding of animal development.
doi:10.1039/c3mb25475e
PMCID: PMC4099485  PMID: 23591446
25.  Global signatures of protein and mRNA expression levels† 
Molecular bioSystems  2009;5(12):1512-1526.
Cellular states are determined by differential expression of the cell’s proteins. The relationship between protein and mRNA expression levels informs about the combined outcomes of translation and protein degradation which are, in addition to transcription and mRNA stability, essential contributors to gene expression regulation. This review summarizes the state of knowledge about large-scale measurements of absolute protein and mRNA expression levels, and the degree of correlation between the two parameters. We summarize the information that can be derived from comparison of protein and mRNA expression levels and discuss how corresponding sequence characteristics suggest modes of regulation.
doi:10.1039/b908315d
PMCID: PMC4089977  PMID: 20023718

Results 1-25 (219)