Molecular BioSystems

Publications in this journal

• Article: Metabolomic analysis of sun exposed skin.

  Manpreet Randhawa, Michael Southall, Samantha Tucker Samaras
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  ABSTRACT: It is very well known that exposure of skin to sun chronically accelerates the mechanism of aging as well as making it more susceptible toward skin cancer. This aspect of aging has been studied very well through genomics and proteomics tools. In this study we have used a metabolomic approach for the first time to determine the differences in the metabolome from full thickness skin biopsies from sun exposed and sun protected sites. We have primarily investigated the energy metabolism and the oxidative pathway in sun exposed skin. Biochemical pathway analysis revealed that energy metabolism in photoexposed skin is predominantly anaerobic. The study also validated the increased oxidative stress in skin.
  Molecular BioSystems 05/2013;
• Article: In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol.

  Tong Hao, Binbin Han, Hongwu Ma, Jing Fu, Hui Wang, Zhiwen Wang, Bincai Tang, Tao Chen, Xueming Zhao
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  ABSTRACT: Bacillus subtilis is a Gram-positive sporiferous bacterium widely used in a variety of industrial fields as a producer of high-quality vitamins, enzymes and proteins. Many genetic modifications and evolutionary engineering optimisations aiming at obtaining a better performing strain for its products have been studied. As genome-scale metabolic network models have gained significant popularity as effective tools in metabolic phenotype studies, we reconstructed a genome-scale metabolic network of B. subtilis - iBsu1147. The accuracy of iBsu1147 is validated by growth on various carbon sources, single gene knockout and large fragment non-essential gene knockout simulations. The model is used for the in silico metabolic engineering design of reactions over/underexpressed or knockout for increasing the production of four important products of B. subtilis: riboflavin, cellulase Egl-237, (R,R)-2,3-butanediol and isobutanol. The simulation predicted candidate reactions related to the improvement of strain performance on related products. The prediction is partly supported by previously published results. Due to the complexity of the biological system, it is difficult to manually find the factors that are not directly related to the production of the target compounds. The in silico predictions provide more choices for further strain improvement for these products.
  Molecular BioSystems 05/2013;
• Article: Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12.

  Rajalakshmi Srinivasan, Deepti Chandraprakash, Revathy Krishnamurthi, Parul Singh, Vittore F Scolari, Sandeep Krishna, Aswin Sai Narain Seshasayee
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  ABSTRACT: A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.
  Molecular BioSystems 05/2013;
• Article: Development of a novel non-radioactive cell-based method for the screening of SGLT1 and SGLT2 inhibitors using 1-NBDG.

  Hung-Chi Chang, Su-Fu Yang, Ching-Chun Huang, Tzung-Sheng Lin, Pi-Hui Liang, Chun-Jung Lin, Lih-Ching Hsu
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  ABSTRACT: Sodium-coupled glucose co-transporters SGLT1 and SGLT2 play important roles in intestinal absorption and renal reabsorption of glucose, respectively. Blocking SGLT2 is a novel mechanism for lowering the blood glucose level by inhibiting renal glucose reabsorption and selective SGLT2 inhibitors are under development for treatment of type 2 diabetes. Furthermore, it has been reported that perturbation of SGLT1 is associated with cardiomyopathy and cancer. Therefore, both SGLT1 and SGLT2 are potential therapeutic targets. Here we report the development of a non-radioactive cell-based method for the screening of SGLT inhibitors using COS-7 cells transiently expressing human SGLT1 (hSGLT1), CHO-K1 cells stably expressing human SGLT2 (hSGLT2), and a novel fluorescent d-glucose analogue 1-NBDG as a substrate. Our data indicate that 1-NBDG can be a good replacement for the currently used isotope-labeled SGLT substrate, (14)C-AMG. The Michaelis constant of 1-NBDG transport (0.55 mM) is similar to that of d-glucose (0.51 mM) and AMG (0.40 mM) transport through hSGLT1. The IC50 values of a SGLT inhibitor phlorizin for hSGLT1 obtained using 1-NBDG and (14)C-AMG were identical (0.11 μM) in our cell-based system. The IC50 values of dapagliflozin, a well-known selective SGLT2 inhibitor, for hSGLT2 and hSGLT1 determined using 1-NBDG were 1.86 nM and 880 nM, respectively, which are comparable to the published results obtained using (14)C-AMG. Compared to (14)C-AMG, the use of 1-NBDG is cost-effective, convenient and potentially more sensitive. Taken together, a non-radioactive system using 1-NBDG has been validated as a rapid and reliable method for the screening of SGLT1 and SGLT2 inhibitors.
  Molecular BioSystems 05/2013;
• Article: Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

  Mahantesha Naika, Khader Shameer, Ramanathan Sowdhamini
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  ABSTRACT: Biotic and abiotic stresses adversely affect agriculture by reducing crop growth and productivity worldwide. To investigate the abiotic stress-responsive genes in Arabidopsis thaliana, we compiled a dataset of stress signals and differentially upregulated genes (>= 2.5 fold change) from Stress-responsive transcription Factors DataBase (STIFDB) with additional set of stress signals and genes curated from PubMed and Gene Expression Omnibus. A dataset of 3091 genes differentially upregulated due to 14 different stress signals (abscisic acid, aluminum, cold, cold-drought-salt, dehydration, drought, heat, iron, light, NaCl, osmotic stress, oxidative stress, UV-B and wounding) were curated and used for the analysis. Details about stress-responsive enriched genes and their association with stress signals can be obtained from STIFDB2 database . The gene-stress-signal data were analyzed using an enrichment-based meta-analysis framework consisting of two different ontologies (Gene Ontology and Plant Ontology), biological pathway and functional domain annotations. We found several shared and distinct biological processes, cellular components and molecular functions associated with stress-responsive genes. Pathway analysis revealed that stress-responsive genes perturbed the pathways under the "Metabolic pathways" category. We also found several shared and stress-signal specific protein domains, suggesting functional mechanisms regulating stress-response. Phenomic characteristics of abiotic stress-responsive genes were ascertained for several stresses and found to be shared by multiple stresses in both anatomy and temporal categories of Plant Ontology. We found several constitutive stress-responsive genes that are differentially upregulated due to perturbation of different stress signals, for example a gene (AT1G68440) involved in phenylpropanoid metabolism and polyamine catabolism as responsive to seven different stress signals. We also performed structure-function prediction of five genes associated responsive to multiple abiotic stress signals. We envisage that results from our analysis that provide insight into functional repertoire, metabolic pathways and phenomic characteristics common and specifically associated with stress signals would help to understand abiotic stress regulome in Arabidopsis thaliana and may also help to develop an improved plant variety using molecular breeding and genetic engineering techniques that are rapidly stress-responsive and tolerant.
  Molecular BioSystems 05/2013;
• Article: Urea in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD).

  Alexander K H Weiss, Thomas S Hofer
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  ABSTRACT: This work presents a quantum mechanical charge field-molecular dynamics (QMCF-MD) simulation of urea in dilute aqueous solution. Detailed data for structure and dynamics are provided and compared to previous works of other groups. Radial and angular distributions are employed, as well as higher degree spatial investigations, two-dimensional particle mapping, volume maps and the previously proposed SLICE formalism. Information on dynamical properties are presented in the form of hydrogen bond correlation functions and mean lifetime analysis based on weighted Voronoi decomposition. Dihedral and tilt/theta angle distributions substantiate the previous findings of other groups, that urea is far from being planar within aqueous solution. In addition to the analysis of the complete hydration shell, several specific regions of hydration have been identified, for which individual analysis has been performed in terms of hydrogen bond lifetime correlation functions and re-orientational times. A decomposition study based on Laguerre tessellation further investigates the structure and dynamics of the individual hydration layers. It is found that urea does not show properties found in the case of typical structure breaking agents, such as Rb(+) or Cs(+), which is in accordance with spectroscopic data of Rezus and Bakker.
  Molecular BioSystems 05/2013;
• Article: Information content and scalability in signal transduction network reconstruction formats.

  Magdalena Rother, Ulrike Münzner, Sebastian Thieme, Marcus Krantz
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  ABSTRACT: One of the first steps towards holistic understanding of cellular networks is the integration of the available information in a human and machine readable format. This network reconstruction process is well established for metabolic networks, and numerous genome wide metabolic reconstructions are already available. Extending these strategies to signalling networks has proven difficult, primarily due to the combinatorial nature of regulatory modifications. The combinatorial nature of possible protein-protein interactions and post translational modifications affects both network size and the correspondence between the reconstructed network and the underlying empirical data. Here, we discuss different approaches to reconstruction of signal transduction networks. We divide the current approaches into topological, specific state based and reaction-contingency based, and discuss their different information content and scalability. The discussion focusses on graphical formats but the points are in general applicable also to mathematical models and databases. While the formats have complementary strengths especially for small networks, reaction-contingency based formats have a number of advantages in the light of global network reconstruction. In particular, they minimise the need for assumptions, maximise the congruence with empirical data, and scale efficiently with network size.
  Molecular BioSystems 05/2013;
• Article: Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis.

  Sharad K Gupta, Souvik Sur, Rajendra Prasad Ojha, Vibha Tandon
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  ABSTRACT: This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA·DNA duplex showed enhanced stability as compared to normal duplex (A-PNA·DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d)pyrimidine moiety (DPP) stabilized the PNA·DNA hybrids compared to A-PNA·DNA. DPP-PNA·DNA duplex showed higher water activity (Δnw = 38.5) in comparison to A-PNA·DNA duplex (Δnw = 14.5). The 50 ns molecular dynamics simulations of PNA·DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 Å (OH-N bond) and 2.91 Å (NH-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 Å (OH-N bond) and 2.97 Å (NH-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 Å (O2H-N2 bond), supporting the higher stability of DPP-PNA·DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA·DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA·DNA duplex make it a better candidate as antisense/antigene therapeutic agents.
  Molecular BioSystems 05/2013;
• Article: Human cathelicidin peptide LL37 binds telomeric G-quadruplex.

  Jagannath Jana, Rajiv Kumar Kar, Anirban Ghosh, Atanu Biswas, Surajit Ghosh, Anirban Bhunia, Subhrangsu Chatterjee
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  ABSTRACT: Stabilization of G-quadruplex inhibits the activity of the enzyme telomerase in cancer cells. We found LL37, a host defense human cathelicidin antimicrobial peptide, to be a potent binder of G-quadruplex structures.
  Molecular BioSystems 05/2013;
• Article: Exploring higher-order EGFR oligomerisation and phosphorylation-a combined experimental and theoretical approach.

  Noga Kozer, Dipak Barua, Suzanne Orchard, Eduoard C Nice, Antony W Burgess, William S Hlavacek, Andrew H A Clayton
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  ABSTRACT: The epidermal growth factor receptor (EGFR) kinase is generally considered to be activated by either ligand-induced dimerisation or a ligand-induced conformational change within pre-formed dimers. Ligand-induced higher-order EGFR oligomerisation or clustering has been reported but it is not clear how EGFR oligomers, as distinct from EGFR dimers, influence signaling outputs. To address this question, we combined measures of receptor clustering (microscopy; image correlation spectroscopy) and phosphorylation (Western blots) with modelling of mass-action chemical kinetics. A stable BaF/3 cell-line that contains a high proportion (>90%) of inactive dimers of EGFR-eGFP but no secreted ligand and no other detectable ErbB receptors was used as the model cell system. EGF at concentrations of greater than 1 nM was found to cluster EGFR-eGFP dimers into higher-order complexes and cause parallel increases in EGFR phosphorylation. The kinetics of EGFR clustering and phosphorylation were both rapid, plateauing within 2 minutes after stimulation with 30 nM EGF. A rule-based model was formulated to interpret the data. This model took into account ligand binding, ligand-induced conformational changes in the cytosolic tail, monomer-dimer-trimer-tetramer transitions via ectodomain- and kinase-mediated interactions, and phosphorylation. The model predicts that cyclic EGFR tetramers are the predominant phosphorylated species, in which activated receptor dimers adopt a cyclic side-by-side orientation, and that receptor kinase activation is stabilised by the intramolecular interactions responsible for cyclic tetramerization.
  Molecular BioSystems 04/2013;
• Article: Digital and analogical reality in proteomics investigation.

  Andrea Urbani, Massimo Castagnola, Mauro Fasano, Luca Bini, Alessandra Modesti, Anna Maria Timperio, Paola Roncada
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  ABSTRACT: Are protein functions continuous or discretized? Proteomics investigations are starting to address this non-trivial awesome question focusing upon determining the nature of biological molecular relationships. In the following editorial we present a number of experimental studies published in this themed Proteomics Issue demonstrating the development of a new analogical vision for the interpretation of genotype-phenotype relationships. New metrics and languages are evolving, which may complement the insufficiency based on a binary digital interpretation of biological phenomena, providing new tools for the interpretation of large scale-experimental studies.
  Molecular BioSystems 04/2013;
• Article: Proteomic analysis of temperature stress-responsive proteins in Arabidopsis thaliana rosette leaves.

  Mariapina Rocco, Simona Arena, Giovanni Renzone, Gabriella Stefania Scippa, Tonia Lomaglio, Francesca Verrillo, Andrea Scaloni, Mauro Marra
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  ABSTRACT: Plants, as sessile organisms, are continuously exposed to temperature changes in the environment. Low and high temperature stresses have a great impact on agricultural productivity, since they significantly alter plant metabolism and physiology. Plant response to temperature stress is a quantitative character, being influenced by the degree of stress, time of exposure, as well as plant adaptation ability; it involves profound cellular changes at the proteomic level. We describe here the quantitative variations of the protein repertoire of Arabidopsis thaliana rosette leaves after exposing seedlings to either short-term cold or heat temperature stress. A proteomic approach, based on two-dimensional electrophoresis and MALDI-TOF peptide mass fingerprinting and/or nanoLC-ESI-LIT-MS/MS experiments, was used for this purpose. The comparison of the resulting proteomic maps highlighted proteins showing quantitative variations induced by temperature treatments. Thirty-eight protein spots exhibited significant quantitative changes under at least one stress condition. Identified, differentially-represented proteins belong to two main broad functional groups, namely energy production/carbon metabolism and response to abiotic and oxidative stresses. The role of the identified proteins is discussed here in relation to plant adaptation to cold or heat stresses. Our results suggest a significant overlapping of the responses to opposite temperature extremes.
  Molecular BioSystems 04/2013;
• Article: Genome-scale reconstruction and in silico analysis of Aspergillus terreus metabolism.

  Jie Liu, Qian Gao, Nan Xu, Liming Liu
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  ABSTRACT: Aspergillus terreus is widely used for industrial production of important chemical compounds such as itaconate and lovastatin. To improve understanding of its physiology, we reconstructed a genome-scale metabolic model, iJL1454, consisting of 1454 genes, 1451 reactions and 1155 metabolites, based on genome annotation and literature mining. The model accurately predicted the growth phenotype of A. terreus on different carbon and nitrogen sources, and after deletion of essential genes. In iJL1454, 69 and 20 (a subset of the 69) genes were identified as growth essential in minimal and rich mediums, respectively. Ten of the genes had previously been suggested as essential by experimental observations. The biosynthetic pathway of itaconate from glucose, in particular the coding genes and the transporters, was elucidated. The pathway included 29 reactions and 55 genes. To guide metabolic engineering, we investigated bottleneck reactions in itaconate production and the effect of perturbations of nutrient and environmental conditions. The results illustrate the value of model iJL1454 as a tool to understand and optimize A. terreus metabolism.
  Molecular BioSystems 04/2013;
• Article: Identification of calcium binding sites on calsequestrin 1 and their implications for polymerization.

  Amit Kumar, Harapriya Chakravarty, Naresh C Bal, Tuniki Balaraju, Nivedita Jena, Gauri Misra, Chandralata Bal, Enrico Pieroni, Muthu Periasamy, Ashoke Sharon
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  ABSTRACT: Biophysical studies have shown that each molecule of calsequestrin 1 (CASQ1) can bind about 70-80 Ca(2+) ions. However, the nature of Ca(2+)-binding sites has not yet been fully characterized. In this study, we employed in silico approaches to identify the Ca(2+) binding sites and to understand the molecular basis of CASQ1-Ca(2+) recognition. We built the protein model by extracting the atomic coordinates for the back-to-back dimeric unit from the recently solved hexameric CASQ1 structure (PDB id: ) and adding the missing C-terminal residues (aa350-364). Using this model we performed extensive 30 ns molecular dynamics simulations over a wide range of Ca(2+) concentrations ([Ca(2+)]). Our results show that the Ca(2+)-binding sites on CASQ1 differ both in affinity and geometry. The high affinity Ca(2+)-binding sites share a similar geometry and interestingly, the majority of them were found to be induced by increased [Ca(2+)]. We also found that the system shows maximal Ca(2+)-binding to the CAS (consecutive aspartate stretch at the C-terminus) before the rest of the CASQ1 surface becomes saturated. Simulated data show that the CASQ1 back-to-back stacking is progressively stabilized by the emergence of an increasing number of hydrophobic interactions with increasing [Ca(2+)]. Further, this study shows that the CAS domain assumes a compact structure with an increase in Ca(2+) binding, which suggests that the CAS domain might function as a Ca(2+)-sensor that may be a novel structural motif to sense metal. We propose the term "Dn-motif" for the CAS domain.
  Molecular BioSystems 04/2013;
• Article: Social networks to biological networks: systems biology of Mycobacterium tuberculosis.

  Rohit Vashisht, Anshu Bhardwaj, Osdd Consortium, Samir K Brahmachari
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  ABSTRACT: Contextualizing relevant information to construct a network that represents a given biological process presents a fundamental challenge in the network science of biology. The quality of network for the organism of interest is critically dependent on the extent of functional annotation of its genome. Mostly the automated annotation pipelines do not account for unstructured information present in volumes of literature and hence large fraction of genome remains poorly annotated. However, if used, this information could substantially enhance the functional annotation of a genome, aiding the development of a more comprehensive network. Mining unstructured information buried in volumes of literature often requires manual intervention to a great extent and thus becomes a bottleneck for most of the automated pipelines. In this review, we discuss the potential of scientific social networking as a solution for systematic manual mining of data. Focusing on Mycobacterium tuberculosis, as a case study, we discuss our open innovative approach for the functional annotation of its genome. Furthermore, we highlight the strength of such collated structured data in the context of drug target prediction based on systems level analysis of pathogen.
  Molecular BioSystems 04/2013;
• Article: Application of proteomics technology in adipocyte biology.

  Johan Renes, Edwin Mariman
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  ABSTRACT: Obesity and its associated complications have reached epidemic proportions in Western-type societies. Concomitantly, the obesity incidence in developing countries is increasing. One hallmark of obesity is the differentiation of pre-adipocytes into mature triglyceride-loaded adipocytes present in subcutaneous and visceral adipose tissue depots. This may ultimately lead to dysfunctional adipose tissue together with detrimental changes in the profiles of (pre-)adipocyte-secreted proteins, known as adipokines. Obesity-induced alterations in adipokine profiles contribute to the development of obesity-associated disorders. Consequently, the interest in the molecular events responsible for adipose tissue modifications during weight gain and weight loss as well as in the aetiology of obesity-associated disorders is growing. Molecular mechanisms involved in pre-adipocyte differentiation and alterations in adipokine profiles have been examined at the gene and protein level by high-throughput technologies. Independent proteomics studies have contributed significantly to further insight into adipocyte biology, particularly with respect to adipokine profiling. In this review novel findings obtained with adipo-proteomics studies are highlighted and the relevance of proteomics technologies to further understand molecular aspects of adipocyte biology is discussed.
  Molecular BioSystems 04/2013;
• Article: Crosstalk between salicylic acid and jasmonate in Arabidopsis investigated by an integrated proteomic and transcriptomic approach.

  Silvia Proietti, Laura Bertini, Anna Maria Timperio, Lello Zolla, Carlo Caporale, Carla Caruso
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  ABSTRACT: Resistance conferred by biotrophic pathogens often requires salicylic acid (SA) signaling, whereas necrotrophic pathogens or wounding mainly activate the jasmonate/ethylene (JA/ET)-dependent pathway. Crosstalk connections between these two independent signaling pathways may lead to synergistic or antagonistic behavior. In order to shed some light on the crosstalk between these two hormones in Arabidopsis plants, a proteomic approach combined with a transcriptomic analysis has been used to identify molecules differentially expressed upon single or simultaneous treatment with both phytohormones. Twenty-five nonredundant differential proteins were revealed upon treatment with SA or JA alone or in combination, which are involved in general metabolic processes as well as in response to stress, in developmental processes, in protein metabolism and transport. Interestingly, gene expression study, carried out on genes involved in oxidative stress and in biotic and/or abiotic stress, highlighted the correspondence between proteomic and transcriptomic approaches, performed here by RT-PCR. Our data clearly demonstrate that almost all genes/proteins involved in oxidative stress as well as in biotic and/or abiotic stress are mainly induced upon JA treatment and only a few of them are overexpressed upon SA treatment. Moreover, we found that a substantially negative crosstalk is established upon the combined action of the two hormones and that generally SA exerts a negative crosstalk compared to the JA pathway. Our study corroborates the hypothesis that the combination of both phytohormones induces reprogramming of the plant transcriptome, but at the same time highlights the presence of a complex network of signaling that is far to be completely elucidated.
  Molecular BioSystems 04/2013;
• Article: Synthesizing oncogenic signal-processing systems that function as both "signal counters" and "signal blockers" in cancer cells.

  Yuchen Liu, Weiren Huang, Dexi Zhou, Yonghua Han, Yonggang Duan, Xiaoyue Zhang, Hu Zhang, Zhimao Jiang, Yaoting Gui, Zhiming Cai
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  ABSTRACT: RNA-protein interaction plays a significant role in regulating eukaryotic translation. This phenomenon raises questions about the ability of artificial biological systems to take the advantage of protein-RNA interaction. Here, we designed an oncogenic signal-processing system expressing both a Renilla luciferase reporter gene controlled by RNA-protein interaction in its 5'-untranslated region (5'-UTR) and a Firefly luciferase normalization gene. To test the ability of the designed system, we then constructed vectors targeting the nuclear factor-κB (NF-κB) or the β-catenin signal. We found that the inhibition (%) of luciferase expression was correlated to the targeted protein content, allowing quantitative measurement of oncogenic signal intensity in cancer cells. The systems inhibited the expression of oncogenic signal downstream genes and induced bladder cancer cell proliferation inhibition and apoptosis without affecting normal urothelial cells. Compared to traditional methods (ELISA and quantitative immunoblotting), the bio-systems provided highly accurate, consistent, and reproducible quantification of protein signals and were able to discriminate between cancerous and non-cancerous cells. In conclusion, the synthetic systems function as both "signal counters" and "signal blockers" in cancer cells. This approach provides a synthetic biology platform for oncogenic signal measurement and cancer treatment.
  Molecular BioSystems 04/2013;
• Article: Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.

  Dobril K Ivanov, Irene Papatheodorou, Matthias Ziehm, Janet M Thornton
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  ABSTRACT: Several components have been previously identified, that modulate longevity in several species, including the target of rapamycin (TOR) and the Insulin/IGF-1 (IIS) signalling pathways. In order to infer paths and transcriptional feedback loops that are likely to modulate ageing, we manually built a comprehensive and computationally efficient signalling network model of the IIS and TOR pathways in worms. The core insulin transduction is signalling from the sole insulin receptor daf-2 to ultimately inhibit the translocation of the transcription factor daf-16 into the nucleus. Reduction in this core signalling is thought to increase longevity in several species. In addition to this core insulin signalling, we have also recorded in our worm model the transcription factors skn-1 and hif-1, those are also thought to modulate ageing in a daf-16 independent manner. Several paths that are likely to modulate ageing were inferred via a web-based service NetEffects, by utilising perturbed components (rheb-1, let-363, aak-2, daf-2;daf-16 and InR;foxo in worms and flies respectively) from freely available gene expression microarrays. These included "routes" from TOR pathway to transcription factors daf-16, skn-1, hif-1 and daf-16 independent paths via skn-1/hif-1. Paths that could be tested by experimental hypotheses, with respect to relative contribution to longevity, are also discussed. Direct comparison of the IIS and TOR pathways in both worm and fly suggest a remarkable similarity. While similarities in the paths that could modulate ageing in both organisms were noted, differences are also discussed. This approach can also be extended to other pathways and processes.
  Molecular BioSystems 04/2013;
• Article: Genomics and proteomics in solving brain complexity.

  Beena M Kadakkuzha, Sathyanarayanan V Puthanveettil
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  ABSTRACT: The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections. Neurons are organized into circuit assemblies that are modulated by specific interneurons and non-neuronal cells, such as glia and astrocytes. Data on human genome sequences predicts that each of these cells in the human brain has the potential of expressing ∼20 000 protein coding genes and tens of thousands of noncoding RNAs. A major challenge in neuroscience is to determine (1) how individual neurons and circuitry utilize this potential during development and maturation of the nervous system, and for higher brain functions such as cognition, and (2) how this potential is altered in neurological and psychiatric disorders. In this review, we will discuss how recent advances in next generation sequencing, proteomics and bioinformatics have transformed our understanding of gene expression and the functions of neural circuitry, memory storage, and disorders of cognition.
  Molecular BioSystems 04/2013;