02757nas a2200181 4500008004100000245009500041210006900136260000800205300002300213490000600236520214100242100001902383700001302402700002302415700001402438700001102452856011202463 2005 eng d00aAnalysis of the use of genomic DNA as a universal reference in two channel DNA microarrays0 aAnalysis of the use of genomic DNA as a universal reference in t cMAY aArticle Number. 660 v63 a

Background: DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used, in which all RNA samples are hybridized to a common reference. Genomic DNA is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. However, genomic DNA, comprising of both the sense and anti-sense strands, is unlike the single stranded cDNA usually used in microarray hybridizations. The presence of the antisense strand in the 'reference' leads to reactions between complementary labeled strands in solution and may cause the assay result to deviate from true values. Results: We have developed a mathematical model to predict the validity of using genomic DNA as a reference in the microarray assay. The model predicts that the assay can accurately estimate relative concentrations for a wide range of initial cDNA concentrations. Experimental results of DNA microarray assay using genomic DNA as a reference correlated well to those obtained by a direct hybridization between two cDNA samples. The model predicts that the initial concentrations of labeled genomic DNA strands and immobilized strands, and the hybridization time do not significantly affect the assay performance. At low values of the rate constant for hybridization between immobilized and mobile strands, the assay performance varies with the hybridization time and initial cDNA concentrations. For the case where a microarray with immobilized single strands is used, results from hybridizations using genomic DNA as a reference will correspond to true ratios under all conditions. Conclusion: Simulation using the mathematical model, and the experimental study presented here show the potential utility of microarray assays using genomic DNA as a reference. We conclude that the use of genomic DNA as reference DNA should greatly facilitate comparative transcriptome analysis.

1 aGadgil, Mugdha1 aLian, W.1 aGadgil, Chetan, J.1 aKapur, V.1 aWu, WS uhttps://library.ncl.res.in/content/analysis-use-genomic-dna-universal-reference-two-channel-dna-microarrays01773nas a2200157 4500008004100000245005500041210005500096260000800151300001400159490000700173520128200180100002301462700002301485700002101508856008601529 2005 eng d00aStochastic model for first order reaction networks0 aStochastic model for first order reaction networks cSEP a901–9460 v673 a

A stochastic model for a general system of first-order reactions in which each reaction may be either a conversion reaction or a catalytic reaction is derived. The governing master equation is formulated in a manner that explicitly separates the effects of network topology from other aspects, and the evolution equations for the first two moments are derived. We find the surprising, and apparently unknown, result that the time evolution of the second moments can be represented explicitly in terms of the eigenvalues and projections of the matrix that governs the evolution of the means. The model is used to analyze the effects of network topology and the reaction type on the moments of the probability distribution. In particular, it is shown that for an open system of first-order conversion reactions, the distribution of all the system components is a Poisson distribution at steady state. Two different measures of the noise have been used previously, and it is shown that different qualitative and quantitative conclusions can result, depending on which measure is used. The effect of catalytic reactions on the variance of the system components is also analyzed, and the master equation for a coupled system of first-order reactions and diffusion is derived.

1 aGadgil, Chetan, J.1 aLee, Chang, Hyeong1 aOthmer, Hans, G. uhttps://library.ncl.res.in/content/stochastic-model-first-order-reaction-networks01077nas a2200133 4500008004100000245004800041210004800089260000800137300001000145490000700155520067800162100002300840856008000863 2008 eng d00aStochastic modeling of biological reactions0 aStochastic modeling of biological reactions cJAN a45-550 v883 a

Several biological systems comprise of reaction networks where the low number of molecules makes it inappropriate to completely characterize system behavior using a continuous approach. Biological systems are also characterized by discrete states (e.g. infected, dead) that are not amenable to the use of a continuous descriptor. This review discusses the need for adopting a discrete stochastic modeling approach for analyzing biological reactions networks. Various stochastic simulation procedures and theoretical studies are presented. The challenges in the theoretical and computational analysis of discrete stochastic biological reaction networks are discussed.

1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/stochastic-modeling-biological-reactions00536nas a2200145 4500008004100000022001400041245005600055210005500111260007900166300000600245490000800251100002300259700002100282856008700303 2009 eng d a0360-727500aAutocatalysis: a unit process of biological systems0 aAutocatalysis a unit process of biological systems a3 PARK AVE, NEW YORK, NY 10016-5901 USAbAMER INST CHEMICAL ENGINEERScMAR a80 v1051 aGadgil, Chetan, J.1 aKulkarni, B., D. uhttps://library.ncl.res.in/content/autocatalysis-unit-process-biological-systems-000486nas a2200145 4500008004100000022001400041245004000055210004000095260006800135300001200203490000700215100002300222700002100245856007400266 2009 eng d a0001-154100aAutocatalysis in biological systems0 aAutocatalysis in biological systems a111 RIVER ST, HOBOKEN, NJ 07030 USAbJOHN WILEY & SONS INCcMAR a556-5620 v551 aGadgil, Chetan, J.1 aKulkarni, B., D. uhttps://library.ncl.res.in/content/autocatalysis-biological-systems-000613nas a2200157 4500008004100000245011600041210006900157260000800226300001300234490000600247100001600253700001600269700002300285700001900308856012800327 2009 eng d00aComparison of feature selection and classification combinations for cancer classification using microarray data0 aComparison of feature selection and classification combinations  cJAN a417-431 0 v51 aVijayan, V.1 aBulsara, B.1 aGadgil, Chetan, J.1 aGadgil, Mugdha uhttps://library.ncl.res.in/content/comparison-feature-selection-and-classification-combinations-cancer-classification-using02374nas a2200205 4500008004100000022001400041245013600055210006900191260005700260300001400317490000700331520153100338653003401869653002301903653003601926653002101962653003301983100002302016856012902039 2009 eng d a0092-824000aSize-independent differences between the mean of discrete stochastic systems and the corresponding continuous deterministic systems0 aSizeindependent differences between the mean of discrete stochas a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcOCT a1599-16110 v713 a

In this paper, it is shown that for a class of reaction networks, the discrete stochastic nature of the reacting species and reactions results in qualitative and quantitative differences between the mean of exact stochastic simulations and the prediction of the corresponding deterministic system. The differences are independent of the number of molecules of each species in the system under consideration. These reaction networks are open systems of chemical reactions with no zero-order reaction rates. They are characterized by at least two stationary points, one of which is a nonzero stable point, and one unstable trivial solution (stability based on a linear stability analysis of the deterministic system). Starting from a nonzero initial condition, the deterministic system never reaches the zero stationary point due to its unstable nature. In contrast, the result presented here proves that this zero-state is a stable stationary state for the discrete stochastic system, and other finite states have zero probability of existence at large times. This result generalizes previous theoretical studies and simulations of specific systems and provides a theoretical basis for analyzing a class of systems that exhibit such inconsistent behavior. This result has implications in the simulation of infection, apoptosis, and population kinetics, as it can be shown that for certain models the stochastic simulations will always yield different predictions for the mean behavior than the deterministic simulations.

10aBiochemical reaction kinetics10aContinuous systems10aDeterministic chemical kinetics10aDiscrete systems10aStochastic reaction kinetics1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/size-independent-differences-between-mean-discrete-stochastic-systems-and-corresponding-002918nas a2200193 4500008004100000022001400041245006200055210006100117260008100178300000700259490000600266520225400272100002502526700001802551700001802569700001802587700002302605856009602628 2010 eng d a1745-615000aKinetic model of TBP auto-regulation exhibits bistability0 aKinetic model of TBP autoregulation exhibits bistability a236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLANDbBIOMED CENTRAL LTDcAUG a500 v53 a

Background: TATA Binding Protein (TBP) is required for transcription initiation by all three eukaryotic RNA polymerases. It participates in transcriptional initiation at the majority of eukaryotic gene promoters, either by direct association to the TATA box upstream of the transcription start site or by indirectly localizing to the promoter through other proteins. TBP exists in solution in a dimeric form but binds to DNA as a monomer. Here, we present the first mathematical model for auto-catalytic TBP expression and use it to study the role of dimerization in maintaining the steady state TBP level. Results: We show that the autogenous regulation of TBP results in a system that is capable of exhibiting three steady states: an unstable low TBP state, one stable state corresponding to a physiological TBP concentration, and another stable steady state corresponding to unviable cells where no TBP is expressed. Our model predicts that a basal level of TBP is required to establish the transcription of the TBP gene, and hence for cell viability. It also predicts that, for the condition corresponding to a typical mammalian cell, the high-TBP state and cell viability is sensitive to variation in DNA binding strength. We use the model to explore the effect of the dimer in buffering the response to changes in TBP levels, and show that for some physiological conditions the dimer is not important in buffering against perturbations. Conclusions: Results on the necessity of a minimum basal TBP level support the in vivo observations that TBP is maternally inherited, providing the small amount of TBP required to establish its ubiquitous expression. The model shows that the system is sensitive to variations in parameters indicating that it is vulnerable to mutations in TBP. A reduction in TBP-DNA binding constant can lead the system to a regime where the unviable state is the only steady state. Contrary to the current hypotheses, we show that under some physiological conditions the dimer is not very important in restoring the system to steady state. This model demonstrates the use of mathematical modelling to investigate system behaviour and generate hypotheses governing the dynamics of such nonlinear biological systems.

1 aGokhale, Sucheta, A.1 aRoshan, Reema1 aKhetan, Vivek1 aPillai, Beena1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/kinetic-model-tbp-auto-regulation-exhibits-bistability-001791nas a2200157 4500008004100000022001400041245008500055210006900140260011500209300001200324490000600336520113600342100002001478700002301498856011201521 2010 eng d a1751-884900aRobustness of the drosophila segment polarity network to transient perturbations0 aRobustness of the drosophila segment polarity network to transie aMICHAEL FARADAY HOUSE SIX HILLS WAY STEVENAGE, HERTFORD SG1 2AY, ENGLANDbINST ENGINEERING TECHNOLOGY-IETcMAR a169-1760 v43 a

Continuous and Boolean models for the Drosophila segment polarity network have shown that the system is able to maintain the wild-type pattern when subjected to sustained changes in the interaction parameters and initial conditions. Embryo development is likely to occur under fluctuating environmental conditions. Here, a well-established Boolean model is used to explore the ability of the segment polarity network to resist transient changes. Paths along which alternate unviable states are reached, and hence critical nodes whose state changes lead the system away from the wild-type state, are identified. It is found that the system appears to be more sensitive to changes that involve activation of normally inactive nodes. Through a simulation of the heat shock response, it is shown how a localised perturbation in one parasegment is more deleterious than a global perturbation affecting all parasegments. The sequence of events involved in the recovery of the system from a global transient heat shock condition is identified. Finally, these results are discussed in terms of the robustness of the system response.

1 aSubramanian, K.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/robustness-drosophila-segment-polarity-network-transient-perturbations-001512nas a2200157 4500008004100000245005100041210005100092260000800143300001400151490000600165520103500171100002501206700002101231700002301252856007901275 2011 eng d00aSystems view of the protein expression process0 aSystems view of the protein expression process cDEC a139–1500 v53 a

Many biological processes are regulated by changing the concentration and activity of proteins. The presence of a protein at a given subcellular location at a given time with a certain conformation is the result of an apparently sequential process. The rate of protein formation is influenced by chromatin state, and the rates of transcription, translation, and degradation. There is an exquisite control system where each stage of the process is controlled both by seemingly unregulated proteins as well as through feedbacks mediated by RNA and protein products. Here we review the biological facts and mathematical models for each stage of the protein production process. We conclude that advances in experimental techniques leading to a detailed description of the process have not been matched by mathematical models that represent the details of the process and facilitate analysis. Such an exercise is the first step towards development of a framework for a systems biology analysis of the protein production process.

1 aGokhale, Sucheta, A.1 aNyayanit, Dimpal1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/systems-view-protein-expression-process01914nas a2200157 4500008004100000022001400041245010800055210006900163260011000232300001200342490000600354520121800360100002501578700002301603856013001626 2012 eng d a1742-206X00aAnalysis of miRNA regulation suggests an explanation for `unexpected' increase in target protein levels0 aAnalysis of miRNA regulation suggests an explanation for unexpec aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcDEC a760-7650 v83 a

MicroRNA (miRNA) has been mostly associated with decrease in target protein expression levels. Recently, `unexpected' observations of increase in target protein expression attributed to microRNA regulation have been reported. We formulate a comprehensive model for regulation by miRNA that includes both reversible mRNA-miRNA binding and selective return of RNA. We use this mathematical model incorporating multiple individual steps in the regulation process to study the simultaneous effects of these steps on the target protein level. We show that four dimensionless numbers obtained from 12 rate constants are sufficient to define the relative change in steady state target protein levels. We quantify the range of these numbers for which such pleiotropic increase in protein levels is possible, and interpret the experimental findings in the framework of our model such that the results are no longer unexpected. Finally, we show through stochastic simulation that the nature of the target protein distribution remains unchanged and the relative steady state noise levels are also completely defined by the values of these dimensionless numbers, irrespective of the individual reaction rate constants.

1 aGokhale, Sucheta, A.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/analysis-mirna-regulation-suggests-explanation-unexpected-increase-target-protein-levels-000561nas a2200133 4500008004100000245012000041210006900161260000800230300001200238490000600250100001600256700002300272856013200295 2012 eng d00aMathematical model identifies conditions for 'unexpected' increase in target protein levels due to miRNA regulation0 aMathematical model identifies conditions for unexpected increase cMAR a760-7650 v81 aGokhale, S.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/mathematical-model-identifies-conditions-unexpected-increase-target-protein-levels-due-mirna00858nas a2200241 4500008004100000022001400041245008500055210006900140260009400209300000900303490000800312100001700320700002200337700001400359700001600373700002100389700001600410700001800426700002300444700001300467700002000480856011600500 2012 eng d a0022-202X00aNovel mechanism involved in temporal regulation of skin pigmentation homeostasis0 aNovel mechanism involved in temporal regulation of skin pigmenta a75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USAbEuropean Soc Dermatol Res (ESDR)cSEP aS1280 v1321 aGanju, Parul1 aNatarajan, V., T.1 aSingh, A.1 aVijayan, V.1 aDani, Prachi, P.1 aKar, H., K.1 aNatarajan, K.1 aGadgil, Chetan, J.1 aRani, R.1 aGokhale, R., S. uhttps://library.ncl.res.in/content/novel-mechanism-involved-temporal-regulation-skin-pigmentation-homeostasis-001831nas a2200181 4500008004100000022001400041245009000055210006900145260011000214300001400324490000600338520108900344100002501433700002101458700002701479700002301506856012001529 2012 eng d a1742-206X00aSimple method for incorporating dynamic effects of intronic miRNA mediated regulation0 aSimple method for incorporating dynamic effects of intronic miRN aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcAPR a2145-21520 v83 a

The importance of microRNA (miRNA) in modulating gene expression at the post-transcriptional level is well known. Such regulation has been shown to influence the dynamics of several regulatory networks including the cell cycle. In this study we incorporated regulatory effects of intronic miRNA into an existing mathematical model of the cell cycle through the use of an existing `proxy' protein - the host protein. It was observed that the incorporation of intronic miRNA mediated regulation improved the performance of the model resulting in a closer match to experimental results. To test the universality of this approach we compared the effects of intronic miRNA mediated regulation and host protein mediated regulation. Further, we compared miRNA mediated and protein mediated positive and negative feedback regulations of the target protein. We found that the target protein profiles were predominantly similar. These observations show the applicability of our method for incorporating intronic miRNA mediated dynamic effects in models for regulation of gene expression.

1 aGokhale, Sucheta, A.1 aHariharan, Manoj1 aBrahmachari, Samir, K.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/simple-method-incorporating-dynamic-effects-intronic-mirna-mediated-regulation-000534nas a2200157 4500008004100000245006900041210006900110260000800179300001000187490000600197100001600203700001800219700002300237700001900260856009700279 2013 eng d00aComparison of methods for identifying periodically varying genes0 aComparison of methods for identifying periodically varying genes cSEP a53-700 v91 aVijayan, V.1 aDeshpande, P.1 aGadgil, Chetan, J.1 aGadgil, Mugdha uhttps://library.ncl.res.in/content/comparison-methods-identifying-periodically-varying-genes02546nas a2200349 4500008004100000022001400041245010800055210006900163260008000232300001400312490000800326520137300334653001401707653002001721653001501741653001201756100002501768700001701793700001901810700002001829700001901849700001901868700002601887700001801913700002101931700002101952700002301973700002901996700001602025700002402041856013102065 2014 eng d a0027-842400aIFN-gamma signaling maintains skin pigmentation homeostasis through regulation of melanosome maturation0 aIFNgamma signaling maintains skin pigmentation homeostasis throu a2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USAbNATL ACAD SCIENCEScFEB a2301-23060 v1113 a

Cellular homeostasis is an outcome of complex interacting processes with nonlinear feedbacks that can span distinct spatial and temporal dimensions. Skin tanning is one such dynamic response that maintains genome integrity of epidermal cells. Although pathways underlying hyperpigmentation cascade are recognized, negative feedback regulatory loops that can dampen the activated melanogenesis process are not completely understood. In this study, we delineate a regulatory role of IFN-gamma in skin pigmentation biology. We show that IFN-gamma signaling impedes maturation of the key organelle melanosome by concerted regulation of several pigmentation genes. Withdrawal of IFN-gamma signal spontaneously restores normal cellular programming. This effect in melanocytes is mediated by IFN regulatory factor-1 and is not dependent on the central regulator microphthalmia-associated transcription factor. Chronic IFN-gamma signaling shows a clear hypopigmentation phenotype in both mouse and human skin. Interestingly, IFN-gamma KO mice display a delayed recovery response to restore basal state of epidermal pigmentation after UV-induced tanning. Together, our studies delineate a new spatiotemporal role of the IFN-gamma signaling network in skin pigmentation homeostasis, which could have implications in various cutaneous depigmentary and malignant disorders.

10adetanning10agene regulation10ainterferon10amelanin1 aNatarajan, Vivek, T.1 aGanju, Parul1 aSingh, Archana1 aVijayan, Vinaya1 aKirty, Kritika1 aYadav, Shalini1 aPuntambekar, Shraddha1 aBajaj, Sonali1 aDani, Prachi, P.1 aKar, Hemanta, K.1 aGadgil, Chetan, J.1 aNatarajan, Krishnamurthy1 aRani, Rajni1 aGokhale, Rajesh, S. uhttps://library.ncl.res.in/content/ifn-gamma-signaling-maintains-skin-pigmentation-homeostasis-through-regulation-melanosome-002927nas a2200265 4500008004100000022001400041245007400055210006900129260008000198300000700278490000600285520204200291653003102333653001102364653001002375653001902385653001002404100002402414700002302438700002902461700002202490700002302512700001802535856010802553 2014 eng d a1662-510200aNon-coding RNA interact to regulate neuronal development and function0 aNoncoding RNA interact to regulate neuronal development and func aPO BOX 110, LAUSANNE, 1015, SWITZERLANDbFRONTIERS RESEARCH FOUNDATIONcFEB a470 v83 a

The human brain is one of the most complex biological systems, and the cognitive abilities have greatly expanded compared to invertebrates without much expansion in the number of protein coding genes. This suggests that gene regulation plays a very important role in the development and function of nervous system, by acting at multiple levels such as transcription and translation. In this article we discuss the regulatory roles of three classes of non-protein coding RNAs (ncRNAs)-microRNAs (miRNAs), piwi-interacting RNA (piRNAs) and long-non-coding RNA (lncRNA), in the process of neurogenesis and nervous function including control of synaptic plasticity and potential roles in neurodegenerative diseases. miRNAs are involved in diverse processes including neurogenesis where they channelize the cellular physiology toward neuronal differentiation. miRNAs can also indirectly influence neurogenesis by regulating the proliferation and self renewal of neural stem cells and are dysregulated in several neurodegenerative diseases. miRNAs are also known to regulate synaptic plasticity and are usually found to be co-expressed with their targets. The dynamics of gene regulation is thus dependent on the local architecture of the gene regulatory network (GRN) around the miRNA and its targets. piRNAs had been classically known to regulate transposons in the germ cells. However, piRNAs have been, recently, found to be expressed in the brain and possibly function by imparting epigenetic changes by DNA methylation. piRNAs are known to be maternally inherited and we assume that they may play a role in early development. We also explore the possible function of piRNAs in regulating the expansion of transposons in the brain. Brain is known to express several lncRNA but functional roles in brain development are attributed to a few lncRNA while functions of most of the them remain unknown. We review the roles of some known lncRNA and explore the other possible functions of lncRNAs including their interaction with miRNAs.

10agene expression regulation10alncRNA10amiRNA10anetwork-motifs10apiRNA1 aIyengar, Bharat, R.1 aChoudhary, Ashwani1 aSarangdhar, Mayuresh, A.1 aVenkatesh, K., V.1 aGadgil, Chetan, J.1 aPillai, Beena uhttps://library.ncl.res.in/content/non-coding-rna-interact-regulate-neuronal-development-and-function-002510nas a2200205 4500008004100000022001400041245017400055210006900229260010600298300001200404490000700416520161600423653002602039653002302065653001002088653003602098100002102134700002302155856012602178 2015 eng d a1355-838200aMathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for mRNA0 aMathematical modeling of combinatorial regulation suggests that  a1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USAbCOLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPTcMAR a307-3190 v213 a

MicroRNAs bind to and regulate the abundance and activity of target messenger RNA through sequestration, enhanced degradation, and suppression of translation. Although miRNA have a predominantly negative effect on the target protein concentration, several reports have demonstrated a positive effect of miRNA, i.e., increase in target protein concentration on miRNA overexpression and decrease in target concentration on miRNA repression. miRNA-target pair-specific effects such as protection of mRNA degradation owing to miRNA binding can explain some of these effects. However, considering such pairs in isolation might be an oversimplification of the RNA biology, as it is known that one miRNA interacts with several targets, and conversely target mRNA are subject to regulation by several miRNAs. We formulate a mathematical model of this combinatorial regulation of targets by multiple miRNA. Through mathematical analysis and numerical simulations of this model, we show that miRNA that individually have a negative effect on their targets may exhibit an apparently positive net effect when the concentration of one miRNA is experimentally perturbed by repression/overexpression in such a multi-miRNA multitarget situation. We show that this apparent unexpected effect is due to competition and will not be observed when miRNA interact noncompetitively with the target mRNA. This result suggests that some of the observed unusual positive effects of miRNA may be due to the combinatorial complexity of the system rather than due to any inherently unusual positive effect of the miRNA on its target.

10acombinatorial binding10amathematical model10amiRNA10apost-transcriptional regulation1 aNyayanit, Dimpal1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/mathematical-modeling-combinatorial-regulation-suggests-apparent-positive-regulation-002323nas a2200157 4500008004100000022001400041245010200055210006900157260009100226300002900317490000700346520164400353100002501997700002302022856012002045 2015 eng d a1932-620300aRanking of reactions based on sensitivity of protein noise depends on the choice of noise measure0 aRanking of reactions based on sensitivity of protein noise depen a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcDEC aArticle Number: e01438670 v103 a

Gene expression is a stochastic process. Identification of the step maximally affecting noise in the protein level is an important aspect of investigation of gene product distribution. There are numerous experimental and theoretical studies that seek to identify this important step. However, these studies have used two different measures of noise, viz. coefficient of variation and Fano factor, and have compared different processes leading to contradictory observations regarding the important step. In this study, we performed systematic global and local sensitivity analysis on two models of gene expression to investigate relative contribution of reaction rate parameters to steady state noise in the protein level using both the measures of noise. We analytically and computationally showed that the ranking of parameters based on the sensitivity of the noise to variation in a given parameter is a strong function of the choice of the noise measure. If the Fano factor is used as the noise measure, translation is the important step whereas for coefficient of variation, transcription is the important step. We derived an analytical expression for local sensitivity and used it to explain the distinct contributions of each reaction parameter to the two measures of noise. We extended the analysis to a generic linear catalysis reaction system and observed that the reaction network topology was an important factor influencing the local sensitivity of the two measures of noise. Our study suggested that, for the analysis of contributions of reactions to the noise, consideration of both the measures of noise is important.

1 aGokhale, Sucheta, A.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/ranking-reactions-based-sensitivity-protein-noise-depends-choice-noise-measure-102099nas a2200181 4500008004100000022001400041245008800055210006900143260010300212300001100315490000800326520137100334100003001705700002101735700002101756700002301777856011701800 2016 eng d a0021-925800aIdentification of unintuitive features of sumoylation through mathematical modeling0 aIdentification of unintuitive features of sumoylation through ma a9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USAbAMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INCcAPR a9458-+0 v2913 a

Sumoylation is a multistep, multienzymatic post-translational modification in which a small ubiquitin-like modifier protein (SUMO) is attached to the target. We present the first mathematical model for sumoylation including enzyme mechanism details such as autosumoylation of E2 and multifunctional nature of SENP. Simulations and analysis reveal three nonobvious properties for the long term response, modeled as an open system: (i) the steady state sumoylation level is robust to variation in several enzyme properties; (ii) even when autosumoylation of E2 results in equal or higher activity, the target sumoylation levels are lower; and (iii) there is an optimal SENP concentration at which steady state target sumoylation level is maximum. These results are qualitatively different for a short term response modeled as a closed system, where e.g. sumoylation always decreases with increasing SENP levels. Simulations with multiple targets suggest that the available SUMO is limiting, indicating a possible explanation for the experimentally observed low fractional sumoylation. We predict qualitative differences in system responses at short post-translational and longer transcriptional time scales. We thus use this mechanism-based model to explain system properties and generate testable hypotheses for existence and mechanism of unexpected responses.

1 aPuntambekar, Shraddha, S.1 aNyayanit, Dimpal1 aSaxena, Priyanka1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/identification-unintuitive-features-sumoylation-through-mathematical-modeling02613nas a2200361 4500008004100000245010900041210006900150260000800219490000600227520145100233100001901684700002801703700001701731700002001748700002001768700001701788700001901805700001901824700002001843700001801863700002501881700002101906700002101927700001801948700001801966700002901984700002302013700002102036700002502057700001602082700002402098856012902122 2017 eng d00aMapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo0 aMapping architectural and transcriptional alterations in nonlesi cAUG0 v73 aIn vitiligo, chronic loss of melanocytes and consequent absence of melanin from the epidermis presents a challenge for long-term tissue maintenance. The stable vitiligo patches are known to attain an irreversible depigmented state. However, the molecular and cellular processes resulting in this remodeled tissue homeostasis is unclear. To investigate the complex interplay of inductive signals and cell intrinsic factors that support the new acquired state, we compared the matched lesional and non-lesional epidermis obtained from stable non-segmental vitiligo subjects. Hierarchical clustering of genome-wide expression of transcripts surprisingly segregated lesional and non-lesional samples in two distinct clades, despite the apparent heterogeneity in the lesions of different vitiligo subjects. Pathway enrichment showed the expected downregulation of melanogenic pathway and a significant downregulation of cornification and keratinocyte differentiation processes. These perturbations could indeed be recapitulated in the lesional epidermal tissue, including blunting of rete-ridges, thickening of stratum corneum and increase in the size of corneocytes. In addition, we identify marked increase in the putrescine levels due to the elevated expression of spermine/spermidine acetyl transferase. Our study provides insights into the intrinsic self-renewing ability of damaged lesional tissue to restore epidermal functionality in vitiligo.1 aSingh, Archana1 aGotherwal, Vishvabandhu1 aJunni, Paivi1 aVijayan, Vinaya1 aTiwari, Manisha1 aGanju, Parul1 aKumar, Avinash1 aSharma, Pankaj1 aFatima, Tanveer1 aGupta, Aayush1 aHolla, Ananthaprasad1 aKar, Hemanta, K.1 aKhanna, Sangeeta1 aThukral, Lipi1 aMalik, Garima1 aNatarajan, Krishnamurthy1 aGadgil, Chetan, J.1 aLahesmaa, Riitta1 aNatarajan, Vivek, T.1 aRani, Rajni1 aGokhale, Rajesh, S. uhttps://library.ncl.res.in/content/mapping-architectural-and-transcriptional-alterations-non-lesional-and-lesional-epidermis01945nas a2200169 4500008004100000245010400041210006900145260000800214300001400222490000900236520131200245100002601557700001801583700002201601700002301623856012901646 2017 eng d00aSystematic comparison of the response properties of protein and RNA mediated gene regulatory motifs0 aSystematic comparison of the response properties of protein and  cJUN a1235-12450 v13 3 aWe present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.1 aIyengar, Bharat, Ravi1 aPillai, Beena1 aVenkatesh, K., V.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/systematic-comparison-response-properties-protein-and-rna-mediated-gene-regulatory-motifs02125nas a2200265 4500008004100000022001400041245009000055210006900145260000800214300000800222490000700230520122000237653002401457653002201481653001901503653003301522653004301555653002501598653002401623653002501647100002201672700003001694700002301724856011201747 2018 eng d a1751-884900aMethod for identification of sensitive nodes in boolean models of biological networks0 aMethod for identification of sensitive nodes in boolean models o cFEB a1-60 v123 a

Biological systems are often represented as Boolean networks and analysed to identify sensitive nodes which on perturbation disproportionately change a predefined output. There exist different kinds of perturbation methods: perturbation of function, perturbation of state and perturbation in update scheme. Nodes may have defects in interpretation of the inputs from other nodes and calculation of the node output. To simulate these defects and systematically assess their effect on the system output, two new function perturbations, referred to as not of function' and function of not', are introduced. In the former, the inputs are assumed to be correctly interpreted but the output of the update rule is perturbed; and in the latter, each input is perturbed but the correct update rule is applied. These and previously used perturbation methods were applied to two existing Boolean models, namely the human melanogenesis signalling network and the fly segment polarity network. Through mathematical simulations, it was found that these methods successfully identified nodes earlier found to be sensitive using other methods, and were also able to identify sensitive nodes which were previously unreported.

10abiological networks10aBoolean functions10aBoolean models10afly segment polarity network10ahuman melanogenesis signalling network10aperturbation methods10aPerturbation theory10aphysiological models1 aDnyane, Pooja, A.1 aPuntambekar, Shraddha, S.1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/method-identification-sensitive-nodes-boolean-models-biological-networks02195nas a2200229 4500008004100000022001400041245010600055210006900161260000800230300001000238490000800248520141500256653002501671653001301696653001401709653002301723653002601746100002001772700001901792700002301811856013101834 2022 eng d a0168-165600aMathematical model of the multi-amino acid multi-transporter system predicts uptake flux in CHO cells0 aMathematical model of the multiamino acid multitransporter syste cJAN a40-490 v3443 aSupply and uptake of amino acids is of great importance to mammalian cell culture processes. Mammalian cells such as Chinese hamster ovary (CHO) cells express several amino acid (AA) transporters including uniporters and exchangers. Each transporter transports multiple AAs, making prediction of the effect of changed medium composition or transporter levels on individual AA transport rate challenging. A general kinetic model for such combinatorial amino acid transport, and a simplified analytical expression for the uptake rate as a function of amino acid concentrations and transporter levels is presented. From this general model, a CHO cell-specific AA transport model, to our knowledge the first such network model for any cell type, is constructed. The model is validated by its prediction of reported uptake flux and dependencies from experiments that were not used in model construction or parameter estimation. The model defines theoretical conditions for synergistic/repressive effect on the uptake rates of other AAs upon external addition of one AA. The ability of the CHO-specific model to predict amino acid interdependencies experimentally observed in other mammalian cell types suggests its robustness. This model will help formulate testable hypotheses of the effect of process changes on AA initial uptake, and serve as the AA transport component of kinetic models for cellular metabolism.10aAmino acid transport10aCHO cell10aExchanger10amathematical model10aMultiple transporters1 aSreejan, Ashley1 aGadgil, Mugdha1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/mathematical-model-multi-amino-acid-multi-transporter-system-predicts-uptake-flux-cho-cells02217nas a2200229 4500008004100000022001400041245006300055210006100118260000900179490000800188520152000196653001501716653002301731653002001754653000901774653001801783100002101801700002001822700002301842700002801865856009401893 2022 eng d a0016-673100aSUMOylation of dorsal attenuates Toll/NF-kappa B signaling0 aSUMOylation of dorsal attenuates TollNFkappa B signaling cJUL 0 v2213 a

In Drosophila, Toll/NF-kappa B signaling plays key roles in both animal development and in host defense. The activation, intensity, and kinetics of Toll signaling are regulated by posttranslational modifications such as phosphorylation, SUMOylation, or ubiquitination that target multiple proteins in the Toll/NF-kappa B cascade. Here, we have generated a CRISPR-Cas9 edited Dorsal (DL) variant that is SUMO conjugation resistant. Intriguingly, embryos laid by dl(SCR) mothers overcome dl haploinsufficiency and complete the developmental program. This ability appears to be a result of higher transcriptional activation by DLSCR. In contrast, SUMOylation dampens DL transcriptional activation, ultimately conferring robustness to the dorso-ventral program. In the larval immune response, dl(SCR) animals show an increase in crystal cell numbers, stronger activation of humoral defense genes, and high cactus levels. A mathematical model that evaluates the contribution of the small fraction of SUMOylated DL (1-5%) suggests that it acts to block transcriptional activation, which is driven primarily by DL that is not SUMO conjugated. Our findings define SUMO conjugation as an important regulator of the Toll signaling cascade, in both development and host defense. Our results broadly suggest that SUMO attenuates DL at the level of transcriptional activation. Furthermore, we hypothesize that SUMO conjugation of DL may be part of a Ubc9-dependent mechanism that restrains Toll/NF-kappa B signaling.

10aDrosophila10ahaploinsufficiency10ainnate immunity10aSUMO10atranscription1 aHegde, Sushmitha1 aSreejan, Ashley1 aGadgil, Chetan, J.1 aRatnaparkhi, Girish, S. uhttps://library.ncl.res.in/content/sumoylation-dorsal-attenuates-tollnf-kappa-b-signaling02394nas a2200157 4500008004100000022001400041245010600055210006900161260000800230300001400238490000700252520180100259100002502060700002302085856012802108 2023 eng d a2163-830600aPhysiologically-based pharmacokinetic model for tuberculosis drug disposition at extrapulmonary sites0 aPhysiologicallybased pharmacokinetic model for tuberculosis drug cSEP a1274-12840 v123 a

Tuberculosis (TB) is a leading cause of mortality attributed to an infectious agent. TB primarily targets the lungs, but in about 16% cases can affect other organs as well, giving rise to extrapulmonary TB (EPTB). However, an optimal regimen for EPTB treatment is not defined. Although the recommended treatment for most forms of EPTB is the same as pulmonary TB, the pharmacokinetics of EPTB therapy are not as well studied. To address this gap, we formulate a whole-body physiologically-based pharmacokinetic (PBPK) model for EPTB that for the first time includes the ability to simulate drug concentrations in the pleura and lymph node, the most commonly affected sites of EPTB. Using this model, we estimate the time-dependent concentrations, at potential EPTB infection sites, of the following four first-line anti-TB drugs: rifampicin, ethambutol, isoniazid, and pyrazinamide. We use reported plasma concentration kinetics data to estimate model parameters for each drug and validate our model using reported concentration data not used for model formulation or parameter estimation. Model predictions match the validation data, and reported pharmacokinetic parameters (maximum plasma concentration, time to reach maximum concentration) for the drugs. The model also predicts ethambutol, isoniazid, and pyrazinamide concentrations in the pleura that match reported experimental values from an independent study. For each drug, the predicted drug concentrations at EPTB sites are compared with their critical concentration. Simulations suggest that although rifampicin and isoniazid concentrations are greater than critical concentration values at most EPTB sites, the concentrations of ethambutol and pyrazinamide are lower than their critical concentrations at most EPTB sites.

1 aRamachandran, Aparna1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/physiologically-based-pharmacokinetic-model-tuberculosis-drug-disposition-extrapulmonary02094nas a2200169 4500008004100000022001400041245008200055210006900137260000800206300001200214490000700226520151500233100002001748700002101768700002301789856011201812 2024 eng d a1072-050200aNetwork motifs exhibiting a differential response to spaced and massed inputs0 aNetwork motifs exhibiting a differential response to spaced and  cJUL aa0540120 v313 a

One characteristic of long-term memory is the existence of an inverted U-shaped response to increasing intervals between training sessions, and consequently, an optimal spacing that maximizes memory formation. Current models of this spacing effect focus on specific molecular components and their interactions. Here, we computationally study the underlying network architecture, in particular, the potential of motif dynamics in qualitatively capturing the spacing effect in a manner that is independent of the animal model, biomolecular components, and the timescales involved. We define a common training and test protocol, and computationally identify network topologies that can qualitatively replicate the experimentally observed characteristics of the spacing effect. For 41 motifs derived from fundamental network architectures such as autoregulation, feedback, and feedforward motifs, we tested their capacity to manifest the spacing effect in terms of an inverted U-shaped response curve, using different combinations of stimulation protocols, response metrics, and kinetic parameters. Our findings indicate that positive feedback motifs where the stimulus enhances conversion reaction in the loop replicate the spacing effect across all response metrics, while feedforward motifs exhibit a metric-specific spacing effect. For some parameter combinations, linear cascades of activation and conversion reactions were found sufficient to qualitatively exhibit spacing effect characteristics.

1 aSreejan, Ashley1 aSaxena, Priyanka1 aGadgil, Chetan, J. uhttps://library.ncl.res.in/content/network-motifs-exhibiting-differential-response-spaced-and-massed-inputs02084nas a2200289 4500008004100000022001400041245009100055210006900146260000800215300001600223490000700239520114900246100001701395700001901412700003301431700002201464700001901486700001601505700002501521700001701546700002101563700002301584700002601607700001601633700002501649856012001674 2025 eng d a0022-262300aMycobacteria-specific prodrug to overcome phenotypic AMR in mycobacterium tuberculosis0 aMycobacteriaspecific prodrug to overcome phenotypic AMR in mycob cDEC a24935-249520 v683 a

Most front-line tuberculosis (TB) drugs are ineffective against hypoxic nonreplicating Mycobacterium tuberculosis (Mtb), largely due to poor permeability, leading to reduced drug accumulation and target engagement. To overcome this phenotypic antimicrobial resistance (AMR), we developed nitroheteroaryl prodrugs for Moxifloxacin (MXF), a front-line TB drug. These prodrugs are activated by bacterial nitroreductases (NTR), which are overexpressed in hypoxic Mtb. NTR-mediated electron transfer and protonation facilitate rapid cleavage of the protective group, releasing active MXF. The lead prodrug exhibited comparable efficacy to MXF in replicating Mtb and significantly enhanced lethality in nonreplicating Mtb. Drug accumulation studies confirmed a modest but significant increase in MXF levels in nonreplicating Mtb treated with the prodrug, suggesting improved permeability. A mathematical model integrating growth and drug-killing kinetics further elucidated how permeability differences impact lethality. Together, these findings highlight enzyme-activated prodrugs as a promising strategy to address phenotypic AMR in Mtb

1 aKumar, Anand1 aBirua, Shalini1 aMallojjala, Sharath, Chandra1 aMukherjee, Piyali1 aSingh, Samsher1 aKaul, Grace1 aRamachandran, Aparna1 aAkhir, Abdul1 aChopra, Sidharth1 aGadgil, Chetan, J.1 aHirschi, Jennifer, S.1 aSingh, Amit1 aChakrapani, Harinath uhttps://library.ncl.res.in/content/mycobacteria-specific-prodrug-overcome-phenotypic-amr-mycobacterium-tuberculosis