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  1. Article ; Online: Joint inference of physiological network and survival analysis identifies factors associated with aging rate.

    Sethi, Anurag / Melamud, Eugene

    Cell reports methods

    2022  Volume 2, Issue 12, Page(s) 100356

    Abstract: We describe methodology for joint reconstruction of physiological-survival networks from observational data capable of identifying key survival-associated variables, inferring a minimal physiological network structure, and bridging this network to the ... ...

    Abstract We describe methodology for joint reconstruction of physiological-survival networks from observational data capable of identifying key survival-associated variables, inferring a minimal physiological network structure, and bridging this network to the Gompertzian survival layer. Using synthetic network structures, we show that the method is capable of identifying aging variables in cohorts as small as 5,000 participants. Applying the methodology to the observational human cohort, we find that interleukin-6, vascular calcification, and red-blood distribution width are strong predictors of baseline fitness. More important, we find that red blood cell counts, kidney function, and phosphate level are directly linked to the Gompertzian aging rate. Our model therefore enables discovery of processes directly linked to the aging rate of our species. We further show that this epidemiological framework can be applied as a causal inference engine to simulate the effects of interventions on physiology and longevity.
    MeSH term(s) Humans ; Gene Regulatory Networks ; Causality ; Aging ; Survival Analysis
    Language English
    Publishing date 2022-12-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2667-2375
    ISSN (online) 2667-2375
    DOI 10.1016/j.crmeth.2022.100356
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genetics implicates overactive osteogenesis in the development of diffuse idiopathic skeletal hyperostosis.

    Sethi, Anurag / Ruby, J Graham / Veras, Matthew A / Telis, Natalie / Melamud, Eugene

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2644

    Abstract: Diffuse idiopathic skeletal hyperostosis (DISH) is a condition where adjacent vertebrae become fused through formation of osteophytes. The genetic and epidemiological etiology of this condition is not well understood. Here, we implemented a machine ... ...

    Abstract Diffuse idiopathic skeletal hyperostosis (DISH) is a condition where adjacent vertebrae become fused through formation of osteophytes. The genetic and epidemiological etiology of this condition is not well understood. Here, we implemented a machine learning algorithm to assess the prevalence and severity of the pathology in ~40,000 lateral DXA scans in the UK Biobank Imaging cohort. We find that DISH is highly prevalent, above the age of 45, ~20% of men and ~8% of women having multiple osteophytes. Surprisingly, we find strong phenotypic and genetic association of DISH with increased bone mineral density and content throughout the entire skeletal system. Genetic association analysis identified ten loci associated with DISH, including multiple genes involved in bone remodeling (RUNX2, IL11, GDF5, CCDC91, NOG, and ROR2). Overall, this study describes genetics of DISH and implicates the role of overactive osteogenesis as a key driver of the pathology.
    MeSH term(s) Male ; Humans ; Female ; Hyperostosis, Diffuse Idiopathic Skeletal/diagnostic imaging ; Hyperostosis, Diffuse Idiopathic Skeletal/genetics ; Hyperostosis, Diffuse Idiopathic Skeletal/complications ; Osteogenesis/genetics ; Osteophyte/complications ; Osteophyte/pathology ; Spine/pathology ; Absorptiometry, Photon
    Language English
    Publishing date 2023-05-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-38279-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Calcification of the abdominal aorta is an under-appreciated cardiovascular disease risk factor in the general population.

    Sethi, Anurag / Taylor, D Leland / Ruby, J Graham / Venkataraman, Jagadish / Sorokin, Elena / Cule, Madeleine / Melamud, Eugene

    Frontiers in cardiovascular medicine

    2022  Volume 9, Page(s) 1003246

    Abstract: Calcification of large arteries is a high-risk factor in the development of cardiovascular diseases, however, due to the lack of routine monitoring, the pathology remains severely under-diagnosed and prevalence in the general population is not known. We ... ...

    Abstract Calcification of large arteries is a high-risk factor in the development of cardiovascular diseases, however, due to the lack of routine monitoring, the pathology remains severely under-diagnosed and prevalence in the general population is not known. We have developed a set of machine learning methods to quantitate levels of abdominal aortic calcification (AAC) in the UK Biobank imaging cohort and carried out the largest to-date analysis of genetic, biochemical, and epidemiological risk factors associated with the pathology. In a genetic association study, we identified three novel loci associated with AAC (
    Language English
    Publishing date 2022-10-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2022.1003246
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The promise and reality of therapeutic discovery from large cohorts.

    Melamud, Eugene / Taylor, D Leland / Sethi, Anurag / Cule, Madeleine / Baryshnikova, Anastasia / Saleheen, Danish / van Bruggen, Nick / FitzGerald, Garret A

    The Journal of clinical investigation

    2020  Volume 130, Issue 2, Page(s) 575–581

    Abstract: Technological advances in rapid data acquisition have transformed medical biology into a data mining field, where new data sets are routinely dissected and analyzed by statistical models of ever-increasing complexity. Many hypotheses can be generated and ...

    Abstract Technological advances in rapid data acquisition have transformed medical biology into a data mining field, where new data sets are routinely dissected and analyzed by statistical models of ever-increasing complexity. Many hypotheses can be generated and tested within a single large data set, and even small effects can be statistically discriminated from a sea of noise. On the other hand, the development of therapeutic interventions moves at a much slower pace. They are determined from carefully randomized and well-controlled experiments with explicitly stated outcomes as the principal mechanism by which a single hypothesis is tested. In this paradigm, only a small fraction of interventions can be tested, and an even smaller fraction are ultimately deemed therapeutically successful. In this Review, we propose strategies to leverage large-cohort data to inform the selection of targets and the design of randomized trials of novel therapeutics. Ultimately, the incorporation of big data and experimental medicine approaches should aim to reduce the failure rate of clinical trials as well as expedite and lower the cost of drug development.
    MeSH term(s) Big Data ; Biomedical Research ; Cohort Studies ; Humans ; Models, Statistical ; Randomized Controlled Trials as Topic
    Language English
    Publishing date 2020-01-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 3067-3
    ISSN 1558-8238 ; 0021-9738
    ISSN (online) 1558-8238
    ISSN 0021-9738
    DOI 10.1172/JCI129196
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex.

    Sethi, Anurag / Goldstein, Byron / Gnanakaran, S

    PLoS computational biology

    2011  Volume 7, Issue 10, Page(s) e1002192

    Abstract: Numerous signaling proteins use multivalent binding to increase the specificity and affinity of their interactions within the cell. Enhancement arises because the effective binding constant for multivalent binding is larger than the binding constants for ...

    Abstract Numerous signaling proteins use multivalent binding to increase the specificity and affinity of their interactions within the cell. Enhancement arises because the effective binding constant for multivalent binding is larger than the binding constants for each individual interaction. We seek to gain both qualitative and quantitative understanding of the multivalent interactions of an adaptor protein, growth factor receptor bound protein-2 (Grb2), containing two SH3 domains interacting with the nucleotide exchange factor son-of-sevenless 1 (Sos1) containing multiple polyproline motifs separated by flexible unstructured regions. Grb2 mediates the recruitment of Sos1 from the cytosol to the plasma membrane where it activates Ras by inducing the exchange of GDP for GTP. First, using a combination of evolutionary information and binding energy calculations, we predict an additional polyproline motif in Sos1 that binds to the SH3 domains of Grb2. This gives rise to a total of five polyproline motifs in Sos1 that are capable of binding to the two SH3 domains of Grb2. Then, using a hybrid method combining molecular dynamics simulations and polymer models, we estimate the enhancement in local concentration of a polyproline motif on Sos1 near an unbound SH3 domain of Grb2 when its other SH3 domain is bound to a different polyproline motif on Sos1. We show that the local concentration of the Sos1 motifs that a Grb2 SH3 domain experiences is approximately 1000 times greater than the cellular concentration of Sos1. Finally, we calculate the intramolecular equilibrium constants for the crosslinking of Grb2 on Sos1 and use thermodynamic modeling to calculate the stoichiometry. With these equilibrium constants, we are able to predict the distribution of complexes that form at physiological concentrations. We believe this is the first systematic analysis that combines sequence, structure, and thermodynamic analyses to determine the stoichiometry of the complexes that are dominant in the cellular environment.
    MeSH term(s) Amino Acid Sequence ; Animals ; GRB2 Adaptor Protein/chemistry ; GRB2 Adaptor Protein/metabolism ; Humans ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Molecular Structure ; Probability ; Protein Binding ; SOS1 Protein/chemistry ; SOS1 Protein/metabolism ; Sequence Homology, Amino Acid
    Chemical Substances GRB2 Adaptor Protein ; SOS1 Protein
    Language English
    Publishing date 2011-10-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1002192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR.

    López, Cesar A / Sethi, Anurag / Goldstein, Byron / Wilson, Bridget S / Gnanakaran, S

    Biophysical journal

    2015  Volume 108, Issue 10, Page(s) 2481–2491

    Abstract: The regulation of T-cell-mediated immune responses depends on the phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) on T-cell receptors. Although many details of the signaling cascades are well understood, the initial mechanism ... ...

    Abstract The regulation of T-cell-mediated immune responses depends on the phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) on T-cell receptors. Although many details of the signaling cascades are well understood, the initial mechanism and regulation of ITAM phosphorylation remains unknown. We used molecular dynamics simulations to study the influence of different compositions of lipid bilayers on the membrane association of the CD3ϵ cytoplasmic tails of the T-cell receptors. Our results show that binding of CD3ϵ to membranes is modulated by both the presence of negatively charged lipids and the lipid order of the membrane. Free-energy calculations reveal that the protein-membrane interaction is favored by the presence of nearby basic residues and the ITAM tyrosines. Phosphorylation minimizes membrane association, rendering the ITAM motif more accessible to binding partners. In systems mimicking biological membranes, the CD3ϵ chain localization is modulated by different facilitator lipids (e.g., gangliosides or phosphoinositols), revealing a plausible regulatory effect on activation through the regulation of lipid composition in cell membranes.
    MeSH term(s) Amino Acid Motifs ; Amino Acid Sequence ; Gangliosides/metabolism ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Phosphatidylinositols/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell/chemistry ; Receptors, Antigen, T-Cell/metabolism
    Chemical Substances Gangliosides ; Intrinsically Disordered Proteins ; Lipid Bilayers ; Phosphatidylinositols ; Receptors, Antigen, T-Cell
    Language English
    Publishing date 2015-05-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2015.03.059
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Using the Seven Bridges Cancer Genomics Cloud to Access and Analyze Petabytes of Cancer Data.

    Malhotra, Raunaq / Seth, Isheeta / Lehnert, Erik / Zhao, Jing / Kaushik, Gaurav / Williams, Elizabeth H / Sethi, Anurag / Davis-Dusenbery, Brandi N

    Current protocols in bioinformatics

    2017  Volume 60, Page(s) 11.16.1–11.16.32

    Abstract: Next-generation sequencing has produced petabytes of data, but accessing and analyzing these data remain challenging. Traditionally, researchers investigating public datasets like The Cancer Genome Atlas (TCGA) would download the data to a high- ... ...

    Abstract Next-generation sequencing has produced petabytes of data, but accessing and analyzing these data remain challenging. Traditionally, researchers investigating public datasets like The Cancer Genome Atlas (TCGA) would download the data to a high-performance cluster, which could take several weeks even with a highly optimized network connection. The National Cancer Institute (NCI) initiated the Cancer Genomics Cloud Pilots program to provide researchers with the resources to process data with cloud computational resources. We present protocols using one of these Cloud Pilots, the Seven Bridges Cancer Genomics Cloud (CGC), to find and query public datasets, bring your own data to the CGC, analyze data using standard or custom workflows, and benchmark tools for accuracy with interactive analysis features. These protocols demonstrate that the CGC is a data-analysis ecosystem that fully empowers researchers with a variety of areas of expertise and interests to collaborate in the analysis of petabytes of data. © 2017 by John Wiley & Sons, Inc.
    MeSH term(s) Cloud Computing ; Computational Biology ; Data Interpretation, Statistical ; Databases, Genetic/statistics & numerical data ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Metadata ; Neoplasms/genetics ; Pilot Projects
    Language English
    Publishing date 2017-12-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1934-340X
    ISSN (online) 1934-340X
    DOI 10.1002/cpbi.39
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Identification of minimally interacting modules in an intrinsically disordered protein.

    Sethi, Anurag / Tian, Jianhui / Vu, Dung M / Gnanakaran, S

    Biophysical journal

    2012  Volume 103, Issue 4, Page(s) 748–757

    Abstract: The conformational characterization of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogeneity and flexibility. If an IDP could somehow be divided into smaller fragments and reconstructed later, theoretical and ... ...

    Abstract The conformational characterization of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogeneity and flexibility. If an IDP could somehow be divided into smaller fragments and reconstructed later, theoretical and spectroscopic studies could probe its conformational variability in detail. Here, we used replica molecular-dynamics simulations and network theory to explore whether such a divide-and-conquer strategy is feasible for α-synuclein, a prototypical IDP. We characterized the conformational variability of α-synuclein by conducting >100 unbiased all-atom molecular-dynamics simulations, for a total of >10 μs of trajectories. In these simulations, α-synuclein formed a heterogeneous ensemble of collapsed coil states in an aqueous environment. These states were stabilized by heterogeneous contacts between sequentially distant regions. We find that α-synuclein contains residual secondary structures in the collapsed states, and the heterogeneity in the collapsed state makes it feasible to split α-synuclein into sequentially contiguous minimally interacting fragments. This study reveals previously unknown characteristics of α-synuclein and provides a new (to our knowledge) approach for studying other IDPs.
    MeSH term(s) Molecular Dynamics Simulation ; Peptide Fragments/chemistry ; Protein Structure, Secondary ; Vibration ; Water/chemistry ; alpha-Synuclein/chemistry ; alpha-Synuclein/metabolism
    Chemical Substances Peptide Fragments ; alpha-Synuclein ; Water (059QF0KO0R)
    Language English
    Publishing date 2012-09-13
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2012.06.052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Taste of Sugar at the Membrane: Thermodynamics and Kinetics of the Interaction of a Disaccharide with Lipid Bilayers

    Tian, Jianhui / Sethi, Anurag / Swanson, Basil I / Goldstein, Byron / Gnanakaran, S

    Biophysical journal. 2013 Feb. 5, v. 104, no. 3

    2013  

    Abstract: Sugar recognition at the membrane is critical in various physiological processes. Many aspects of sugar-membrane interaction are still unknown. We take an integrated approach by combining conventional molecular-dynamics simulations with enhanced sampling ...

    Abstract Sugar recognition at the membrane is critical in various physiological processes. Many aspects of sugar-membrane interaction are still unknown. We take an integrated approach by combining conventional molecular-dynamics simulations with enhanced sampling methods and analytical models to understand the thermodynamics and kinetics of a di-mannose molecule in a phospholipid bilayer system. We observe that di-mannose has a slight preference to localize at the water-phospholipid interface. Using umbrella sampling, we show the free energy bias for this preferred location to be just −0.42 kcal/mol, which explains the coexistence of attraction and exclusion mechanisms of sugar-membrane interaction. Accurate estimation of absolute entropy change of water molecules with a two-phase model indicates that the small energy bias is the result of a favorable entropy change of water molecules. Then, we incorporate results from molecular-dynamics simulation in two different ways to an analytical diffusion-reaction model to obtain association and dissociation constants for di-mannose interaction with membrane. Finally, we verify our approach by predicting concentration dependence of di-mannose recognition at the membrane that is consistent with experiment. In conclusion, we provide a combined approach for the thermodynamics and kinetics of a weak ligand-binding system, which has broad implications across many different fields.
    Keywords analytical methods ; dissociation ; energy ; entropy ; lipid bilayers ; models ; molecular dynamics ; phospholipids ; prediction ; sugars ; taste
    Language English
    Dates of publication 2013-0205
    Size p. 622-632.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2012.12.011
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: A coarse-grained model for synergistic action of multiple enzymes on cellulose

    Asztalos Andrea / Daniels Marcus / Sethi Anurag / Shen Tongye / Langan Paul / Redondo Antonio / Gnanakaran Sandrasegaram

    Biotechnology for Biofuels, Vol 5, Iss 1, p

    2012  Volume 55

    Abstract: Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D- ... ...

    Abstract Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis .
    Keywords Cellulose degradation ; Synergy ; Exo-cellulase ; Endo-cellulase ; Agent-based model ; Spatial heterogeneity ; Biotechnology ; TP248.13-248.65 ; Chemical technology ; TP1-1185 ; Technology ; T ; DOAJ:Biotechnology ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences ; Fuel ; TP315-360
    Subject code 540
    Language English
    Publishing date 2012-08-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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