Fields, patterns and information: R.L. Brahmachary’s contributions during the infancy of molecular embryology

The contribution of Professor Ratan Lal Brahmachary’s research during the early years of molecular embryology, its theoretical underpinnings, and its connection with those of other contemporary research efforts, are traced in this article as a part of the history of developmental biology research in India

Fields, patterns and information: R.L. Brahmachary’s contributions during the infancy of molecular embryology

The contribution of Professor Ratan Lal Brahmachary’s research during the early years of molecular embryology, its theoretical underpinnings, and its connection with those of other contemporary research efforts, are traced in this article as a part of the history of developmental biology research in India

BiologicalNetworks: visualization and analysis tool for systems biology

Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of databases [Baitaluk et al. (2006) BMC Bioinformatics 7, 55]. Here we describe a server, BiologicalNetworks, which provides visualization, analysis services and an information management framework over PathSys. The server allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein–protein, protein–DNA and genetic interactions. Most importantly, BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks. BiologicalNetworks Server is available at

Dangling and hydrolyzed ligand arms in [Mn3] and [Mn6] coordination assemblies: synthesis, characterization, and functional activity

Two flexible, branched, and sterically constrained di- and tripodal side arms around a phenol backbone were utilized in ligands H3L1 and H5L2 to isolate {Mn6} and {Mn3} coordination aggregates. 2,6-Bis{(1-hydroxy-2-methylpropan-2-ylimino)methyl}-4-methylphenol (H3L1) gave trinuclear complex [Mn3(μ-H2L1)2(μ1,3-O2CCH3)4(CH3OH)2](ClO4)2·4CH3OH (1), whereas 2,6-bis[{1-hydroxy-2-(hydroxymethyl)butan-2-ylimino}methyl]-4-methylphenol (H5L2) provided hexanuclear complex [Mn6(μ4-H2L2)2(μ-HL3)2(μ3-OH)2(μ1,3-O2CC2H5)4](ClO4)2·2H2O (2). Binding of acetates and coordination of {H2L1}− provided a linear MnIIIMnIIMnIII arrangement in 1. A MnIII6 fused diadamantane-type assembly was obtained in 2 from propionate bridges, coordination of {H2L2}3–, and in situ generated {HL3}2–. The magnetic characterization of 1 and 2 revealed the properties dominated by intramolecular anti-ferromagnetic exchange interactions, and this was confirmed using density functional theory calculations. Complex 1 exhibited field-induced slow magnetic relaxation at 2 K due to the axial anisotropy of MnIII centers. Both the complexes show effective solvent-dependent catechol oxidation toward 3,5-di-tert-butylcatechol in air. The catechol oxidation abilities are comparable from two complexes of different nuclearity and structure

PathSys: integrating molecular interaction graphs for systems biology

BACKGROUND: The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. RESULTS: Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. CONCLUSION: Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at

BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies

<p>Abstract</p> <p>Background</p> <p>Understanding of immune response mechanisms of pathogen-infected host requires multi-scale analysis of genome-wide data. Data integration methods have proved useful to the study of biological processes in model organisms, but their systematic application to the study of host immune system response to a pathogen and human disease is still in the initial stage.</p> <p>Results</p> <p>To study host-pathogen interaction on the systems biology level, an extension to the previously described BiologicalNetworks system is proposed. The developed methods and data integration and querying tools allow simplifying and streamlining the process of integration of diverse experimental data types, including molecular interactions and phylogenetic classifications, genomic sequences and protein structure information, gene expression and virulence data for pathogen-related studies. The data can be integrated from the databases and user's files for both public and private use.</p> <p>Conclusions</p> <p>The developed system can be used for the systems-level analysis of host-pathogen interactions, including host molecular pathways that are induced/repressed during the infections, co-expressed genes, and conserved transcription factor binding sites. Previously unknown to be associated with the influenza infection genes were identified and suggested for further investigation as potential drug targets. Developed methods and data are available through the Java application (from BiologicalNetworks program at <url>http://www.biologicalnetworks.org</url>) and web interface (at <url>http://flu.sdsc.edu</url>).</p

Haemophagocytic lymphohistiocytosis in patients with human immunodeficiency virus infection: to treat or not to treat

Haemophagocytic lymphohistiocytosis (HLH) in Human Immunodeficiency Virus (HIV) infected individuals can either be due to the disease itself or due to associated infections/malignancies. The treatment for HLH requires immunosuppressive therapy but administering immunosuppressive therapy to an already immunosuppressed patient (HIV infection) is complex. We present two such cases of HLH in patients infected with HIV. In the first case, no alternate cause for HLH was found even after extensive investigations and it was attributed to the uncontrolled HIV replication. Patient was started on dexamethasone for the same but succumbed to hospital acquired pneumonia. The second patient was diagnosed with Hodgkin's lymphoma but he succumbed to his illness before initiating immunosuppressive therapy for HLH. We report these cases to highlight the dilemma and a need for further research in this direction