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Orexins are excitatory neuropeptides, which are predominantly associated with feeding behavior, sleep-wake cycle and energy homeostasis. The orexinergic system comprises of HCRTR1 and HCRTR2, G-protein-coupled receptors of rhodopsin family and the endogenous ligands processed from HCRT pro-hormone, Orexin A and Orexin B. These neuropeptides are biosynthesized by the orexin neurons present in the lateral hypothalamus area, with dense projections to other brain regions. The orexin-receptor signaling is implicated in various metabolic as well as neurological disorders, making it a promising target for pharmacological interventions. However, there is limited information available on the collective representation of the signal transduction pathways pertaining to the orexin-orexin receptor signaling system. Here, we depict a compendium of the Orexin A/B stimulated reactions in the form of a basic signaling pathway map. This map catalogs the reactions into five categories: molecular association, activation/inhibition, catalysis, transport, and gene regulation. A total of 318 downstream molecules were annotated adhering to the guidelines of NetPath curation. This pathway map can be utilized for further assessment of signaling events associated with orexin-mediated physiological functions and is freely available on WikiPathways, an open-source pathway database (https://www.wikipathways.org/index.php/Pathway:WP5094). GRAPHICAL ABSTRACT: [Figure: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12079-022-00700-3.

Interleukin-17A (IL-17A) is one of the member of IL-17 family consisting of other five members (IL-17B to IL-17F). The Gamma delta (γδ) T cells and T helper 17 (Th17) cells are the major producers of IL-17A. Aberrant signaling by IL-17A has been implicated in the pathogenesis of several autoimmune diseases including idiopathic pulmonary fibrosis, acute lung injury, chronic airway diseases, and cancer. Activation of the IL-17A/IL-17 receptor A (IL-17RA) system regulates phosphoinositide 3-kinase/AKT serine/threonine kinase/mammalian target of rapamycin (PI3K/AKT/mTOR), mitogen-activated protein kinases (MAPKs) and activation of nuclear factor-κB (NF-κB) mediated signaling pathways. The IL-17RA activation orchestrates multiple downstream signaling cascades resulting in the release of pro-inflammatory cytokines such as interleukins (IL)-1β, IL-6, and IL-8, chemokines (C-X-C motif) and promotes neutrophil-mediated immune response. Considering the biomedical importance of IL-17A, we developed a pathway resource of signaling events mediated by IL-17A/IL-17RA in this study. The curation of literature data pertaining to the IL-17A system was performed manually by the NetPath criteria. Using data mined from the published literature, we describe an integrated pathway reaction map of IL-17A/IL-17RA consisting of 114 proteins and 68 reactions. That includes detailed information on IL-17A/IL-17RA mediated signaling events of 9 activation/inhibition events, 17 catalysis events, 3 molecular association events, 68 gene regulation events, 109 protein expression events, and 6 protein translocation events. The IL-17A signaling pathway map data is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway : WP5242).

An efficient and elegant assembly of pyrene/aryl fused pyrrolo[2,3-b]quinolinone and pyrrolizino[3,2-b]quinolinone hybrid heterocycles was achieved via a domino multicomponent reaction strategy using a solid state melt reaction (SSMR) condition.

CHK-1 kinase belongs to the serine/threonine family of kinases, which play a vital role in cell cycle arrest and proved to be a promising therapeutic target to control cancer development and progression. Many potent and selective CHK-1 inhibitors have been reported, but only a few are currently in clinical trial. In this era, drug re-profiling has proved to be a major step in drug discovery and development that is cost and time beneficial. In this study, we have incorporated a combined in silico computational approach to widen the chemical range of CHK-1 inhibitors from the existing FDA approved drugs. An e-pharmacophore model was created from 3D crystal coordinates of CHK-1 protein complex with the clinical trial inhibitor (CCT245737). The hypothesis with seven molecular features was screened with FDA drugs and the obtained drugs were subjected into Glide XP molecular docking. The top 10% scored ligands were visualized and Procaterol was best identified which showed similar interaction patterns with enzyme active sites as the clinical trial inhibitor. Furthermore, total binding free energy, pharmacokinetic properties and molecular dynamics were also evaluated. The results consolidated showed better binding affinity, acceptable kinetic profile and significant stability of Procaterol binding with CHK-1 kinase. In conclusion, we highlight that Procaterol is a re-provable potent CHK-1 inhibitor and appears as a new structural scaffold for further optimisation.

Discoidin domain receptor 1 (DDR1) is one of the receptors that belong to a family of non-integrin collagen receptors. In common, DDR1 is predominantly found in epithelial and smooth muscle cells and its mainly involved in organogenesis during embryonic development. However, it's also overexpressed in several pathological conditions, including cancer and inflammation. The DDR1 is reported in numerous cancers, including breast, prostate, pancreatic, bladder, lung, liver, pituitary, colorectal, skin, gastric, glioblastoma, and inflammation. DDR1 activates through the collagen I, IV, IGF-1/IGF1R, and IGF2/IR, regulating downstream signaling molecules such as MAPKs, PI3K/Akt, and NF-kB in diseases. Despite its biomedical importance, there is a lack of consolidated network map of the DDR1 signaling pathway, which prompted us for curation of literature data pertaining to the DDR1 system following the NetPath criteria. We present here the compiled pathway map comprises 39 activation/inhibition events, 17 catalysis events, 22 molecular associations, 65 gene regulation events, 35 types of protein expression, and two protein translocation events. The detailed DDR1 signaling pathway map is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/ Pathway: https://www.wikipathways.org/index.php/Pathway:WP5288 ).

Oral cancer is common worldwide but lacks robust diagnostics and therapeutics. Lifestyle factors, such as tobacco chewing and smoking, are significantly associated with oral cancers. Mapping the changes in the global proteome, secretome and post-translational modifications (PTMs) during tobacco exposure of oral keratinocytes hold great potential for understanding the mechanisms of oral carcinogenesis, not to mention for innovation toward clinical interventions in the future. On the other hand, although advances in mass spectrometry (MS)-based techniques have enabled the deep mining of complex proteomes, a large portion of the mass spectrometric data remains unassigned. These unassigned spectral data can be researched for multiple post-translational modifications (multiPTMs). Using data mining of publicly available proteomics data, we report, in this study, a multiPTM analysis of high-resolution MS-derived datasets on cellular proteome and secretome of chronic tobacco-treated oral keratinocytes. We identified 800 PTM sites in 496 proteins. Among them, 43 PTM sites in 37 proteins were found to be differentially expressed, accounting for their protein-level expression. Enrichment analysis of the proteins with altered phosphosite expression and the known kinases of these phosphosites discovered the overrepresentation of certain biological processes such as splicing and hemidesmosome assembly. These findings contribute to a deeper understanding of omics level changes in chronic tobacco-treated oral keratinocytes, and by extension, pathophysiology of oral cancers.

Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has been declared a pandemic by WHO. The clinical manifestation and disease progression in COVID-19 patients varies from minimal symptoms to severe respiratory issues with multiple organ failure. Understanding the mechanism of SARS-CoV-2 interaction with host cells will provide key insights into the effective molecular targets for the development of novel therapeutics. Recent studies have identified virus-mediated phosphorylation or activation of some major signaling pathways, such as ERK1/2, JNK, p38, PI3K/AKT and NF-κB signaling, that potentially elicit the cytokine storm that serves as a major cause of tissue injuries. Several studies highlight the aggressive inflammatory response particularly ‘cytokine storm’ in SARS-CoV-2 patients. A depiction of host molecular dynamics triggered by SARS-CoV-2 in the form of a network of signaling molecules will be helpful for COVID-19 research. Therefore, we developed the signaling pathway map of SARS-CoV-2 infection using data mined from the recently published literature. This integrated signaling pathway map of SARS-CoV-2 consists of 326 proteins and 73 reactions. These include information pertaining to 1,629 molecular association events, 30 enzyme catalysis events, 43 activation/inhibition events, and 8,531 gene regulation events. The pathway map is publicly available through WikiPathways: https://www.wikipathways.org/index.php/Pathway:WP5115. Supplementary Information The online version contains supplementary material available at 10.1007/s12079-021-00632-4.

Metabolomics is a leading frontier of systems science and biomedical innovation. However, metabolite identification in mass spectrometry (MS)-based global metabolomics investigations remains a formidable challenge. Moreover, lack of comprehensive spectral databases hinders accurate identification of compounds in global MS-based metabolomics. Creating experiment-derived metabolite spectral libraries tailored to each experiment is labor-intensive. Therefore, predicted spectral libraries could serve as a better alternative. User-friendly tools are much needed, as the currently available metabolomic analysis tools do not offer adequate provision for users to create or choose context-specific databases. Here, we introduce the MS2Compound, a metabolite identification tool, which can be used to generate a custom database of predicted spectra using the Competitive Fragmentation Modeling-ID (CFM-ID) algorithm, and identify metabolites or compounds from the generated database. The database generator can create databases of the model/context/species used in the metabolomics study. The MS2Compound is also powered with mS-score, a scoring function for matching raw fragment spectra to a predicted spectra database. We demonstrated that mS-score is robust in par with dot product and hypergeometric score in identifying metabolites using benchmarking datasets. We evaluated and highlight here the unique features of the MS2Compound by a re-analysis of a publicly available metabolomic dataset (MassIVE id: MSV000086784) for a complex traditional drug formulation called Triphala. In conclusion, we believe that the omics systems science and biomedical research and innovation community in the field of metabolomics will find the MS2Compound as a user-friendly analysis tool of choice to accelerate future metabolomic analyses.

An expedient regioselectivesynthesis of novel mono, C2-symmetric bis-triazole and acridinedione bridged macromolecules has been achieved in good yields employing intermolecular Cu(I) catalyzed azide and alkyne click reaction. Synthesis of O-propargyl acridinedione was achieved in three good yielding steps starting from dimedone, while the symmetrical aliphatic and aryl bis-azides were derived from appropriate dibromides in the presence of sodium azide in dry DMF. The synthesized mono and C2-symmetric bis-macromolecules have been elucidated by 1H, 13C, elemental and mass spectroscopic analysis. The antioxidant activity of synthesized compounds has also been investigated. ____________________________________________________________________________

Opioid receptors belong to the class A G-protein-coupled receptors and are activated by alkaloid opiates such as morphine, and endogenous ligands such as endorphins and enkephalins. Opioid receptors are widely distributed in the human body and are involved in numerous physiological processes through three major classical opioid receptor subtypes; the mu, delta and kappa along with a lesser characterized subtype, opioid receptor-like (ORL1). Opioids are the most potent analgesics and have been extensively used as a therapeutic drug for the treatment of pain and related disorders. Chronic administration of clinically used opioids is associated with adverse effects such as drug tolerance, addiction and constipation. Several investigations attempted to identify the molecular signaling networks associated with endogenous as well as synthetic opiates, however, there is a paucity of a cumulative depiction of these signaling events. Here, we report a systemic collection of downstream molecules pertaining to four subtypes of opioid receptors (MOR, KOR, DOR and ORL1) in the form of a signaling pathway map. We manually curated reactions induced by the activation of opioid receptors from the literature into five categories- molecular association, activation/inhibition, catalysis, transport, and gene regulation. This led to a dataset of 180 molecules, which is collectively represented in the opioid receptor signaling network following NetPath criteria. We believe that the public availability of an opioid receptor signaling pathway map can accelerate biomedical research in this area because of its high therapeutic significance. The opioid receptors signaling pathway map is uploaded to a freely available web resource, WikiPathways enabling ease of access (https://www.wikipathways.org/index.php/Pathway:WP5093). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12079-021-00653-z.

Kanchanara Guggulu (KG) is an important traditional medicine that is prescribed by the Ayurveda physicians for the treatment of swellings in various organs such as the thyroid, and lymph nodes. High-resolution mass-spectrometry-based metabolomics found metabolites in KG. LC-MS/MS-based metabolomics analysis of KG identified 2,579 compounds including quercetin and kaempferol derivatives. The molecular docking and dynamics analysis of quercetin pentaacetate with aldose reductase is documented for further consideration in drug discovery.

The G-quadruplexes (G4s) are a class of DNA secondary structures with guanine rich DNA sequences that can fold into four stranded non-canonical structures. At the genomic level, their pivotal role is well established in DNA replication, telomerase functions, constitution of topologically associating domains, and the regulation of gene expression. Genome instability mediated by altered G4 formation and assembly has been associated with multiple disorders including cancers and neurodegenerative disorders. Multiple tools have also been developed to predict the potential G4 regions in genomes and the whole genome G4 maps are also being derived through sequencing approaches. Enrichment of G4s in the cis-regulatory elements of genes associated with tumorigenesis has accelerated the quest for identification of G4-DNA binding ligands (G4DBLs) that can selectively bind and regulate the expression of such specific genes. In this context, the analysis of G4DBL responsive transcriptome in diverse cancer cell lines is inevitable for assessment of the specificity of novel G4DBLs. Towards this, we assembled the transcripts differentially regulated by different G4DBLs and have also identified a core set of genes regulated in diverse cancer cell lines in response to 3 or more of these ligands. With the mode of action of G4DBLs towards topology shifts, folding, or disruption of G4 structure being currently visualized, we believe that this dataset will serve as a platform for assembly of G4DBL responsive transcriptome for comparative analysis of G4DBLs in multiple cancer cells based on the expression of specific cis-regulatory G4 associated genes in the future. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12079-021-00637-z.

The C–C Motif Chemokine Ligand 18 (CCL18) is a beta-chemokine sub-family member with immunomodulatory functions in primates. CCL18-dependent migration and epithelial-to-mesenchymal transition of oral squamous cell carcinoma, squamous cell carcinoma of head and neck, breast cancer, hepatocellular carcinoma, non-small cell lung carcinoma, ovarian cancer, pancreatic ductal carcinoma and bladder cancer cells are well-established. In the tumor niche, tumor-associated macrophages produce CCL18 and its overexpression is correlated with reduced patient survival in multiple cancers. Although multiple receptors including C–C chemokine receptor type 3 (CCR3), type 6 (CCR6), type 8 (CCR8) and G-protein coupled estrogen receptor (GPER1) are reported for CCL18, the Phosphatidylinositol Transfer Protein, Membrane-Associated 3 (PITPNM3) receptor is currently considered as its predominant receptor. Characterization of the molecular events and check points associated with the immunosuppressive and cancer progression support functions induced by CCL18 for their potential towards therapeutic applications is an area of active research. Hence, in this study, we assembled 917 signaling events reported to be induced by CCL18 through their studied receptors in diverse cell types as an integrated knowledgebase for reference, data integration and gene-set enrichment analysis of global transcriptomic and/or proteomics datasets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12079-021-00633-3.

Background Healthcare-associated infections (HAI) are prime health task worldwide and issue of patient safety besides intensifying antimicrobial drug resistance. It is essential to formulate structurally fascinating novel, active and cost-effective anti-microbial drugs possessing a peculiar way of action and capable of overcoming the resistance to effectively combat this disease. Materials and methods The synthesized spiro-heterocyclic hybrids (SHHs) were elucidated through spectroscopic analysis and were assessed for their in vitro antimicrobial activity by agar diffusion method and minimal inhibitory concentration (MIC) value was also determined. In addition, antioxidant potential was also evaluated through DPPH radical scavenging assays. Results The novel class of SHHs 4a and 4b displayed significant antibacterial activity against selected healthcare associated microbial pathogens (HAMPs). In addition, SHH 4b showed potent antioxidant properties. Conclusion Antibacterial and antifungal activity of dispirooxindolopyrrolidine fused acenaphthenone heterocyclic hybrids were examined. Interestingly, SHH 4b exhibited potent antimicrobial activity against selected HAMPs. Further, these compounds were also showed potent antioxidant properties. These results revealed that SHH 4b is a promising lead for the development of new antimicrobial drugs.

The vast potential of organic materials for electronic, optoelectronic and spintronic devices entails substantial interest in the fabrication of π-conjugated systems with tailored functionality directly at insulating interfaces. On-surface fabrication of such materials on non-metal surfaces remains to be demonstrated with high yield and selectivity. Here we present the synthesis of polyaromatic chains on metallic substrates, insulating layers, and in the solid state. Scanning probe microscopy shows the formation of azaullazine repeating units on Au(111), Ag(111), and h-BN/Cu(111), stemming from intermolecular homo-coupling via cycloaddition reactions of CN-substituted polycyclic aromatic azomethine ylide (PAMY) intermediates followed by subsequent dehydrogenation. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry demonstrates that the reaction also takes place in the solid state in the absence of any catalyst. Such intermolecular cycloaddition reactions are promising methods for direct synthesis of regioregular polyaromatic polymers on arbitrary insulating surfaces.

Tympanoplasty is a surgical procedure performed for the closure of tympanic membrane perforation. The present study was conducted to compare the outcomes of a newer technique of cartilage tympanoplasty which the author has named as half disc cartilage tympanoplasty and temporalis fascia tympanoplasty in the following areas—the improvement in hearing, frequency specific improvement in hearing, graft uptake rate. Retrospective study was conducted in the Department of Otorhinolaryngology Rajagiri Hospital from February 2018 to February 2020. 40 patients with moderate central, subtotal and anterior perforation were included in the study. 20 patients (group A) underwent tympanoplasty with temporalis fascia graft and 20 patients (group B) underwent tympanoplasty with temporalis fascia and cymba concha with perichondrium as the support in the anterior half. Both groups were compared for the improvement in hearing and frequency specific improvement in hearing. Follow up period for the study was 6 months. Chi square and t tests were used to assess association and as tests of significance. In our present study hearing improvement following half disc cartilage tympanoplasty was better than temporalis fascia tympanoplasty. In post half disc cartilage tympanoplasty and post temporalis fascia tympanoplasty hearing gain was maximum in low frequencies. Half disc cartilage tympanoplasty is superior to temporalis fascia tympanoplasty in terms of hearing gain. Low frequency hearing shows significant improvement following tympanoplasty.

The vast potential of organic materials for electronic, optoelectronic and spintronic devices entails substantial interest in the fabrication of π-conjugated systems with tailored functionality directly at insulating interfaces. On-surface fabrication of such materials on non-metal surfaces remains to be demonstrated with high yield and selectivity. Here we present the synthesis of polyaromatic chains on metallic substrates, insulating layers, and in the solid state. Scanning probe microscopy shows the formation of azaullazine repeating units on Au(111), Ag(111), and h-BN/Cu(111), stemming from intermolecular homo-coupling via cycloaddition reactions of CN-substituted polycyclic aromatic azomethine ylide (PAMY) intermediates followed by subsequent dehydrogenation. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry demonstrates that the reaction also takes place in the solid state in the absence of any catalyst. Such intermolecular cycloaddition reactions are promising methods for direct synthesis of regioregular polyaromatic polymers on arbitrary insulating surfaces., This work was financially supported by the European Research Council Consolidator Grant NanoSurfs (no. 615233), the Advanced Grant (no. 694097), the Horizon 2020 research and innovation program 2D ink (no. 664878) and the National Science Foundation of China (no. 11974403 and Sino-German Project no. 51761135130). W.A. acknowledges funding by the DFG via a Heisenberg professorship. M.R., R.B., and X.F. thank the German Research Foundation (DFG) within the Cluster of Excellence “Center for Advancing Electronics Dresden (cfaed)” and EnhanceNano (No. 391979941). A.P.P. and A.Ru. thank the Cluster of Excellence "Advanced Imaging of Matter (AIM)" and Grupos Consolidados (IT1249-19). M.G. acknowledges funding by the H2020-MSCA-IF−2014 program under GA no. 658070 (2DNano).

Interleukin-33 (IL-33) is a member of the IL-1 family of cytokines that play a central role in the regulation of immune responses. Its release from epithelial and endothelial cells is mediated by pro-inflammatory cytokines, cell damage and by recognition of pathogen-associated molecular patterns (PAMPs). The activity of IL-33 is mediated by binding to the IL-33 receptor complex (IL-33R) and activation of NF-κB signaling via the classical MyD88/IRAK/TRAF6 module. IL-33 also induces the phosphorylation and activation of ERK1/2, JNK, p38 and PI3K/AKT signaling modules resulting in the production and release of pro-inflammatory cytokines. Aberrant signaling by IL-33 has been implicated in the pathogenesis of several acute and chronic inflammatory diseases, including asthma, atopic dermatitis, rheumatoid arthritis and ulcerative colitis among others. Considering the biomedical importance of IL-33, we developed a pathway resource of signaling events mediated by IL-33/IL-33R in this study. Using data mined from the published literature, we describe an integrated pathway reaction map of IL-33/IL-33R consisting of 681 proteins and 765 reactions. These include information pertaining to 19 physical interaction events, 740 enzyme catalysis events, 6 protein translocation events, 4 activation/inhibition events, 9 transcriptional regulators and 2492 gene regulation events. The pathway map is publicly available through NetPath ( http://www.netpath.org /), a resource of human signaling pathways developed previously by our group. This resource will provide a platform to the scientific community in facilitating identification of novel therapeutic targets for diseases associated with dysregulated IL-33 signaling. Database URL: http://www.netpath.org/pathways?path_id=NetPath_120 .

This study is an integrated analysis of the transcriptome profile microRNA (miRNA) and its experimentally validated mRNA targets differentially expressed in the tumorigenic stem-like fraction of oral squamous cell carcinoma (OSCC). We had previously reported the coexistence of multiple drug-resistant tumorigenic fractions, termed side population (SP1, SP2, and MP2), and a nontumorigenic fraction, termed main population (MP1), in oral cancer. These fractions displayed a self-renewal, regenerative potential and expressed known stemness-related cell surface markers despite functional differences. Flow cytometrically sorted pure fractions of SP1 and MP1 cells were subjected to differential expression analysis of both mRNAs and miRNAs. A significant upregulation of genes associated with inflammation, cell survival, cell proliferation, drug transporters, and antiapoptotic pathways, in addition to enhanced transcriptome reprogramming mediated by DNA‐histone binding proteins and pattern recognition receptor-mediated signaling, was found to play a crucial role in the transformation of the nontumorigenic MP1 fraction to the tumorigenic SP1 fraction. We also identified several differentially expressed miRNAs that specifically target genes distinctive of tumorigenic SP1 fraction. miRNA-mediated downregulation of stemness-associated markers CD44 and CD147 and upregulation of CD151 may also account for the emergence and persistence of multiple tumorigenic stem cell fractions with varying degrees of malignancy. The phenotypic switch of cancer cells to stem-like OSCC cells mediated by transcriptomal regulation is effectual in addressing biological tumor heterogeneity and subsequent therapeutic resistance leading to a minimal residual disease (MRD) condition in oral cancer. A detailed study of the interplay of miRNAs, mRNA, and the cellular phases involved in the gradual transition of nontumorigenic cancer cells to tumorigenic stem-like cells in solid tumors would enable detection and development of a treatment regimen that targets and successfully eliminates multiple, drug-resistant fractions of cancer cells.

The present work focuses on optimization of biodiesel combustion phenomena through parametric approach using response surface methodology. Physical properties of biodiesel play a vital role for accurate simulations of the fuel spray, atomization, combustion, and emission formation processes. Typically methyl based biodiesel consists of five main types of esters: methyl palmitate, methyl oleate, methyl stearate, methyl linoleate, and methyl linolenate in its composition. Based on the amount of methyl esters present the properties of pongamia bio-diesel and its blends were estimated. CONVERGETM computational fluid dynamics software was used to simulate the fuel spray, turbulence and combustion phenomena. The simulation responses such as indicated specific fuel consumption, NOx, and soot were analyzed using design of experiments. Regression equations were developed for each of these responses. The optimum parameters were found out to be compression ratio ? 16.75, start of injection ? 21.9? before top dead center, and exhaust gas re-circulation ? 10.94%. Results have been compared with baseline case.

Vascular Endothelial Growth Factor-A (VEGFA) signaling is crucial to the cellular processes involved in angiogenesis. Previously, we assembled a network of molecular reactions induced by VEGFA in human umbilical vein endothelial cell populations. Considering transcriptome as a read-out of the transcriptional and epigenomic regulatory network, we now present an analysis of VEGFA-induced temporal transcriptome datasets from 6 non-synchronized studies. From these datasets, applying a confidence criterion, a set of early VEGFA-responsive signature genes were derived and evaluated for their co-expression potential with respect to multiple cancer gene expression datasets. Further, inclusive of a set of ligand-receptor pairs, a list of ligand and receptor signaling systems that potentially fine-tune the endothelial cell functions subsequent to VEGFA signaling were also derived. We believe that a number of these signaling systems would concurrently and/or hierarchically fine-tune the signaling network of endothelial cell populations towards the processes associated with angiogenesis through autocrine, paracrine, juxtacrine, and matricrine modes. By further analysis of published literature on VEGFA signaling, we also present an improved update-version of our previous VEGFA signaling network model in endothelial cells as a platform for analysis of cross-talk with these signaling systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12079-019-00541-7) contains supplementary material, which is available to authorized users.

Glioblastoma multiforme (GBM) is one of the most lethal brain tumors with an inadequately understood pathophysiology. Biomarkers that guide accurate diagnosis and treatment decisions would greatly support precision medicine for GBM. Previous studies of GBM have focused on signaling pathways such as epidermal growth factor receptor (EGFR), platelet-derived growth factor receptors (PDGFRs), notch, wnt, and others, identified with single omics technology platforms (genomics, transcriptomics, or proteomics), but not with their integrated use. In this context, we report here a multi-omics pathway view, expanded through integration of the expression data at transcriptomic and proteomic levels, followed by selection of a functionally related group of proteins such as kinases deregulated in GBM. By using this strategy, we observed a highly significant enrichment of the gonadotropin-releasing hormone (GnRH) signaling pathway that was not deciphered with single omics datasets. The curation of the GnRH pathway with extensive literature analysis brought about a comprehensive annotation of the pathway, which included several additional pathway members that were not previously annotated. A targeted search resulted in identification of additional nonkinase members of the pathway in the GBM multi-omics datasets. We found evidence of GnRH receptor expression in GBM and other cancers. We offer here an updated generic pathway map of GnRH signaling, show its enrichment in the context of GBM, and discuss its plausible cross-connectivity with EGFR, wnt, calcium, and focal adhesion kinase signaling pathways that were earlier shown to be the top deregulated pathways in GBM. In conclusion, this study demonstrates the promise of multi-omics research and analyses to better understand complex cancers and suggests continued efforts and research in this direction in the field of integrative biology.

Here, a synthetic method has been optimized for the synthesis of thermoresponsive and pH-responsive poly(N-isopropylacrylamide-co-acrylic acid) nanogels which are subsequently loaded with cytochrome C by using a modified breathing-in mechanism. Physico-chemical properties mapped by using dynamic light scattering (DLS) and differential scanning calorimetry (DSC) confirm the swelling/deswelling kinetics as reversible with a volume phase transition temperature (VPTT) of ~39 °C. Fe@Au nanoparticles were incorporated inside the nanogel networks by using two different methods: coating and in situ growth. The latter bears closer resemblance to the nanogels only, while the former follows the trend of bare Fe@Au nanoparticles. High loading (~96 %) and encapsulation (500 μg/mg of nanogels) of cytochrome C were obtained. Release experiments performed by using a dialysis set-up and monitored by using UV-vis spectroscopy show the highest release at 40 °C and pH 3.2 (high temperature, low pH), with maximum release from the Fe@Au-coated nanogels that also show a reverse swelling-collapse trend. The location of the drug, the incorporation and presence of Fe@Au nanoparticles and the drug incorporation method are found to control both the drug release mechanism and kinetics. This is a post-peer-review, pre-copyedit version of an article published in [Colloid and Polymer Science]. The final authenticated version is available online at: http://dx.doi.org/10.1007/s00396-016-3944-1

Vascular endothelial growth factor-A (VEGF-A) is essential for endothelial cell functions associated with angiogenesis. Signal transduction networks initiated by VEGFA/VEGFR2, the most prominent ligand-receptor complex in the VEGF system, leads to endothelial cell proliferation, migration, survival and new vessel formation involved in angiogenesis. Considering its biomedical importance, we have developed the first comprehensive map of endothelial cell-specific signaling events of VEGFA/VEGFR2 system pertaining to angiogenesis. Screening over 20,000 published research articles and following the post-translational modification (PTM) and site specificity of VEGFR2, we have documented 240 proteins and their diverse PTM-dependent reactions involved in VEGFA/VEGFR2 signal transduction. From the ligand-receptor complex, this map has been extended to the level of major transcriptionally regulated genes for which the signaling cascades leading to their transcription factors are reported. We believe that this map would serve as a novel platform for reference, integration, and representation and more significantly, the progressive analysis of dynamic features of VEGF signaling in endothelial cells including their cross-talks with other ligand-receptor systems involved in angiogenesis.

Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases and bioinformatic tools that leverage PTM site-specific information. Here we present the first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications. We adapted the widely used single sample Gene Set Enrichment Analysis approach to utilize PTMsigDB, enabling PTM Signature Enrichment Analysis (PTM-SEA) of quantitative MS data. We used a well-characterized data set of epidermal growth factor (EGF)-perturbed cancer cells to evaluate our approach and demonstrated better representation of signaling events compared with gene-centric methods. We then applied PTM-SEA to analyze the phosphoproteomes of cancer cells treated with cell-cycle inhibitors and detected mechanism-of-action specific signatures of cell cycle kinases. We also applied our methods to analyze the phosphoproteomes of PI3K-inhibited human breast cancer cells and detected signatures of compounds inhibiting PI3K as well as targets downstream of PI3K (AKT, MAPK/ERK) covering a substantial fraction of the PI3K pathway. PTMsigDB and PTM-SEA can be freely accessed at https://github.com/broadinstitute/ssGSEA2.0.

Background Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, electrolyte, electrodes and additives among others leading to varying experimental configurations. A large number of metal-based and metal-free dye sensitizers have now been reported and tools using such data to indicate new directions for design and development are on the rise. Description DSSCDB, the first of its kind dye-sensitized solar cell database, aims to provide users with up-to-date information from publications on the molecular structures of the dyes, experimental details and reported measurements (efficiencies and spectral properties) and thereby facilitate a comprehensive and critical evaluation of the data. Currently, the DSSCDB contains over 4000 experimental observations spanning multiple dye classes such as triphenylamines, carbazoles, coumarins, phenothiazines, ruthenium and porphyrins. Conclusion The DSSCDB offers a web-based, comprehensive source of property data for dye sensitized solar cells. Access to the database is available through the following URL: www.dyedb.com.

We report the synthesis and properties of temperature- and pH-responsive p([NIPAm-co-PEGMA] (core)/[NIPAm-co-AAc] (shell)) nanogels with narrow size distributions, tunable sizes and increased drug loading efficiencies. The core-shell nanogels were synthesized using an optimized two-stage seeded polymerization methodology. The core-shell nanogels show a narrow size distribution and controllable physico-chemical properties. The hydrodynamic sizes, charge distributions, temperature-induced volume phase transition behaviors, pH-responsive behaviors and drug loading capabilities of the core-shell nanogels were investigated using transmission electron microscopy, zeta potential measurements, dynamic light scattering and UV-Vis spectroscopy. The size of the core-shell nanogels was controlled by polymerizing NIPAm with crosslinker poly(ethylene glycol) dimethacrylate (PEGDMA) of different molecular weights (Mn-200, 400, 550 and 750 g/mol) during the core synthesis. It was found that the swelling/deswelling kinetics of the nanogels was sharp and reversible; with its volume phase transition temperature in the range of 40–42 °C. Furthermore, the nanogels loaded with l-3,4-dihydroxyphenylalanine (L-DOPA), using a modified breathing-in mechanism, showed high loading and encapsulation efficiencies, providing potential possibilities of such nanogels for biomedical applications. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

Interleukin-17 (IL-17) belongs to a relatively new family of cytokines that has garnered attention as the signature cytokine of Th17 cells. This cytokine family consists of 6 ligands, which bind to 5 receptor subtypes and induce downstream signaling. Although the receptors are ubiquitously expressed, cellular responses to ligands vary across tissues. The cytokine family is associated with various autoimmune disorders including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, asthma and psoriasis in addition to being implicated in the pathogenesis of cancer. In addition, this family plays a role in host defense against bacterial and fungal infections. The signaling mechanisms of the IL-17 family of proinflammatory cytokines are not well explored. In this study, we present a resource of literature-annotated reactions induced by IL-17. The reactions are catalogued under 5 categories, namely; molecular association, catalysis, transport, activation/inhibition and gene regulation. A total of 93 molecules and 122 reactions have been annotated. The IL-17 pathway is freely available through NetPath, a resource of signal transduction pathways previously developed by our group.

Here, we report three different methods to determine the volume phase transition temperature (VPTT) of various systems including poly(N-isopropylacrylamide) (pNIPAm) based nanogels, Au nanoclusters and a combination of inorganic and polymeric systems. Although all the methods reveal close VPTT values, we suggest that method III is the least computation dependent and most reliable. In an attempt to define the overall system reversibility, a predictive reversibility parameter (RP) was defined that explains the system behavior at each state point. RP takes into consideration all the system states during both heating and cooling cycles. Reversible systems were found to have RP values less than 1, while irreversible systems were observed to have RP values of 2. We predict that real systems will show RP values between 1 and 2. Thus, by knowing both the system's VPTT and its reversibility, a particular application can be designed or upgraded. This journal is © The Royal Society of Chemistry 2017. This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite Leishmania major, which results in disfiguration and scars. L. major genome was the first to be sequenced within the genus Leishmania. Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of L. major and also annotate its genome. In this study, we searched L. major promastigote proteomic data against the annotated L. major protein database. Additionally, we searched the proteomic data against six-frame translated L. major genome. In all, we identified 3613 proteins in L. major promastigotes, which covered 43% of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in L. major. We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in L. major, one of the largest acetylated peptide datasets thus far in Leishmania. This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.

Pancreatic cancer is the fourth leading cause of cancer-related death in the world. The etiology of pancreatic cancer is heterogeneous with a wide range of alterations that have already been reported at the level of the genome, transcriptome, and proteome. The past decade has witnessed a large number of experimental studies using high-throughput technology platforms to identify genes whose expression at the transcript or protein levels is altered in pancreatic cancer. Based on expression studies, a number of molecules have also been proposed as potential biomarkers for diagnosis and prognosis of this deadly cancer. Currently, there are no repositories which provide an integrative view of multiple Omics data sets from published research on pancreatic cancer. Here, we describe the development of a web-based resource, Pancreatic Cancer Database (http://www.pancreaticcancerdatabase.org), as a unified platform for pancreatic cancer research. PCD contains manually curated information pertaining to quantitative alterations in miRNA, mRNA, and proteins obtained from small-scale as well as high-throughput studies of pancreatic cancer tissues and cell lines. We believe that PCD will serve as an integrative platform for scientific community involved in pancreatic cancer research.