Orion

Sarajlic, Semir; Edirisinghe, Neranjan; Yuriy, Lukinov; Walters, Michael; Brock, Davis; Faroux, Gregori

doi:10.1145/2949550.2952770

Cited by 14 publications

(4 citation statements)

References 11 publications

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“…Screening for IRs and iGluRs was performed with TMHMM v2.0 for transmembrane domain prediction and domain region screened with InterProScan 5 (v5.28-67.0) [70] for conserved Pfam [71] and InterPro [72] domains on high performance computing systems at Georgia State University [73,74]. IRs have several distinctive domains: an extracellular amino-terminal domain (ATD) involved in assembly of the heteromeric channel; an extracellular ligand binding domain (LBD) consisting of two half-domains (S1 and S2) to which agonists bind; an ion channel domain (ICD) that forms the ion channel, consisting of three transmembrane domains (M1, M2, M3) and a pore loop (P); and an intracellular carboxyl-termination domain (CTD).…”

Section: Ir Identification Sequence Alignment and Phylogenetic Analmentioning

confidence: 99%

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins

et al. 2020

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Crustaceans express genes for at least three classes of putative chemosensory proteins. These are: Ionotropic Receptors (IRs), derived from the heterotetrameric ionotropic glutamate receptors (iGluRs); Transient Receptor Potential (TRP) channels, a diverse set of sensor-channels that include several families of chemoreceptor channels; and Gustatory Receptor Like receptors (GRLs), ionotropic receptors that are homologues of Gustatory Receptors (GRs) of insects and are expressed sparingly in most crustaceans so far studied. IRs are typically numerically the most dominant of these receptor proteins in crustaceans and include two classes: co-receptor IRs, which are necessary for making a functional receptor-channel; and tuning IRs, whose specific combination in the IR subunits in the heterotetramer confers chemical specificity. Previous work showed that the transcriptomes from two major chemosensory organs-the lateral flagellum of the antennule (LF) and the tips of the legs (dactyls)-of the Caribbean spiny lobster Panulirus argus express four coreceptor IRs and over 100 tuning IRs. In this paper, we examined and compared the transcriptomes from the LF and dactyls of P. argus and three other decapod crustaceans-the clawed lobster Homarus americanus, red swamp crayfish Procambarus clarkii, and the blue crab Callinectes sapidus. Each species has at least ca. 100 to 250 IRs, 1 to 4 GRLs, and ca. 15 TRP channels including those shown to be involved in chemoreception in other species. The IRs show different degrees of phylogenetic conservation: some are arthropod-conserved, others are pancrustacean-conserved, others appear to be crustacean-conserved, and some appear to be species-specific. Many IRs appear to be more highly expressed in the LF than dactyl. Our results show that decapod crustaceans express an abundance of

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Section: Ir Identification Sequence Alignment and Phylogenetic Analmentioning

confidence: 99%

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins

et al. 2020

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“…All data were acquired using the computing resources at Georgia State University49. After assembly, TransDecoder (https://transdecoder.github.io/)48 was used to identify coding domain sequences with a minimum cut-off of 50 amino acids28.…”

Section: Methodsmentioning

confidence: 99%

De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters

McCann

Sinkiewicz

Norvelle

et al. 2017

Sci Rep

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Hamsters are an ideal animal model for a variety of biomedical research areas such as cancer, virology, circadian rhythms, and behavioural neuroscience. The use of hamsters has declined, however, most likely due to the dearth of genetic tools available for these animals. Our laboratory uses hamsters to study acute social stress, and we are beginning to investigate the genetic mechanisms subserving defeat-induced behavioural change. We have been limited, however, by the lack of genetic resources available for hamsters. In this study, we sequenced the brain transcriptome of male and female Syrian hamsters to generate the necessary resources to continue our research. We completed a de novo assembly and after assembly optimization, there were 113,329 transcripts representing 14,530 unique genes. This study is the first to characterize transcript expression in both female and male hamster brains and offers invaluable information to promote understanding of a host of important biomedical research questions for which hamsters are an excellent model.

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“…The small molecule's 3D structure was optimized with Omega2 [ 31 , 32 ]. Docking study was conducted using OEDocking module FRED [ 33 , 34 ] with default parameters on GSU cluster Orion [ 35 ] and XSEDE [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Discovery and evaluation of triple inhibitors of VEGFR-2, TIE-2 and EphB4 as anti-angiogenic and anti-cancer agents

Zhang

Shan

et al. 2017

Oncotarget

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Receptor tyrosine kinases (RTKs), especially VEGFR-2, TIE-2, and EphB4, play a crucial role in both angiogenesis and tumorigenesis. Moreover, complexity and heterogeneity of angiogenesis make it difficult to treat such pathological traits with single-target agents. Herein, we developed two classes of multi-target RTK inhibitors (RTKIs) based on the highly conserved ATP-binding pocket of VEGFR-2/TIE-2/EphB4, using previously reported BPS-7 as a lead compound. These multi-target RTKIs exhibited considerable potential as novel anti-angiogenic and anticancer agents. Among them, QDAU5 displayed the most promising potency and selectivity. It significantly suppressed viability of EA.hy926 and proliferation of several cancer cells. Further investigations indicated that QDAU5 showed high affinity to VEGFR-2 and reduced the phosphorylation of VEGFR-2. We identified QDAU5 as a potent multiple RTKs inhibitor exhibiting prominent anti-angiogenic and anticancer potency both in vitro and in vivo. Moreover, quinazolin-4(3H)-one has been identified as an excellent hinge binding moiety for multi-target inhibitors of angiogenic VEGFR-2, Tie-2, and EphB4.

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Orion

Cited by 14 publications

References 11 publications

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins

De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters

Discovery and evaluation of triple inhibitors of VEGFR-2, TIE-2 and EphB4 as anti-angiogenic and anti-cancer agents

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