RESUMO
Background: In Latin America, epilepsy in the elderly is a neglected issue that has never been studied. The epidemiological transition has significantly altered the demographics of epilepsy, and therefore, we would like to draw attention to this topic. Objective: We require local real-world evidence, as the literature often depicts a different scenario, including pharmacological management. Methods: From 2007 to 2018, we recruited all patients with new-onset geriatric epilepsy (first seizure after the age of 60) tracked from ten Mexican hospitals, adding them to patients with similar characteristics from a previously published study. The diagnosis was confirmed in all patients by a certified neurologist, and they were also studied using a conventional electroencephalogram and imaging workup. Results: A diagnosis of new-onset geriatric epilepsy (Elderly patients was established in 100 cases. No specific cause was found in 26% of patients, while 42% had a stroke and 10% had neurocysticercosis (NCC). Monotherapy was the choice in 83 patients, and phenytoin was the most used drug (50%), followed by carbamazepine (25%). Conclusion: NCC remains a frequent cause of new-onset geriatric epilepsy. This distribution is not seen in the literature, mainly representing patients from wealthy economies. In our setting, financial constraints influence the choice of the drug, and newer antiepileptic drugs should be made more affordable to this population with economic and physical frailty.
Assuntos
Epilepsia , Fragilidade , Idoso , Humanos , Eletroencefalografia , Epilepsia/tratamento farmacológico , Epilepsia/epidemiologia , Epilepsia/etiologia , América Latina/epidemiologia , México/epidemiologiaRESUMO
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.
Assuntos
Bases de Dados Factuais , Biologia Celular , Biologia Computacional , Curadoria de Dados , Bases de Dados Genéticas , Epigenômica , Humanos , Metadados , Proteômica , Software , Biologia de Sistemas , Interface Usuário-ComputadorRESUMO
Immunomodulatory nucleic acids have extraordinary promise for treating disease, yet clinical progress has been limited by a lack of tools to safely increase activity in patients. Immunomodulatory nucleic acids act by agonizing or antagonizing endosomal toll-like receptors (TLR3, TLR7/8, and TLR9), proteins involved in innate immune signaling. Immunomodulatory spherical nucleic acids (SNAs) that stimulate (immunostimulatory, IS-SNA) or regulate (immunoregulatory, IR-SNA) immunity by engaging TLRs have been designed, synthesized, and characterized. Compared with free oligonucleotides, IS-SNAs exhibit up to 80-fold increases in potency, 700-fold higher antibody titers, 400-fold higher cellular responses to a model antigen, and improved treatment of mice with lymphomas. IR-SNAs exhibit up to eightfold increases in potency and 30% greater reduction in fibrosis score in mice with nonalcoholic steatohepatitis (NASH). Given the clinical potential of SNAs due to their potency, defined chemical nature, and good tolerability, SNAs are attractive new modalities for developing immunotherapies.
Assuntos
Neoplasias Experimentais/terapia , Hepatopatia Gordurosa não Alcoólica/terapia , Ácidos Nucleicos/química , Receptores Toll-Like/agonistas , Animais , Antígenos/química , Linhagem Celular , Feminino , Humanos , Imunidade Inata , Cirrose Hepática/patologia , Linfoma/terapia , Camundongos , Camundongos Endogâmicos C57BL , Nanomedicina/métodos , Nanopartículas/química , Conformação de Ácido Nucleico , Ácidos Nucleicos/uso terapêutico , Oligonucleotídeos/uso terapêuticoRESUMO
The closely related Abl family kinases, Arg and Abl, play important non-redundant roles in the regulation of cell morphogenesis and motility. Despite similar N-terminal sequences, Arg and Abl interact with different substrates and binding partners with varying affinities. This selectivity may be due to slight differences in amino acid sequence leading to differential interactions with target proteins. We report that the Arg Src homology (SH) 2 domain binds two specific phosphotyrosines on cortactin, a known Abl/Arg substrate, with over 10-fold higher affinity than the Abl SH2 domain. We show that this significant affinity difference is due to the substitution of arginine 161 and serine 187 in Abl to leucine 207 and threonine 233 in Arg, respectively. We constructed Abl SH2 domains with R161L and S187T mutations alone and in combination and find that these substitutions are sufficient to convert the low affinity Abl SH2 domain to a higher affinity "Arg-like" SH2 domain in binding to a phospho-cortactin peptide. We crystallized the Arg SH2 domain for structural comparison to existing crystal structures of the Abl SH2 domain. We show that these two residues are important determinants of Arg and Abl SH2 domain binding specificity. Finally, we expressed Arg containing an "Abl-like" low affinity mutant Arg SH2 domain (L207R/T233S) and find that this mutant, although properly localized to the cell periphery, does not support wild type levels of cell edge protrusion. Together, these observations indicate that these two amino acid positions confer different binding affinities and cellular functions on the distinct Abl family kinases.
Assuntos
Cortactina/química , Proteínas Proto-Oncogênicas c-abl/química , Substituição de Aminoácidos , Animais , Células Cultivadas , Cortactina/genética , Cortactina/metabolismo , Cristalografia por Raios X , Fibroblastos , Humanos , Camundongos , Camundongos Knockout , Mutação de Sentido Incorreto , Ligação Proteica , Proteínas Proto-Oncogênicas c-abl/genética , Proteínas Proto-Oncogênicas c-abl/metabolismo , Relação Estrutura-Atividade , Domínios de Homologia de srcRESUMO
We report the development of a powerful analytical method that utilizes a tilted elastomeric pyramidal pen array in the context of a scanning probe lithography experiment to rapidly prepare libraries having as many as 25 million features over large areas with a range of feature sizes from the nano- to microscale. This technique can be used to probe important chemical and biological processes, opening up the field of nanocombinatorics. In a proof-of-concept investigation of mesenchymal stem cell (MSC) differentiation, combinatorial patterns first enabled a rapid and systematic screening of MSC adhesion, as a function of feature size, while uniform patterns were used to study differentiation with statistically significant sample sizes. Without media containing osteogenic-inducing chemical cues, cells cultured on nanopatterned fibronectin substrates direct MSC differentiation towards osteogenic fates when compared to nonpatterned fibronectin substrates. This powerful and versatile approach enables studies of many systems spanning biology, chemistry, and engineering areas.
Assuntos
Fibronectinas/química , Microscopia de Varredura por Sonda/métodos , Adesão Celular , Diferenciação Celular , Células Cultivadas , Adesões Focais , Humanos , Células-Tronco Mesenquimais/citologia , Microscopia Confocal/métodos , Microscopia Eletrônica de Varredura/métodos , Microscopia de Fluorescência/métodos , Nanotecnologia/métodos , Osteogênese , Polímeros/química , Células-Tronco/citologiaRESUMO
BACKGROUND: This study employed bibliometric analysis to ascertain the research focus areas among a group of Mexican physicians affiliated with the Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE). ISSSTE, a healthcare institution catering to a diverse range of diseases, offers a distinctive perspective on the investigated specialties within the realm of health. The primary objective was to identify knowledge gaps in medical care disciplines through a comprehensive examination of scholarly publications. METHODS: We retrieved Scopus papers affiliated with "ISSSTE" and saved them as .CSV files. Subsequently, we employed VOSviewer, biblioshiny, and bibliometrix for bibliometric analysis. This enabled us to identify prominent institutions, prolific authors, highly cited researchers, and their respective affiliations. RESULTS: Our analysis identified 2063 publications; the specialty internal medicine accounted for the greatest proportion with 831 publications. Original papers accounted for 82% of the total, with 52% of them being written in Spanish. The majority of scientific output, 92%, originated from Mexico City. The annual production has steadily increased since 2010, peaking in 2021 with over 200 publications. However, papers on prevalent conditions, such as metabolic syndrome, received limited citations, and the L0 index (percentage of uncited items) for all papers is close to 60%. Scopus mislabeled one affiliation, and some cases show a low paper-to-author ratio of 0.5 Discussion: Additional concerns, such as honorary authorship due to excessive authors per paper, and the underlying causes of low citation rates in Mexican publications, warrant further examination. Moreover, our research emphasizes the urgency of bolstering research and development funding, which was consistently below 0.5% of GDP for the past four decades, falling short of legal mandates and international benchmarks. We endorse the establishment of robust research collectives in Latin America to address these challenges, foster regional scientific output, and transition from knowledge consumers to knowledge producers, thereby reducing dependence on foreign technology.
RESUMO
Invadopodia are matrix-degrading membrane protrusions in invasive carcinoma cells enriched in proteins that regulate actin polymerization. The on-off regulatory switch that initiates actin polymerization in invadopodia requires phosphorylation of tyrosine residues 421, 466, and 482 on cortactin. However, it is unknown which of these cortactin tyrosine phosphorylation sites control actin polymerization. We investigated the contribution of individual tyrosine phosphorylation sites (421, 466, and 482) on cortactin to the regulation of actin polymerization in invadopodia. We provide evidence that the phosphorylation of tyrosines 421 and 466, but not 482, is required for the generation of free actin barbed ends in invadopodia. In addition, these same phosphotyrosines are important for Nck1 recruitment to invadopodia via its SH2 domain, for the direct binding of Nck1 to cortactin in vitro, and for the FRET interaction between Nck1 and cortactin in invadopodia. Furthermore, matrix proteolysis-dependent tumor cell invasion is dramatically inhibited in cells expressing a mutation in phosphotyrosine 421 or 466. Together, these results identify phosphorylation of tyrosines 421 and 466 on cortactin as the crucial residues that regulate Nck1-dependent actin polymerization in invadopodia and tumor cell invasion, and suggest that specifically blocking either tyrosine 421 or 466 phosphorylation might be effective at inhibiting tumor cell invasion in vivo.
Assuntos
Actinas/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Neoplasias da Mama/metabolismo , Carcinoma/metabolismo , Cortactina/metabolismo , Citoesqueleto/metabolismo , Proteínas Oncogênicas/metabolismo , Pseudópodes/metabolismo , Actinas/genética , Carcinoma/patologia , Linhagem Celular Tumoral , Cortactina/genética , Feminino , Humanos , Invasividade Neoplásica/genética , Fosforilação , Ligação Proteica , Tirosina/genética , Domínios de Homologia de src/genéticaRESUMO
The vacuolar-ATPase (v-ATPase) is a proton transporter found on many intracellular organelles and the plasma membrane (PM). The v-ATPase on PMs of cancer cells may contribute to their invasive properties in vitro. Its relevance to human cancer tissues remains unclear. We investigated whether the expression and cellular localization of v-ATPase corresponded to the stage of human pancreatic cancer, and its effect on matrix metalloproteinase (MMP) activation in vitro. The intensity of v-ATPase staining increased significantly across the range of pancreatic histology from normal ducts to pancreatic intraepithelial neoplasms (PanIN), and finally pancreatic ductal adenocarcinoma (PDAC). Low-grade PanIN lesions displayed polarized staining confined to the basal aspect of the cell in the majority (86%) of fields examined. High-grade PanIN lesions and PDAC showed intense and diffuse v-ATPase localization. In pancreatic cancer cells, PM-associated v-ATPase colocalized with cortactin, a component of the leading edge that helps direct MMP release. Blockade of the v-ATPase with concanamycin or short-hairpin RNA targeting the V1E subunit reduced MMP-9 activity; this effect was greatest in cells with prominent PM-associated v-ATPase. In cells with detectable MMP-2 activities, however, treatment with concanamycin markedly increased MMP-2's most activated forms. V-ATPase blockade inhibited functional migration and invasion in those cells with predominantly MMP-9 activity. These results indicate that human PDAC specimens show loss of v-ATPase polarity and increased expression that correlates with increasing invasive potential. Thus, v-ATPase selectively modulates specific MMPs that may be linked to an invasive cancer phenotype.
Assuntos
Isoenzimas/metabolismo , Metaloproteinases da Matriz/metabolismo , Neoplasias Pancreáticas/enzimologia , ATPases Vacuolares Próton-Translocadoras/metabolismo , Linhagem Celular Tumoral , Ativação Enzimática , Técnicas de Silenciamento de Genes , Humanos , Imuno-Histoquímica , Invasividade Neoplásica , Neoplasias Pancreáticas/patologia , ATPases Vacuolares Próton-Translocadoras/antagonistas & inibidores , ATPases Vacuolares Próton-Translocadoras/genéticaRESUMO
Standardized protocols for wastewater-based surveillance (WBS) for the RNA of SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, are being developed and refined worldwide for early detection of disease outbreaks. We report here on lessons learned from establishing a WBS program for SARS-CoV-2 integrated with a human surveillance program for COVID-19. We have established WBS at three campuses of a university, including student residential dormitories and a hospital that treats COVID-19 patients. Lessons learned from this WBS program address the variability of water quality, new detection technologies, the range of detectable viral loads in wastewater, and the predictive value of integrating environmental and human surveillance data. Data from our WBS program indicated that water quality was statistically different between sewer sampling sites, with more variability observed in wastewater coming from individual buildings compared to clusters of buildings. A new detection technology was developed based upon the use of a novel polymerase called V2G. Detectable levels of SARS-CoV-2 in wastewater varied from 102 to 106 genomic copies (gc) per liter of raw wastewater (L). Integration of environmental and human surveillance data indicate that WBS detection of 100 gc/L of SARS-CoV-2 RNA in wastewater was associated with a positivity rate of 4% as detected by human surveillance in the wastewater catchment area, though confidence intervals were wide (ß ~ 8.99 ∗ ln(100); 95% CI = 0.90-17.08; p < 0.05). Our data also suggest that early detection of COVID-19 surges based on correlations between viral load in wastewater and human disease incidence could benefit by increasing the wastewater sample collection frequency from weekly to daily. Coupling simpler and faster detection technology with more frequent sampling has the potential to improve the predictive potential of using WBS of SARS-CoV-2 for early detection of the onset of COVID-19.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Pandemias , RNA Viral , Águas ResiduáriasRESUMO
Cultured cell lines are the workhorse of cancer research, but the extent to which they recapitulate the heterogeneity observed among malignant cells in tumors is unclear. Here we used multiplexed single-cell RNA-seq to profile 198 cancer cell lines from 22 cancer types. We identified 12 expression programs that are recurrently heterogeneous within multiple cancer cell lines. These programs are associated with diverse biological processes, including cell cycle, senescence, stress and interferon responses, epithelial-mesenchymal transition and protein metabolism. Most of these programs recapitulate those recently identified as heterogeneous within human tumors. We prioritized specific cell lines as models of cellular heterogeneity and used them to study subpopulations of senescence-related cells, demonstrating their dynamics, regulation and unique drug sensitivities, which were predictive of clinical response. Our work describes the landscape of heterogeneity within diverse cancer cell lines and identifies recurrent patterns of heterogeneity that are shared between tumors and specific cell lines.
Assuntos
Linhagem Celular Tumoral , Heterogeneidade Genética , Neoplasias/genética , Lesões Pré-Cancerosas/genética , Linhagem Celular Tumoral/efeitos dos fármacos , Senescência Celular/genética , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , RNA-Seq , Estresse Fisiológico/genética , Microambiente TumoralRESUMO
Anti-cancer uses of non-oncology drugs have occasionally been found, but such discoveries have been serendipitous. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. We used PRISM, a molecular barcoding method, to screen drugs against cell lines in pools. An unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines in a manner predictable from the cell lines' molecular features. Our findings include compounds that killed by inducing PDE3A-SLFN12 complex formation; vanadium-containing compounds whose killing depended on the sulfate transporter SLC26A2; the alcohol dependence drug disulfiram, which killed cells with low expression of metallothioneins; and the anti-inflammatory drug tepoxalin, which killed via the multi-drug resistance protein ABCB1. The PRISM drug repurposing resource (https://depmap.org/repurposing) is a starting point to develop new oncology therapeutics, and more rarely, for potential direct clinical translation.
Assuntos
Neoplasias , Linhagem Celular , Dissulfiram , Reposicionamento de Medicamentos , Humanos , Neoplasias/tratamento farmacológicoRESUMO
In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.
Assuntos
Mapeamento Cromossômico , Simulação por Computador , Camundongos Endogâmicos/genética , Locos de Características Quantitativas , Algoritmos , Animais , Bases de Dados Genéticas , Genoma , Haplótipos , Desequilíbrio de Ligação , Camundongos , Modelos Genéticos , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The use of microtechnique for studying cell division is well established (Begg & Ellis, 1979; Wadsworth, 1999; Zhang & Nicklas, 1999). The advantage of microinjection in cell division research is the timed delivery of a macromolecules at a particular stage of mitosis (for example, pre- vs postanaphase), which can circumvent the spindle assembly checkpoint (Hinchcliffe et al., 2016). Micromanipulation can be used to remove whole organelles, such as the centrosome or nucleus and examine the effects on cell division (Hinchcliffe et al., 2001; Hornick et al., 2011). The focus of this chapter is on methods for microinjection and micromanipulation of cultured mammalian cells. We describe pulling and shaping microneedles, as well as the imaging chambers we use. We also provide information on cell culture conditions, and imaging techniques used for our long-term observation studies, which allow cells to be followed on the order of several days.
Assuntos
Microinjeções/métodos , Microcirurgia/métodos , Mitose/fisiologia , Animais , Centrossomo/fisiologia , Humanos , Micromanipulação/métodos , Fuso Acromático/fisiologiaRESUMO
ABSTRACT Background: In Latin America, epilepsy in the elderly is a neglected issue that has never been studied. The epidemiological transition has significantly altered the demographics of epilepsy, and therefore, we would like to draw attention to this topic. Objective: We require local real-world evidence, as the literature often depicts a different scenario, including pharmacological management. Methods: From 2007 to 2018, we recruited all patients with new-onset geriatric epilepsy (first seizure after the age of 60) tracked from ten Mexican hospitals, adding them to patients with similar characteristics from a previously published study. The diagnosis was confirmed in all patients by a certified neurologist, and they were also studied using a conventional electroencephalogram and imaging workup. Results: A diagnosis of new-onset geriatric epilepsy (Elderly patients was established in 100 cases. No specific cause was found in 26% of patients, while 42% had a stroke and 10% had neurocysticercosis (NCC). Monotherapy was the choice in 83 patients, and phenytoin was the most used drug (50%), followed by carbamazepine (25%). Conclusion: NCC remains a frequent cause of new-onset geriatric epilepsy. This distribution is not seen in the literature, mainly representing patients from wealthy economies. In our setting, financial constraints influence the choice of the drug, and newer antiepileptic drugs should be made more affordable to this population with economic and physical frailty.
RESUMO
Adherent cells cultured on flat, homogeneous surfaces typically maintain an intact cell body with a polygonal or fan shape, despite active migration and strong mechanical interactions with the substratum. We hypothesized that, in addition to the constraint of the surface membrane, an active mechanism may be involved in maintaining the shape and integrity of the cell body particularly where cells encounter complex topographic patterns of guidance cues. To detect if there is a mechanism that constrains cell shape, we plated NIH 3T3 fibroblasts on ring-patterned substrata 8-17.5 microns in width and 53-133 microns in outer diameter. Untreated cells have a limited angular span, encompassing an average of 108 degrees around the ring, even though these cells were able to cover a much larger surface when plated on flat surfaces of the same material. Treatment of 3T3 cells with a myosin II inhibitor, blebbistatin, induced a striking increase in the bending ability, causing cells to cover more than 60% of the ring. Inhibition of the Rho-dependent kinase with Y-27632 caused a similar but smaller increase in the angular span. Our results suggest that cell shape is controlled not only by the passive constraint of the surface membrane but also by an active mechanism driven by myosin II-mediated contractility under the regulation of Rho-dependent kinase. The inward surface tension-like forces allow the cell to maintain its integrity while navigating through complex physiological environments.
RESUMO
Breast carcinoma cells use specialized, actin-rich protrusions called invadopodia to degrade and invade through the extracellular matrix. Phosphorylation of the actin nucleation-promoting factor and actin-stabilizing protein cortactin downstream of the epidermal growth factor receptor-Src-Arg kinase cascade is known to be a critical trigger for invadopodium maturation and subsequent cell invasion in breast cancer cells. The functions of cortactin phosphorylation in this process, however, are not completely understood. We identify the Rho-family guanine nucleotide exchange factor Vav2 in a comprehensive screen for human SH2 domains that bind selectively to phosphorylated cortactin. We demonstrate that the Vav2 SH2 domain binds selectively to phosphotyrosine-containing peptides corresponding to cortactin tyrosines Y421 and Y466 but not to Y482. Mutation of the Vav2 SH2 domain disrupts its recruitment to invadopodia, and an SH2-domain mutant form of Vav2 cannot support efficient matrix degradation in invasive MDA-MB-231 breast cancer cells. We show that Vav2 function is required for promoting invadopodium maturation and consequent actin polymerization, matrix degradation, and invasive migratory behavior. Using biochemical assays and a novel Rac3 biosensor, we show that Vav2 promotes Rac3 activation at invadopodia. Rac3 knockdown reduces matrix degradation by invadopodia, whereas a constitutively active Rac3 can rescue the deficits in invadopodium function in Vav2-knockdown cells. Together these data indicate that phosphorylated cortactin recruits Vav2 to activate Rac3 and promote invadopodial maturation in invasive breast cancer cells.
Assuntos
Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Cortactina/metabolismo , Podossomos/metabolismo , Proteínas Proto-Oncogênicas c-vav/metabolismo , Actinas/metabolismo , Linhagem Celular Tumoral , Matriz Extracelular/metabolismo , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Humanos , Invasividade Neoplásica , Fosforilação , Fosfotirosina/metabolismo , Podossomos/fisiologia , Proteínas Tirosina Quinases/metabolismo , Pseudópodes/metabolismo , Proteínas rac de Ligação ao GTP/metabolismoRESUMO
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome. RESULTS: As part of that effort, we have developed a framework to integrate, navigate, and analyze drug discovery data based on formalized and standardized classifications and annotations of druggable protein targets, the Drug Target Ontology (DTO). DTO was constructed by extensive curation and consolidation of various resources. DTO classifies the four major drug target protein families, GPCRs, kinases, ion channels and nuclear receptors, based on phylogenecity, function, target development level, disease association, tissue expression, chemical ligand and substrate characteristics, and target-family specific characteristics. The formal ontology was built using a new software tool to auto-generate most axioms from a database while supporting manual knowledge acquisition. A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem of biomedical ontologies. As a formal OWL-DL ontology, DTO contains asserted and inferred axioms. Modeling data from the Library of Integrated Network-based Cellular Signatures (LINCS) program illustrates the potential of DTO for contextual data integration and nuanced definition of important drug target characteristics. DTO has been implemented in the IDG user interface Portal, Pharos and the TIN-X explorer of protein target disease relationships. CONCLUSIONS: DTO was built based on the need for a formal semantic model for druggable targets including various related information such as protein, gene, protein domain, protein structure, binding site, small molecule drug, mechanism of action, protein tissue localization, disease association, and many other types of information. DTO will further facilitate the otherwise challenging integration and formal linking to biological assays, phenotypes, disease models, drug poly-pharmacology, binding kinetics and many other processes, functions and qualities that are at the core of drug discovery. The first version of DTO is publically available via the website http://drugtargetontology.org/ , Github ( http://github.com/DrugTargetOntology/DTO ), and the NCBO Bioportal ( http://bioportal.bioontology.org/ontologies/DTO ). The long-term goal of DTO is to provide such an integrative framework and to populate the ontology with this information as a community resource.
Assuntos
Ontologias Biológicas , Biologia Computacional/métodos , Sistemas de Liberação de Medicamentos/métodos , Descoberta de Drogas/métodos , Humanos , Proteínas/classificação , Proteínas/genética , Proteínas/metabolismo , Semântica , SoftwareRESUMO
African Americans and Hispanics in the United States have much higher rates of HIV than non-minorities. There is now strong evidence that a range of behavioral interventions are efficacious in reducing sexual risk behavior in these populations. Although a handful of these programs are just beginning to be disseminated widely, we still have not implemented effective programs to a level that would reduce the population incidence of HIV for minorities. We proposed that innovative approaches involving computational technologies be explored for their use in both developing new interventions and in supporting wide-scale implementation of effective behavioral interventions. Mobile technologies have a place in both of these activities. First, mobile technologies can be used in sensing contexts and interacting to the unique preferences and needs of individuals at times where intervention to reduce risk would be most impactful. Second, mobile technologies can be used to improve the delivery of interventions by facilitators and their agencies. Systems science methods including social network analysis, agent-based models, computational linguistics, intelligent data analysis, and systems and software engineering all have strategic roles that can bring about advances in HIV prevention in minority communities. Using an existing mobile technology for depression and 3 effective HIV prevention programs, we illustrated how 8 areas in the intervention/implementation process can use innovative computational approaches to advance intervention adoption, fidelity, and sustainability.
Assuntos
Metodologias Computacionais , Infecções por HIV/prevenção & controle , Implementação de Plano de Saúde , Promoção da Saúde/métodos , Grupos Minoritários , Negro ou Afro-Americano , Telefone Celular , Previsões , Infecções por HIV/etnologia , Hispânico ou Latino , Humanos , Avaliação de Programas e Projetos de Saúde , Comportamento de Redução do Risco , Comportamento Sexual , Estados UnidosRESUMO
The role of centrosomes and centrioles during mitotic spindle assembly in vertebrates remains controversial. In cell-free extracts and experimentally derived acentrosomal cells, randomly oriented microtubules (MTs) self-organize around mitotic chromosomes and assemble anastral spindles. However, vertebrate somatic cells normally assemble a connected pair of polarized, astral MT arrays--termed an amphiaster ("a star on both sides")--that is formed by the splitting and separation of the microtubule-organizing center (MTOC) well before nuclear envelope breakdown (NEB). Whether amphiaster formation requires splitting of duplicated centrosomes is not known. We found that when centrosomes were removed from living vertebrate cells early in their cell cycle, an acentriolar MTOC reassembled, and, prior to NEB, a functional amphiastral spindle formed. Cytoplasmic dynein, dynactin, and pericentrin are all recruited to the interphase aMTOC, and the activity of kinesin-5 is needed for amphiaster formation. Mitosis proceeded on time and these karyoplasts divided in two. However, ~35% of aMTOCs failed to split and separate before NEB, and these entered mitosis with persistent monastral spindles. Chromatin-associated RAN-GTP--the small GTPase Ran in its GTP bound state--could not restore bipolarity to monastral spindles, and these cells exited mitosis as single daughters. Our data reveal the novel finding that MTOC separation and amphiaster formation does not absolutely require the centrosome, but, in its absence, the fidelity of bipolar spindle assembly is highly compromised.