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1.
ALTEX ; 37(1): 64-74, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31453632

RESUMO

New approaches, like the Adverse Outcome Pathway (AOP) framework, have been developed to describe how chemicals cause toxicity by linking in vitro assays to adverse health outcomes. However, approaches, tools and resources for development of AOPs have not been well described. Here we review information resources for AOP development and define a streamlined process for linking a chemical to an existing AOP. We propose a four step process to facilitate AOP development: link the uncharacterized chemical directly to Molecular Initiating Events, Key Events, or Adverse Outcomes; identify analogs with toxicological information for the uncharacterized chemical; link the characterized chemical (initial chemical if characterized, a characterized analog if initial chemical is not) to Molecular Initiating Events, Key Events, or Adverse Outcomes; and identify AOPs that contain the Molecular Initiating Events, Key Events, or Adverse Outcomes that were found in Steps 1 and 3. The process and library of informational resources proposed and tested here served as the foundation for an informational online tool (AOPERA) that helps practitioners identify their current-state knowledge gaps, navigate the four-step process, and connect to relevant resources. AOPERA can be found at https://igbb.github.io/AOPERA_HTML. Additionally, we anticipate that by simplifying and standardizing the process of linking a chemical to a known AOP, we will lower the barrier to entry for this objective and increase its accessibility to new practitioners. In turn, this may increase the demand for new or improved AOPs to which practitioners can link chemicals, thereby contributing to the expansion of the library of known AOPs.

2.
PLoS One ; 14(12): e0226687, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31877201

RESUMO

Large scale biological responses are inherently uncertain, in part as a consequence of noisy systems that do not respond deterministically to perturbations and measurement errors inherent to technological limitations. As a result, they are computationally difficult to model and current approaches are notoriously slow and computationally intensive (multiscale stochastic models), fail to capture the effects of noise across a system (chemical kinetic models), or fail to provide sufficient biological fidelity because of broad simplifying assumptions (stochastic differential equations). We use a new approach to modeling multiscale stationary biological processes that embraces the noise found in experimental data to provide estimates of the parameter uncertainties and the potential mis-specification of models. Our approach models the mean stationary response at each biological level given a particular expected response relationship, capturing variation around this mean using conditional Monte Carlo sampling that is statistically consistent with training data. A conditional probability distribution associated with a biological response can be reconstructed using this method for a subset of input values, which overcomes the parameter identification problem. Our approach could be applied in addition to dynamical modeling methods (see above) to predict uncertain biological responses over experimental time scales. To illustrate this point, we apply the approach to a test case in which we model the variation associated with measurements at multiple scales of organization across a reproduction-related Adverse Outcome Pathway described for teleosts.

3.
Risk Anal ; 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31721239

RESUMO

Adverse outcome pathway Bayesian networks (AOPBNs) are a promising avenue for developing predictive toxicology and risk assessment tools based on adverse outcome pathways (AOPs). Here, we describe a process for developing AOPBNs. AOPBNs use causal networks and Bayesian statistics to integrate evidence across key events. In this article, we use our AOPBN to predict the occurrence of steatosis under different chemical exposures. Since it is an expert-driven model, we use external data (i.e., data not used for modeling) from the literature to validate predictions of the AOPBN model. The AOPBN accurately predicts steatosis for the chemicals from our external data. In addition, we demonstrate how end users can utilize the model to simulate the confidence (based on posterior probability) associated with predicting steatosis. We demonstrate how the network topology impacts predictions across the AOPBN, and how the AOPBN helps us identify the most informative key events that should be monitored for predicting steatosis. We close with a discussion of how the model can be used to predict potential effects of mixtures and how to model susceptible populations (e.g., where a mutation or stressor may change the conditional probability tables in the AOPBN). Using this approach for developing expert AOPBNs will facilitate the prediction of chemical toxicity, facilitate the identification of assay batteries, and greatly improve chemical hazard screening strategies.

4.
Mol Ther Methods Clin Dev ; 13: 463-473, 2019 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-31193384

RESUMO

Gene delivery vehicles currently in the clinic for treatment of monogenic disorders lack sufficient carrying capacity to efficiently address complex polygenic diseases. Thus, to engineer multifaceted genetic circuits for bioengineering human cells as a therapeutic option for polygenic diseases, we require new tools that are currently in their infancy. Mammalian artificial chromosomes, or synthetic chromosomes, represent a viable approach for delivery of large genetic payloads that are mitotically stable and remain independent of the host genome. Previously, we described a mammalian synthetic chromosome platform, termed the ACE system, that requires a single unidirectional integrase for the introduction of multiple genes onto the ACE platform chromosome. In this report, we provide a proof of concept that the ACE synthetic chromosome bioengineering platform is amenable to sequential delivery of off-the-shelf large genomic fragments. Specifically, large genomic clones spanning the human solute carrier family 2, facilitated glucose transporter member 1 (SLC2A1 or GLUT1, 169 kbp), and human monocarboxylate transporter 1 (SLC16A1 or MCT1, 144 kbp) genetic loci were engineered onto the ACE platform and demonstrated to express and correctly splice both gene transcripts. Thus, the ACE system provides a facile and tractable engineering platform for the development of gene-based therapeutic agents targeting polygenic diseases.

5.
Chem Res Toxicol ; 32(6): 1212-1222, 2019 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-31074622

RESUMO

Exposure to certain chemicals such as disinfectants through inhalation is suspected to be involved in the development of pulmonary fibrosis, a lung disease in which lung tissue becomes damaged and scarred. Pulmonary fibrosis is known to be regulated by transforming growth factor ß (TGF-ß) and peroxisome proliferator-activated receptor gamma (PPARγ). Here, we developed an adverse outcome pathway (AOP) to better define the linkage of PPARγ antagonism to the adverse outcome of pulmonary fibrosis. We then conducted a systematic analysis to identify potential chemicals involved in this AOP, using the ToxCast database and deep learning artificial neural network models. We identified chemicals bearing a potential inhalation hazard and exposure hazards from the database that could be related to this AOP. For chemicals that were not present in the ToxCast database, multilayer perceptron models were developed based on the ToxCast assays related to the AOP. The reactivity of ToxCast untested chemicals was then predicted using these deep learning models. Both approaches identified a set of chemicals that could be used to validate the AOP. This study suggests that chemicals categorized using an existing database such as ToxCast can be used to validate an AOP and that deep learning approaches can be used to characterize a range of potential active chemicals for an AOP of interest.

6.
Environ Toxicol Chem ; 38(9): 1850-1865, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31127958

RESUMO

An important goal in toxicology is the development of new ways to increase the speed, accuracy, and applicability of chemical hazard and risk assessment approaches. A promising route is the integration of in vitro assays with biological pathway information. We examined how the adverse outcome pathway (AOP) framework can be used to develop pathway-based quantitative models useful for regulatory chemical safety assessment. By using AOPs as initial conceptual models and the AOP knowledge base as a source of data on key event relationships, different methods can be applied to develop computational quantitative AOP models (qAOPs) relevant for decision making. A qAOP model may not necessarily have the same structure as the AOP it is based on. Useful AOP modeling methods range from statistical, Bayesian networks, regression, and ordinary differential equations to individual-based models and should be chosen according to the questions being asked and the data available. We discuss the need for toxicokinetic models to provide linkages between exposure and qAOPs, to extrapolate from in vitro to in vivo, and to extrapolate across species. Finally, we identify best practices for modeling and model building and the necessity for transparent and comprehensive documentation to gain confidence in the use of qAOP models and ultimately their use in regulatory applications. Environ Toxicol Chem 2019;38:1850-1865. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

7.
BMC Bioinformatics ; 20(Suppl 2): 103, 2019 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-30871459

RESUMO

BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier. RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska. CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .


Assuntos
Metagenômica/métodos , Biodiversidade
8.
Crit Rev Biotechnol ; 39(3): 351-365, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30727764

RESUMO

Emerging technologies research often covers various perspectives in disciplines and research areas ranging from hard sciences, engineering, policymaking, and sociology. However, the interrelationship between these different disciplinary domains, particularly the physical and social sciences, often occurs many years after a technology has matured and moved towards commercialization. Synthetic biology may serve an exception to this idea, where, since 2000, the physical and the social sciences communities have increasingly framed their research in response to various perspectives in biological engineering, risk assessment needs, governance challenges, and the social implications that the technology may incur. This paper reviews a broad collection of synthetic biology literature from 2000-2016, and demonstrates how the co-development of physical and social science communities has grown throughout synthetic biology's earliest stages of development. Further, this paper indicates that future co-development of synthetic biology scholarship will assist with significant challenges of the technology's risk assessment, governance, and public engagement needs, where an interdisciplinary approach is necessary to foster sustainable, risk-informed, and societally beneficial technological advances moving forward.


Assuntos
Bioengenharia/tendências , Política Pública/tendências , Sociologia/tendências , Biologia Sintética/tendências , Humanos , Pesquisa/tendências , Ciências Sociais
9.
ALTEX ; 36(3): 353-362, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30662994

RESUMO

The adverse outcome pathway (AOP) framework is a conceptual construct that mechanistically links molecular initiating events to adverse biological outcomes through a series of causal key events (KEs) that represent the perturbation of the biological system. Quantitative, predictive AOPs are necessary for screening emerging contaminants and potential substitutes to inform their prioritization for testing. In practice, they are not widely used because they can be costly to develop and validate. A modular approach for assembly of quantitative AOPs, based on existing knowledge, would allow for rapid development of biological pathway models to screen contaminants for potential hazards and prioritize them for subsequent testing and modeling. For each pair of KEs, a quantitative KE relationship (KER) can be derived as a response-response function or a conditional probability matrix describing the anticipated change in a KE based on the response of the prior KE. This transfer of response across KERs can be used to assemble a quantitative AOP. Here we demonstrate the use of proposed approach in two cases: inhibition of cytochrome P450 aromatase leading to reduced fecundity in fathead minnows and ionic glutamate receptor mediated excitotoxicity leading to memory impairment in rodents. The model created from these chains have value in characterizing the pathway and the potential or relative level of toxicological effect anticipated. This approach to simplistic, modular AOP models has wide applicability for rapid development of biological pathway models.


Assuntos
Rotas de Resultados Adversos , Pesquisa Biomédica , Toxicologia , Animais , Humanos
10.
ALTEX ; 36(1): 103-120, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30415271

RESUMO

There is a need for fast, efficient, and cost-effective hazard identification and characterization of chemical hazards. This need is generating increased interest in the use of zebrafish embryos as both a screening tool and an alternative to mammalian test methods. A Collaborative Workshop on Aquatic Models and 21st Century Toxicology identified the lack of appropriate and consistent testing protocols as a challenge to the broader application of the zebrafish embryo model. The National Toxicology Program established the Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) initiative to address the lack of consistent testing guidelines and identify sources of variability for zebrafish-based assays. This report summarizes initial SEAZIT information-gathering efforts. Investigators in academic, government, and industry laboratories that routinely use zebrafish embryos for chemical toxicity testing were asked about their husbandry practices and standard protocols. Information was collected about protocol components including zebrafish strains, feed, system water, disease surveillance, embryo exposure conditions, and endpoints. Literature was reviewed to assess issues raised by the investigators. Interviews revealed substantial variability across design parameters, data collected, and analysis procedures. The presence of the chorion and renewal of exposure media (static versus static-renewal) were identified as design parameters that could potentially influence study outcomes and should be investigated further with studies to determine chemical uptake from treatment solution into embryos. The information gathered in this effort provides a basis for future SEAZIT activities to promote more consistent practices among researchers using zebrafish embryos for toxicity evaluation.


Assuntos
Embrião não Mamífero , Testes de Toxicidade/métodos , Peixe-Zebra/embriologia , Animais , Córion/metabolismo , Avaliação Pré-Clínica de Medicamentos/métodos , Desenvolvimento Embrionário/efeitos dos fármacos , Ensaios de Triagem em Larga Escala
11.
ALTEX ; 36(1): 91-102, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30332685

RESUMO

Current efforts in chemical safety are focused on utilizing human in vitro or alternative animal data in biological pathway context. However, it remains unclear how biological pathways, and toxicology data developed in that context, can be used to quantitatively facilitate decision-making.  The objective of this work is to determine if hypothesis testing using Adverse Outcome Pathways (AOPs) can provide quantitative chemical hazard predictions.  Current methods for predicting hazards of chemicals in a biological pathway context were extensively reviewed, specific case studies examined and computational modeling used to demonstrate quantitative hazard prediction based on an AOP. Since AOPs are chemically agnostic, we propose that AOPs function as hypotheses for how specific chemicals may cause adverse effects via specific pathways. Three broad approaches were identified for testing the hypothesis with AOPs, semi-quantitative weight of evidence, probabilistic, and mechanistic modeling. We then demonstrate how these approaches could be used to test hypotheses using high throughput in vitro data and alternative animal data. Finally, we discuss standards in development and documentation that would facilitate use in a regulatory context. We conclude that quantitative AOPs provide a flexible hypothesis framework for predicting chemical hazards. It accommodates a wide range of approaches that are useful at many stages and build upon one another to become increasingly quantitative.


Assuntos
Rotas de Resultados Adversos , Alternativas aos Testes com Animais , Simulação por Computador , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Substâncias Perigosas/toxicidade , Animais , Tomada de Decisões , Humanos , Projetos de Pesquisa , Medição de Risco
12.
BMC Genomics ; 19(1): 877, 2018 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-30518325

RESUMO

BACKGROUND: The health and resilience of species in natural environments is increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizards (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays. RESULTS: Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms linking transcript expression and toxicological phenotypes. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to TNT-induced anemia and/or methemoglobinemia and caused dose-specific effects on genes involved in lipid and overall energy metabolism consistent with a hormesis response of growth stimulation at low doses and adverse decreases in lizard growth at high doses. Functional enrichment results were indicative of inhibited potential for lipid mobilization and catabolism in TNT exposures which corresponded with increased inguinal fat weights and was suggestive of a decreased overall energy budget. Malaria infection elicited enriched expression of multiple immune-related functions likely corresponding to increased white blood cell (WBC) counts. Food limitation alone enriched functions related to cellular energy production and decreased expression of immune responses consistent with a decrease in WBC levels. CONCLUSIONS: Despite these findings, the lizards demonstrated immune resilience to malaria infection under food limitation with transcriptional results indicating a fully competent immune response to malaria, even under bio-energetic constraints. Interestingly, both TNT and malaria individually increased transcriptional expression of immune-related genes and increased overall WBC concentrations in blood; responses that were retained in the TNT x malaria combined exposure. The results demonstrate complex and sometimes unexpected responses to multiple stressors where the lizards displayed remarkable resiliency to the stressor combinations investigated.


Assuntos
Poluentes Ambientais/toxicidade , Lagartos/metabolismo , Transcriptoma/efeitos dos fármacos , Animais , Peso Corporal/efeitos dos fármacos , Mudança Climática , Análise por Conglomerados , Ecossistema , Metabolismo Energético/efeitos dos fármacos , Eritropoese/efeitos dos fármacos , Hemólise/efeitos dos fármacos , Fígado/efeitos dos fármacos , Fígado/metabolismo , Lagartos/genética , Lagartos/parasitologia , Linfócitos/citologia , Linfócitos/imunologia , Linfócitos/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Fenótipo , Plasmodium/patogenicidade , RNA/química , RNA/isolamento & purificação , RNA/metabolismo , Análise de Sequência de RNA , Baço/parasitologia , Baço/fisiologia , Trinitrotolueno/toxicidade
13.
Clin Lymphoma Myeloma Leuk ; 18(9): 569-575.e1, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30122201

RESUMO

BACKGROUND: The proteasome inhibitor bortezomib has demonstrated marked preclinical activity when combined with the histone deacetylase inhibitor vorinostat in leukemia, multiple myeloma, and mantle cell lymphoma (MCL) cells. The present study evaluated the efficacy and safety of the combination in patients with relapsed or refractory MCL and diffuse large B-cell lymphoma (DLBCL). PATIENTS AND METHODS: The present multicenter, nonrandomized phase II trial used a Simon 2-stage design with 3 cohorts: cohort A, MCL with no previous bortezomib (including untreated MCL); cohort B, MCL with previous bortezomib; and cohort C, relapsed or refractory DLBCL with no previous bortezomib. Vorinostat (400 mg) was administered orally on days 1 to 5 and 8 to 12 before bortezomib (1.3 mg/m2), which was administered intravenously on days 1, 4, 8, and 11 of each 21-day cycle. RESULTS: For the 65 treated patients (22 in cohort A, 4 in cohort B, and 39 in cohort C), the overall response rate was 31.8%, 0%, and 7.7%, respectively. The median progression-free survival was 7.6 months for cohort A and 1.8 months for cohort C. In cohort A, 7 patients had a partial response (PRs), 5 had stable disease (SD), 7 had progressive disease (PD), 1 was not assessed, and 2 were not evaluable. In cohort B, 2 had SD and 2 had PD. In cohort C, 3 had a PR, 8 had SD, 23 had PD, and 5 were not assessed. Baseline NF-κB activation, measured as nuclear RelA by immunohistochemistry, did not correlate with clinical response. CONCLUSION: The combination of bortezomib and vorinostat is safe and has modest activity in MCL and limited activity in DLBCL.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Linfoma Difuso de Grandes Células B/tratamento farmacológico , Linfoma de Célula do Manto/tratamento farmacológico , Recidiva Local de Neoplasia/tratamento farmacológico , Terapia de Salvação , Adulto , Idoso , Idoso de 80 Anos ou mais , Bortezomib/administração & dosagem , Feminino , Seguimentos , Humanos , Linfoma Difuso de Grandes Células B/patologia , Linfoma de Célula do Manto/patologia , Masculino , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/patologia , Prognóstico , Estudos Prospectivos , Taxa de Sobrevida , Vorinostat/administração & dosagem
14.
Colloids Surf B Biointerfaces ; 161: 210-218, 2018 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-29080505

RESUMO

This effort utilizes a genetically tunable system of bacteriophage to evaluate the effect of charge, temperature and particle concentration on biomaterial synthesis utilizing the coffee ring (CR) effect. There was a 1.6-3 fold suppression of the CR at higher temperatures while maintaining self-assembled structures of thin films. This suppression was observed in phage with charged and uncharged surface chemistry, which formed ordered and disordered assemblies respectively, indicating CR suppression is not dependent on short-range ordering or surface chemistry. Analysis of the drying process suggests weakened capillary flow at elevated temperatures caused CR suppression and could be further enhanced for controlled assembly for advanced biomaterials.


Assuntos
Bacteriófago M13/química , Nanoestruturas/química , Volatilização , Algoritmos , Bacteriófago M13/genética , Bacteriófago M13/ultraestrutura , Microscopia Eletrônica de Varredura , Nanoestruturas/ultraestrutura , Tamanho da Partícula , Propriedades de Superfície , Temperatura Ambiente
15.
Genes Dev ; 31(18): 1858-1869, 2017 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-29021243

RESUMO

The piRNA pathway represses transposable elements in the gonads and thereby plays a vital role in protecting the integrity of germline genomes of animals. Mature piRNAs are processed from longer transcripts, piRNA precursors (pre-piRNAs). In Drosophila, processing of pre-piRNAs is initiated by piRNA-guided Slicer cleavage or the endonuclease Zucchini (Zuc). As Zuc does not have any sequence or structure preferences in vitro, it is not known how piRNA precursors are selected and channeled into the Zuc-dependent processing pathway. We show that a heterologous RNA that lacks complementary piRNAs is processed into piRNAs upon recruitment of several piRNA pathway factors. This processing requires Zuc and the helicase Armitage (Armi). Aubergine (Aub), Argonaute 3 (Ago3), and components of the nuclear RDC complex, which are required for normal piRNA biogenesis in germ cells, are dispensable. Our approach allows discrimination of proteins involved in the transcription and export of piRNA precursors from components required for the cytoplasmic processing steps. piRNA processing correlates with localization of the substrate RNA to nuage, a distinct membraneless cytoplasmic compartment, which surrounds the nucleus of germ cells, suggesting that sequestration of RNA to this subcellular compartment is both necessary and sufficient for selecting piRNA biogenesis substrates.


Assuntos
Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Endorribonucleases/metabolismo , RNA Helicases/metabolismo , Precursores de RNA/metabolismo , Processamento Pós-Transcricional do RNA , RNA Interferente Pequeno/biossíntese , Animais , Proteínas Argonauta/genética , Proteínas Argonauta/metabolismo , Citoplasma/metabolismo , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Endorribonucleases/genética , Feminino , Células Germinativas/metabolismo , Ovário/metabolismo , Fatores de Iniciação de Peptídeos/genética , Fatores de Iniciação de Peptídeos/metabolismo , RNA Helicases/genética
16.
Nat Protoc ; 12(9): 1999-2013, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28858289

RESUMO

Large-scale fabrication of precisely defined nanostructures with tunable functions is critical to the exploitation of nanoscience and nanotechnology for production of electronic devices, energy generators, biosensors, and bionanomedicines. Although self-assembly processes have been developed to exploit biological molecules for functional materials, the resulting nanostructures and functions are still very limited, and scalable synthesis is far from being realized. Recently, we have established a bacteriophage-based biomimetic process, called 'self-templating assembly'. We used bacteriophage as a nanofiber model system to exploit its liquid crystalline structure for the creation of diverse hierarchically organized structures. We have also demonstrated that genetic modification of functional peptides of bacteriophage results in structures that can be used as soft and hard tissue-regenerating materials, biosensors, and energy-generating materials. Here, we describe a comprehensive protocol to perform genetic engineering of phage, liter-scale amplification, purification, and self-templating assembly, and suggest approaches for characterizing hierarchical phage nanostructures using optical microscopy, atomic-force microscopy (AFM), and scanning electron microscopy (SEM). We also discuss sources of contamination, common mistakes during the fabrication process, and quality-control measures to ensure reproducible material production. The protocol takes ∼8-10 d to complete.


Assuntos
Bacteriófago M13/química , Bacteriófago M13/metabolismo , Biomimética/métodos , Engenharia Genética/métodos , Nanofibras/química , Nanotecnologia/métodos , Microscopia de Força Atômica , Nanofibras/virologia
17.
Gen Comp Endocrinol ; 252: 79-87, 2017 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-28736226

RESUMO

Cytochrome P450 aromatase catalyzes conversion of C19 androgens to C18 estrogens and is critical for normal reproduction in female vertebrates. Fadrozole is a model aromatase inhibitor that has been shown to suppress estrogen production in the ovaries of fish. However, little is known about the early impacts of aromatase inhibition on steroid production and gene expression in fish. Adult female fathead minnows (Pimephales promelas) were exposed via water to 0, 5, or 50µg fadrozole/L for a time-course of 0.5, 1, 2, 4, and 6h, or 0 or 50µg fadrozole/L for a time-course of 6, 12, and 24h. We examined ex vivo ovarian 17ß-estradiol (E2) and testosterone (T) production, and plasma E2 concentrations from each study. Expression profiles of genes known or hypothesized to be impacted by fadrozole including aromatase (cytochrome P450 [cyp] 19a1a), steriodogenic acute regulatory protein (star), cytochrome P450 side-chain cleavage (cyp11a), cytochrome P450 17 alpha hydroxylase/17,20 lyase (cyp17), and follicle stimulating hormone receptor (fshr) were measured in the ovaries by quantitative real-time polymerase chain reaction (QPCR). In addition, broader ovarian gene expression was examined using a 15k fathead minnow microarray. The 5µg/L exposure significantly reduced ex vivo E2 production by 6h. In the 50µg/L treatment, ex vivo E2 production was significantly reduced after just 2h of exposure and remained depressed at all time-points examined through 24h. Plasma E2 concentrations were significantly reduced as early as 4h after initiation of exposure to either 5 or 50µg fadrozole/L and remained depressed throughout 24h in the 50µg/L exposure. Ex vivo T concentrations remained unchanged throughout the time-course. Expression of transcripts involved in steroidogenesis increased within the first 24h suggesting rapid induction of a mechanism to compensate for fadrozole inhibition of aromatase. Microarray results also showed fadrozole exposure caused concentration- and time-dependent changes in gene expression profiles in many HPG-axis pathways as early as 4h. This study provides insights into the very rapid effects of aromatase inhibition on steroidogenic processes in fish.


Assuntos
Inibidores da Aromatase/farmacologia , Cyprinidae/genética , Fadrozol/farmacologia , Regulação da Expressão Gênica/efeitos dos fármacos , Ovário/metabolismo , Esteroides/biossíntese , Animais , Cyprinidae/sangue , Cyprinidae/metabolismo , Estradiol/sangue , Feminino , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/genética , Testosterona/sangue , Transcriptoma/genética
18.
Environ Sci Technol ; 51(15): 8701-8712, 2017 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-28651047

RESUMO

We examined whether contaminants present in surface waters could be prioritized for further assessment by linking the presence of specific chemicals to gene expression changes in exposed fish. Fathead minnows were deployed in cages for 2, 4, or 8 days at three locations near two different wastewater treatment plant discharge sites in the Saint Louis Bay, Duluth, MN and one upstream reference site. The biological impact of 51 chemicals detected in the surface water of 133 targeted chemicals was determined using biochemical endpoints, exposure activity ratios for biological and estrogenic responses, known chemical:gene interactions from biological pathways and knowledge bases, and analysis of the covariance of ovary gene expression with surface water chemistry. Thirty-two chemicals were significantly linked by covariance with expressed genes. No estrogenic impact on biochemical endpoints was observed in male or female minnows. However, bisphenol A (BPA) was identified by chemical:gene covariation as the most impactful estrogenic chemical across all exposure sites. This was consistent with identification of estrogenic effects on gene expression, high BPA exposure activity ratios across all test sites, and historical analysis of the study area. Gene expression analysis also indicated the presence of nontargeted chemicals including chemotherapeutics consistent with a local hospital waste stream. Overall impacts on gene expression appeared to be related to changes in treatment plant function during rain events. This approach appears useful in examining the impacts of complex mixtures on fish and offers a potential route in linking chemical exposure to adverse outcomes that may reduce population sustainability.


Assuntos
Cyprinidae/genética , Águas Residuárias , Poluentes Químicos da Água/toxicidade , Animais , Monitoramento Ambiental , Estrona , Feminino , Masculino , Testes de Mutagenicidade , Medição de Risco
19.
Environ Toxicol Chem ; 36(6): 1411-1421, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28543973

RESUMO

Our ability to conduct whole-organism toxicity tests to understand chemical safety has been outpaced by the synthesis of new chemicals for a wide variety of commercial applications. As a result, scientists and risk assessors are turning to mechanistically based studies to increase efficiencies in chemical risk assessment and making greater use of in vitro and in silico methods to evaluate potential environmental and human health hazards. In this context, the adverse outcome pathway (AOP) framework has gained traction in regulatory science because it offers an efficient and effective means for capturing available knowledge describing the linkage between mechanistic data and the apical toxicity end points required for regulatory assessments. A number of international activities have focused on AOP development and various applications to regulatory decision-making. These initiatives have prompted dialogue between research scientists and regulatory communities to consider how best to use the AOP framework. Although expert-facilitated discussions and AOP development have been critical in moving the science of AOPs forward, it was recognized that a survey of the broader scientific and regulatory communities would aid in identifying current limitations while guiding future initiatives for the AOP framework. To that end, a global horizon scanning exercise was conducted to solicit questions concerning the challenges or limitations that must be addressed to realize the full potential of the AOP framework in research and regulatory decision-making. The questions received fell into several broad topical areas: AOP networks, quantitative AOPs, collaboration on and communication of AOP knowledge, AOP discovery and development, chemical and cross-species extrapolation, exposure/toxicokinetics considerations, and AOP applications. Expert ranking was then used to prioritize questions for each category, where 4 broad themes emerged that could help inform and guide future AOP research and regulatory initiatives. In addition, frequently asked questions were identified and addressed by experts in the field. Answers to frequently asked questions will aid in addressing common misperceptions and will allow for clarification of AOP topics. The need for this type of clarification was highlighted with surprising frequency by our question submitters, indicating that improvements are needed in communicating the AOP framework among the scientific and regulatory communities. Overall, horizon scanning engaged the global scientific community to help identify key questions surrounding the AOP framework and guide the direction of future initiatives. Environ Toxicol Chem 2017;36:1411-1421. © 2017 SETAC.


Assuntos
Medição de Risco/métodos , Animais , Organismos Aquáticos/efeitos dos fármacos , Organismos Aquáticos/fisiologia , Regulamentação Governamental , Substâncias Perigosas/toxicidade , Humanos , Modelos Teóricos , Inquéritos e Questionários
20.
Toxicol Sci ; 158(2): 252-262, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28525648

RESUMO

In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (United Kingdom) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (eg, transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments. In light of the growing number of examples of the application of omics data in the context of ecological risk assessment, we considered how omics datasets might continue to support the AOP framework. In particular, the role of omics in identifying potential AOP molecular initiating events and providing supportive evidence of key events at different levels of biological organization and across taxonomic groups was discussed. Areas with potential for short and medium-term breakthroughs were also discussed, such as providing mechanistic evidence to support chemical read-across, providing weight of evidence information for mode of action assignment, understanding biological networks, and developing robust extrapolations of species-sensitivity. Key challenges that need to be addressed were considered, including the need for a cohesive approach towards experimental design, the lack of a mutually agreed framework to quantitatively link genes and pathways to key events, and the need for better interpretation of chemically induced changes at the molecular level. This article was developed to provide an overview of ecological risk assessment process and a perspective on how high content molecular-level datasets can support the future of assessment procedures through the AOP framework.


Assuntos
Rotas de Resultados Adversos , Metabolismo dos Lipídeos , Metabolômica , Proteômica , Transcriptoma , Animais , Humanos , Medição de Risco
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