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1.
Toxicol Res (Camb) ; 13(1): tfad120, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38223529

RESUMO

Fialuridine (FIAU) is a nucleoside-based drug that caused liver failure and deaths in a human clinical trial that were not predicted by nonclinical safety studies. A recent report concluded that a TK-NOG humanized liver (hu-liver) mouse model detected human-specific FIAU liver toxicity, and broader use of that model could improve drug safety testing. We further evaluated this model at similar dose levels to assess FIAU sensitivity and potential mechanistic biomarkers. Although we were unable to reproduce the marked acute liver toxicity with two separate studies (including one with a "sensitized" donor), we identified molecular biomarkers reflecting the early stages of FIAU mitochondrial toxicity, which were not seen with its stereoisomer (FIRU). Dose dependent FIAU-induced changes in hu-liver mice included more pronounced reductions in mitochondrial to nuclear DNA (mtDNA/nucDNA) ratios in human hepatocytes compared to mouse hepatocytes and kidneys of the same animals. FIAU treatment also triggered a p53 transcriptional response and opposing changes in transcripts of nuclear- and mitochondrial-encoded mitochondrial proteins. The time dependent accumulation of FIAU into mtDNA is consistent with the ≥9-week latency of liver toxicity observed for FIAU in the clinic. Similar changes were observed in an in vitro micro-patterned hepatocyte coculture system. In addition, FIAU-dependent mtDNA/nucDNA ratio and transcriptional alterations, especially reductions in mitochondrially encoded transcripts, were seen in livers of non-engrafted TK-NOG and CD-1 mice dosed for a shorter period. Conclusion: These mechanistic biomarker findings can be leveraged in an in vitro model and in a more routine preclinical model (CD-1 mice) to identify nucleosides with such a FIAU-like mitochondrial toxicity mechanistic liability potential. Further optimization of the TK-NOG hu-liver mouse model is necessary before broader adoption for drug safety testing.

2.
RNA Biol ; 10(4): 502-15, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23558773

RESUMO

Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost. We report the development of a new RNA-Seq library preparation technique that produces representative, strand-specific RNA-Seq libraries from small amounts of starting material in a fast, simple and cost-effective manner. Additionally, we have developed a new quantitative PCR-based assay for precisely determining the number of PCR cycles to perform for optimal enrichment of the final library, a key step in all SGS library preparation workflows.


Assuntos
Escherichia coli/genética , Perfilação da Expressão Gênica/métodos , Biblioteca Gênica , Reação em Cadeia da Polimerase/métodos , Transcrição Reversa , Análise de Sequência de RNA/métodos , Sequência de Bases , Linhagem Celular Tumoral , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos
3.
Microorganisms ; 11(3)2023 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-36985359

RESUMO

Loss of algal production from the crashes of algal mass cultivation systems represents a significant barrier to the economic production of microalgal-based biofuels. Current strategies for crash prevention can be too costly to apply broadly as prophylaxis. Bacteria are ubiquitous in microalgal mass production cultures, however few studies investigate their role and possible significance in this particular environment. Previously, we demonstrated the success of selected protective bacterial communities to save Microchloropsis salina cultures from grazing by the rotifer Brachionus plicatilis. In the current study, these protective bacterial communities were further characterized by fractionation into rotifer-associated, algal-associated, and free-floating bacterial fractions. Small subunit ribosomal RNA amplicon sequencing was used to identify the bacterial genera present in each of the fractions. Here, we show that Marinobacter, Ruegeria, and Boseongicola in algae and rotifer fractions from rotifer-infected cultures likely play key roles in protecting algae from rotifers. Several other identified taxa likely play lesser roles in protective capability. The identification of bacterial community members demonstrating protective qualities will allow for the rational design of microbial communities grown in stable co-cultures with algal production strains in mass cultivation systems. Such a system would reduce the frequency of culture crashes and represent an essentially zero-cost form of algal crop protection.

4.
Biotechnol Bioeng ; 109(5): 1146-54, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22161571

RESUMO

Algal biofuels are a growing interest worldwide due to their potential in terms of sustainable greenhouse gas displacement and energy production. This article describes a comparative survey of biodiesel production and conversion yields of biodiesel via alkaline transesterification of acylglycerols extracted from the microalgae Thalassiosira pseudonana and Phaeodactylum tricornutum, grown under silicate or nitrate limitation, and that of model vegetable oils: soybean, and rapeseed oil. Acylglycerols were extracted with n-hexane and the total yield per biomass was determined by gravimetric assay. Under our conditions, the total acylglycerol yield from the microalgae studied was 13-18% of total dry weight. The biodiesel samples were analyzed using gas chromatography-flame ionization detector to determine quantitative information of residual glycerol, mono-, di-, and tri-acylglycerol concentrations in the biodiesel. All of the algal-based biodiesel demonstrated less mono-, di-, and tri-acylglycerol concentrations than the vegetable-based biodiesel under identical transesterification conditions. The fatty acid compositions of all the feedstock oils and their resultant biodiesel were also analyzed and reported. Based on the fatty acid methyl ester compositions of our samples we qualitatively assessed the suitability of the algal-derived biodiesel in terms of cetane number (CN), cold-flow properties, and oxidative stability.


Assuntos
Biocombustíveis , Diatomáceas/metabolismo , Glicerídeos/análise , Glicerídeos/isolamento & purificação , Óleos de Plantas/química , Óleo de Soja/química , Cromatografia Gasosa , Diatomáceas/crescimento & desenvolvimento , Ácidos Graxos Monoinsaturados , Nitrogênio/metabolismo , Óleo de Brassica napus , Silicatos/metabolismo
5.
J Neurosurg ; : 1-9, 2022 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-35061981

RESUMO

OBJECTIVE: In this article, the authors describe the impact of the COVID-19 virtual match cycle and discuss approaches to optimize future cycles through applicant and neurosurgical education leadership insights. METHODS: Anonymous surveys of neurosurgery program leaders (program directors and program chairs), program administrators (PAs), and 2020-2021 neurosurgery residency match applicants were distributed by the SNS, in conjunction with the Association of Resident Administrators in Neurological Surgery and AANS Young Neurosurgeons Committee. RESULTS: Responses were received from 77 (67.0%) of 115 PAs, 119 (51.7%) of 230 program leaders, and 124 (44.3%) of 280 applicants representing geographically diverse regions. During the virtual application cycle relative to the previous year, programs received more Electronic Residency Application Service applications (mean 314.8 vs 285.3, p < 0.0001) and conducted more applicant interviews (mean 45.2 vs 39.9, p = 0.0003). More than 50% of applicants applied to > 80 programs; 60.3% received ≤ 20 interview invitations, and 9% received > 40 invitations. Overall, 65% of applicants completed ≤ 20 interviews, whereas 34.7% completed > 20 interviews. Program leaders described one 4-week home subinternship (93.3%) and two 4-week external subinternships (68.9%) as optimal neurosurgical exposure; 62.8% of program leaders found the standardized letter of recommendation template to be somewhat (47.5%) or significantly (15.3%) helpful. Applicants, PAs, and program leaders all strongly preferred a hybrid model of in-person and virtual interview options for future application cycles over all in-person or all virtual options. Ninety-three percent of applicants reported matching within their top 10-ranked programs, and 52.9% of programs matched residents within the same decile ranking as in previous years. CONCLUSIONS: Optimizing a national strategy for the neurosurgery application process that prioritizes equity and reduces costs, while ensuring adequate exposure for applicants to gain educational opportunities and evaluate programs, is critical to maintain a successful training system.

6.
Metabolites ; 11(10)2021 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-34677422

RESUMO

Open microalgal ponds used in industrial biomass production are susceptible to a number of biotic and abiotic environmental stressors (e.g., grazers, pathogens, pH, temperature, etc.) resulting in pond crashes with high economic costs. Identification of signature chemicals to aid in rapid, non-invasive, and accurate identification of the stressors would facilitate targeted and effective treatment to save the algal crop from a catastrophic crash. Specifically, we were interested in identifying volatile organic compounds (VOCs) that can be used to as an early diagnostic for algal crop damage. Cultures of Microchloropsis gaditana were subjected to two forms of algal crop damage: (1) active grazing by the marine rotifer, Brachionus plicatilis, or (2) repeated freeze-thaw cycles. VOCs emitted above the headspace of these algal cultures were collected using fieldable solid phase microextraction (SPME) fibers. An untargeted analysis and identification of VOCs was conducted using gas chromatography-mass spectrometry (GC-MS). Diagnostic VOCs unique to each algal crop damage mechanism were identified. Active rotifer grazing of M. gaditana was characterized by the appearance of carotenoid degradation products, including ß-cyclocitral and various alkenes. Freeze-thaw algae produced a different set of VOCs, including palmitoleic acid. Both rotifer grazing and freeze-thawed algae produced ß-ionone as a VOC, possibly suggesting a common stress-induced cellular mechanism. Importantly, these identified VOCs were all absent from healthy algal cultures of M. gaditana. Early detection of biotic or abiotic environmental stressors will facilitate early diagnosis and application of targeted treatments to prevent algal pond crashes. Thus, our work further supports the use of VOCs for monitoring the health of algal ponds to ultimately enhance algal crop yields for production of biofuel.

7.
Toxicol Sci ; 181(2): 148-159, 2021 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-33837425

RESUMO

A new safety testing paradigm that relies on gene expression biomarker panels was developed to easily and quickly identify drug-induced injuries across tissues in rats prior to drug candidate selection. Here, we describe the development, qualification, and implementation of gene expression signatures that diagnose tissue degeneration/necrosis for use in early rat safety studies. Approximately 400 differentially expressed genes were first identified that were consistently regulated across 4 prioritized tissues (liver, kidney, heart, and skeletal muscle), following injuries induced by known toxicants. Hundred of these "universal" genes were chosen for quantitative PCR, and the most consistent and robustly responding transcripts selected, resulting in a final 22-gene set from which unique sets of 12 genes were chosen as optimal for each tissue. The approach was extended across 4 additional tissues (pancreas, gastrointestinal tract, bladder, and testes) where toxicities are less common. Mathematical algorithms were generated to convert each tissue's 12-gene expression values to a single metric, scaled between 0 and 1, and a positive threshold set. For liver, kidney, heart, and skeletal muscle, this was established using a training set of 22 compounds and performance determined by testing a set of approximately 100 additional compounds, resulting in 74%-94% sensitivity and 94%-100% specificity for liver, kidney, and skeletal muscle, and 54%-62% sensitivity and 95%-98% specificity for heart. Similar performance was observed across a set of 15 studies for pancreas, gastrointestinal tract, bladder, and testes. Bundled together, we have incorporated these tissue signatures into a 4-day rat study, providing a rapid assessment of commonly seen compound liabilities to guide selection of lead candidates without the necessity to perform time-consuming histopathologic analyses.


Assuntos
Perfilação da Expressão Gênica , Preparações Farmacêuticas , Animais , Fígado , Ratos , Medição de Risco , Transcriptoma
8.
Metabolites ; 10(9)2020 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-32899747

RESUMO

Microalgae produce specific chemicals indicative of stress and/or death. The aim of this study was to perform non-destructive monitoring of algal culture systems, in the presence and absence of grazers, to identify potential biomarkers of incipient pond crashes. Here, we report ten volatile organic compounds (VOCs) that are robustly generated by the marine alga, Microchloropsis salina, in the presence and/or absence of the marine grazer, Brachionus plicatilis. We cultured M. salina with and without B. plicatilis and collected in situ volatile headspace samples using thermal desorption tubes over the course of several days. Data from four experiments were aggregated, deconvoluted, and chromatographically aligned to determine VOCs with tentative identifications made via mass spectral library matching. VOCs generated by algae in the presence of actively grazing rotifers were confirmed via pure analytical standards to be pentane, 3-pentanone, 3-methylhexane, and 2-methylfuran. Six other VOCs were less specifically associated with grazing but were still commonly observed between the four replicate experiments. Through this work, we identified four biomarkers of rotifer grazing that indicate algal stress/death. This will aid machine learning algorithms to chemically define and diagnose algal mass production cultures and save algae cultures from imminent crash to make biofuel an alternative energy possibility.

9.
Sci Rep ; 9(1): 13866, 2019 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-31554867

RESUMO

Algae ponds used in industrial biomass production are susceptible to pathogen or grazer infestation, resulting in pond crashes with high economic costs. Current methods to monitor and mitigate unhealthy ponds are hindered by a lack of early indicators that precede culture crash. We used solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS) to identify volatiles emitted from healthy and rotifer infested cultures of Microchloropsis salina. After 48 hours of algal growth, marine rotifers, Brachionus plicatilis, were added to the algae cultures and volatile organic compounds (VOC) were sampled from the headspace using SPME fibers. A GC-MS approach was used in an untargeted analysis of VOCs, followed by preliminary identification. The addition of B. plicatilis to healthy cultures of M. salina resulted in decreased algal cell numbers, relative to uninfected controls, and generated trans-ß-ionone and ß-cyclocitral, which were attributed to carotenoid degradation. The abundances of the carotenoid-derived VOCs increased with rotifer consumption of algae. Our results indicate that specific VOCs released by infected algae cultures may be early indicators for impending pond crashes, providing a useful tool to monitor algal biomass production and pond crash prevention.


Assuntos
Eutrofização , Lagoas/química , Compostos Orgânicos Voláteis/análise , Animais , Biomarcadores/análise , Ecologia , Biomarcadores Ambientais , Lagoas/microbiologia , Rotíferos , Compostos Orgânicos Voláteis/metabolismo
10.
Bioresour Technol ; 283: 350-357, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30933901

RESUMO

Improving the economic feasibility is necessary for algae-based processes to achieve commercial scales for biofuels and bioproducts production. A closed-loop system for fusel alcohol production from microalgae biomass with integrated nutrient recycling was developed, which enables the reuse of nitrogen and phosphorus for downstream application and thus reduces the operational requirement for external major nutrients. Mixed fusel alcohols, primarily isobutanol and isopentanol were produced from Microchloropsis salina hydrolysates by an engineered E. coli co-culture. During the process, cellular nitrogen from microalgae biomass was converted into ammonium, whereas cellular phosphorus was liberated by an osmotic shock treatment. The formation of struvite from the liberated ammonium and phosphate, and the subsequent utilization of struvite to support M. salina cultivation was demonstrated. The closed loop system established here should help overcome one of the identified economic barriers to scale-up of microalgae production, and enhance the sustainability of microalgae-based chemical commodities production.


Assuntos
Álcoois/metabolismo , Biomassa , Microalgas/metabolismo , Nutrientes/metabolismo , Estramenópilas/metabolismo , Escherichia coli/metabolismo , Microalgas/crescimento & desenvolvimento , Nitrogênio/metabolismo , Fósforo/metabolismo , Reciclagem , Estramenópilas/crescimento & desenvolvimento , Estruvita/metabolismo
11.
Toxicol Sci ; 168(1): 110-125, 2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30496518

RESUMO

Liver and skeletal muscle-specific microRNAs (miRNAs) are currently being evaluated as novel plasma biomarkers that may out-perform or add value to the conventional liver injury biomarkers alanine aminotransferase (ALT) and aspartate aminotransferase (AST), and to the skeletal muscle injury biomarkers AST and creatine kinase (CK). A comprehensive evaluation was conducted to assess the relative performance of these miRNAs to detect and distinguish liver from muscle tissue injury. The performance of miR-122 and miR-192 for liver and miR-1, miR-133a, miR-133b, and miR-206 for skeletal muscle was compared with 10 enzymatic or protein biomarkers across 27 compounds causing specific types of tissue injury in rat. Receiver operator characteristic analyses were performed comparing the relative sensitivity and specificity of each of the biomarkers in individual animals with histopathology observations of necrosis and/or degeneration in various organs. All of the miRNAs outperformed ALT, AST, and/or CK in studies with either liver or skeletal muscle injury and demonstrated superior specificity in organs without type-specific injury (eg, liver biomarkers assessed with compounds that cause skeletal muscle injury). When additional protein biomarkers were included, glutamate dehydrogenase, arginase I, alpha-glutathione S-transferase for liver and skeletal troponin I, myosin light chain 3, fatty acid-binding protein 3, and creatine kinase M isoform for skeletal muscle, the miRNAs demonstrated equal or superior performance to the extended panel. Taken together, this comprehensive evaluation demonstrates that these novel miRNA toxicity biomarkers outperform and add value with respect to sensitivity and specificity over ALT, AST in monitoring the liver and over CK for monitoring skeletal muscle drug-induced injury.


Assuntos
Doença Hepática Induzida por Substâncias e Drogas/diagnóstico , Fígado/metabolismo , MicroRNAs/sangue , Músculo Esquelético/metabolismo , Doenças Musculares/diagnóstico , Alanina Transaminase/sangue , Animais , Aspartato Aminotransferases/sangue , Biomarcadores/sangue , Doença Hepática Induzida por Substâncias e Drogas/sangue , Creatina Quinase Forma MM/sangue , Feminino , Masculino , Doenças Musculares/sangue , Doenças Musculares/induzido quimicamente , Ratos , Ratos Sprague-Dawley , Ratos Wistar
12.
Am J Infect Control ; 46(3): 246-252, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29499788

RESUMO

BACKGROUND: The Ebola virus disease outbreak highlighted the lack of consistent guidelines and training for workers outside of hospital settings. Specifically, emergency medical services (EMS) workers, who are frequently the first professionals to evaluate patients, often do not have advanced notice of patient diagnosis, and have limited time in their national curricula devoted to highly infectious disease (HID) identification and containment. All of these can place them at increased risk. To explore the depth of US EMS practitioners' HID training and education, a pilot gap analysis survey was distributed to determine where the aforementioned can be bolstered to increase occupational safety. METHODS: Electronic surveys were distributed to EMS organization members. The survey collected respondent willingness to encounter HID scenarios; current policies and procedures; and levels of knowledge, training, and available resources to address HIDs. RESULTS: A total of 2,165 surveys were initiated and collected. Eighty percent of frontline personnel were aware that their agency had an HID standard operating guideline. Almost 85% of respondents correctly marked routes of exposure for select HIDs. More than half of respondents indicated no maximum shift times in personal protective equipment. DISCUSSION: This research suggests EMS practitioners could benefit from enhanced industry-specific education, training, and planning on HID mitigation and management. CONCLUSION: Strengthening EMS preparedness in response to suspected or confirmed HID cases may not only improve patient outcomes, but also worker and community safety.


Assuntos
Controle de Doenças Transmissíveis/métodos , Controle de Doenças Transmissíveis/normas , Serviços Médicos de Emergência/métodos , Serviços Médicos de Emergência/normas , Pessoal de Saúde/educação , Doenças Transmissíveis/transmissão , Coleta de Dados , Serviço Hospitalar de Emergência , Tratamento de Emergência , Guias como Assunto , Humanos , Estados Unidos
13.
Toxicol Sci ; 156(2): 422-427, 2017 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-28115646

RESUMO

The skeletal muscle (SKM) injury biomarkers, skeletal troponin I (sTnI), myosin light chain 3 (Myl3), and creatine kinase muscle isoform (Ckm) have been shown recently to be more sensitive and specific for monitoring drug-induced SKM injury than the conventional biomarkers, aspartate transaminase (AST) and creatine kinase (CK) enzymatic assays in rat toxicology studies. To evaluate the utility of these SKM biomarkers across species, they were assessed in 2 dog models: a drug-induced injury study in Beagle dogs and a 160 km endurance exercise run completed by Alaskan sled dogs. In the drug-induced injury model, mean sTnI and Myl3 plasma levels were 6- and 18-fold, respectively, compared with baseline as early as Study Day (SD) 15, while mean plasma AST and CK levels did not increase, and biopsy samples were non-remarkable for histopathology prior to SD 29 when degeneration was first noted. Peak group mean plasma responses over baseline for sTnI, Myl3, and Ckm biomarkers were 96-, 103-, and 11-fold, respectively, compared with 2.5-fold for AST and 3.8-fold for CK-enzymatic (CK-enz) assay. In the sled dog sustained exercise model, the peak response for all biomarkers was observed at the first sampling (2 h) after the completion of the run. The sTnI, Myl3, and Ckm mean fold peak values compared with baseline were 170-, 120-, and 150-fold, respectively, while AST increased 7-fold and CK-enz increased 29-fold. These findings support the conclusion that sTnI, Myl3, and Ckm are sensitive early tissue leakage biomarkers for monitoring SKM injury and effects of exercise in dog, extending their utility across preclinical species beyond the rat, and provide further support to investigate their translational utility to clinical trial settings to monitor for drug-induced SKM injury and ensure patient safety.


Assuntos
Biomarcadores/sangue , Músculo Esquelético/efeitos dos fármacos , Músculo Esquelético/lesões , Doenças Musculares/sangue , Resistência Física , Animais , Creatina Quinase Forma MM/sangue , Cães , Masculino , Músculo Esquelético/patologia , Doenças Musculares/induzido quimicamente , Doenças Musculares/etiologia , Doenças Musculares/patologia , Cadeias Leves de Miosina/sangue , Especificidade da Espécie , Troponina I/sangue
14.
Protein Sci ; 15(6): 1303-17, 2006 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-16731966

RESUMO

Recent work using chemical cross-linking to define interresidue distance constraints in proteins has shown that these constraints are useful for testing tertiary structural models. We applied this approach to the G-protein-coupled receptor bovine rhodopsin in its native membrane using lysine- and cysteine-targeted bifunctional cross-linking reagents. Cross-linked proteolytic peptides of rhodopsin were identified by combined liquid chromatography and FT-ICR mass spectrometry with automated data-reduction and assignment software. Tandem mass spectrometry was used to verify cross-link assignments and locate the exact sites of cross-link attachment. Cross-links were observed to form between 10 pairs of residues in dark-state rhodopsin. For each pair, cross-linkers with a range of linker lengths were tested to determine an experimental distance-of-closest-approach (DCA) between reactive side-chain atoms. In all, 28 cross-links were identified using seven different cross-linking reagents. Molecular mechanics procedures were applied to published crystal structure data to calculate energetically achievable theoretical DCAs between reactive atoms without altering the position of the protein backbone. Experimentally measured DCAs are generally in good agreement with the theoretical DCAs. However, a cross-link between C316 and K325 in the C-terminal region cannot be rationalized by DCA simulations and suggests that backbone reorientation relative to the crystal coordinates occurs on the timescale of cross-linking reactions. Biochemical and spectroscopic data from other studies have found that the C-terminal region is highly mobile in solution and not fully represented by X-ray crystallography data. Our results show that chemical cross-linking can provide reliable three-dimensional structural information and insight into local conformational dynamics in a membrane protein.


Assuntos
Rodopsina/química , Sequência de Aminoácidos , Animais , Bovinos , Cromatografia Líquida , Reagentes de Ligações Cruzadas/química , Cristalografia por Raios X , Cisteína/química , Lisina/química , Espectrometria de Massas , Dados de Sequência Molecular , Conformação Proteica , Rodopsina/metabolismo , Espectroscopia de Infravermelho com Transformada de Fourier , Succinimidas/química
15.
Toxicol Sci ; 150(1): 247-56, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26721300

RESUMO

Novel skeletal muscle (SKM) injury biomarkers that have recently been identified may outperform or add value to the conventional SKM injury biomarkers aspartate transaminase (AST) and creatine kinase (CK). The relative performance of these novel biomarkers of SKM injury including skeletal troponin I (sTnI), myosin light chain 3 (Myl3), CK M Isoform (Ckm), and fatty acid binding protein 3 (Fabp3) was assessed in 34 rat studies including both SKM toxicants and compounds with toxicities in tissues other than SKM. sTnI, Myl3, Ckm, and Fabp3 all outperformed CK or AST and/or added value for the diagnosis of drug-induced SKM injury (ie, myocyte degeneration/necrosis). In addition, when used in conjunction with CK and AST, sTnI, Myl3, CKm, and Fabp3 individually and collectively improved diagnostic sensitivity and specificity, as well as diagnostic certainty, for SKM injury and responded in a sensitive manner to low levels of SKM degeneration/necrosis in rats. These findings support the proposal that sTnI, Myl3, Ckm, and Fabp3 are suitable for voluntary use, in conjunction with CK and AST, in regulatory safety studies in rats to monitor drug-induced SKM injury and the potential translational use of these exploratory biomarkers in early clinical trials to ensure patient safety.


Assuntos
Biomarcadores/sangue , Músculo Esquelético/efeitos dos fármacos , Doenças Musculares/sangue , Doenças Musculares/induzido quimicamente , Animais , Creatina Quinase Forma MM/sangue , Relação Dose-Resposta a Droga , Proteína 3 Ligante de Ácido Graxo , Proteínas de Ligação a Ácido Graxo/sangue , Feminino , Masculino , Músculo Esquelético/enzimologia , Músculo Esquelético/metabolismo , Doenças Musculares/enzimologia , Doenças Musculares/metabolismo , Cadeias Leves de Miosina/sangue , Preparações Farmacêuticas/administração & dosagem , Preparações Farmacêuticas/química , Ratos Endogâmicos F344 , Ratos Sprague-Dawley , Ratos Wistar , Projetos de Pesquisa , Sensibilidade e Especificidade , Troponina I/sangue
16.
Biotechniques ; 53(6): 373-80, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23227988

RESUMO

Second-generation sequencing (SGS) has become the preferred method for RNA transcriptome profiling of organisms and single cells. However, SGS analysis of transcriptome diversity (including protein-coding transcripts and regulatory non-coding RNAs) is inefficient unless the sample of interest is first depleted of nucleic acids derived from ribosomal RNA (rRNA), which typically account for up to 95% of total intracellular RNA content. Here we describe a novel microscale hydroxyapatite chromatography (HAC) normalization method to remove eukaryotic and prokaryotic high abundant rRNA species, thereby increasing sequence coverage depth and transcript diversity across non-rRNA populations. RNA-seq analysis of Escherichia coli K-12 and human intracellular total RNA showed that HAC-based normalization enriched for all non-ribosomal RNA species regardless of RNA transcript abundance or length when compared with untreated controls. Microcolumn HAC normalization generated rRNA-depleted cDNA libraries comparable to the well-established duplex specific nuclease (DSN) normalization and Ribo-Zero rRNA-depletion methods, thus establishing microscale HAC as an effective, cost saving, and non-destructive alternative normalization technique.


Assuntos
Cromatografia de Afinidade/métodos , Durapatita/química , Biblioteca Gênica , RNA/genética , Análise de Sequência de RNA/métodos , Transcriptoma , Sequência de Bases , Cromatografia por Troca Iônica/métodos , Mapeamento Cromossômico , Escherichia coli K12/genética , Humanos , Leucócitos Mononucleares/química , RNA/análise , RNA/química
17.
Electrophoresis ; 28(24): 4697-704, 2007 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-18008300

RESUMO

A rapid microanalytical protein-based approach to bacterial characterization is presented. Chip gel electrophoresis (CGE) coupled with LIF detection was used to analyze lysates from different bacterial cell lines to obtain signature profiles of the soluble protein composition. The study includes Escherichia coli, Bacillus subtilis, and Bacillus anthracis (Delta Sterne strain) vegetative cells as well as endospores formed from the latter two species as model organisms to demonstrate the method. A unified protein preparation protocol was developed for both cell types to streamline the benchtop process and aid future automation. Cells and spores were lysed and proteins solubilized using a combination of thermal and chemical lysis methods. Reducing agents, necessary to solubilize spore proteins, were eliminated using a small-scale rapid size-exclusion chromatography step to eliminate interference with down-stream protein labeling. This approach was found to be compatible with nonspore cells (i.e., vegetative cells) as well, not adversely impacting the protein signatures. Data are presented demonstrating distinct CGE protein signatures for our model organisms, suggesting the potential for discrimination of organisms on the basis of empirical protein patterns. The goal of this work is to develop a fast and field-portable method for characterizing bacteria via their proteomes.


Assuntos
Bactérias/classificação , Proteínas de Bactérias/isolamento & purificação , Eletroforese em Microchip/métodos , Bactérias/metabolismo
18.
J Bacteriol ; 184(8): 2116-22, 2002 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-11914342

RESUMO

Many bacteria employ the nonmevalonate pathway for synthesis of isopentenyl diphosphate, the monomer unit for isoprenoid biosynthesis. However, gram-positive cocci exclusively use the mevalonate pathway, which is essential for their growth (E. I. Wilding et al., J. Bacteriol. 182:4319-4327, 2000). Enzymes of the mevalonate pathway are thus potential targets for drug intervention. Uniquely, the enterococci possess a single open reading frame, mvaE, that appears to encode two enzymes of the mevalonate pathway, acetoacetyl-coenzyme A thiolase and 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase. Western blotting revealed that the mvaE gene product is a single polypeptide in Enterococcus faecalis, Enterococcus faecium, and Enterococcus hirae. The mvaE gene was cloned from E. faecalis and was expressed with an N-terminal His tag in Escherichia coli. The gene product was then purified by nickel affinity chromatography. As predicted, the 86.5-kDa mvaE gene product catalyzed both the acetoacetyl-CoA thiolase and HMG-CoA reductase reactions. Temperature optima, DeltaH(a) and K(m) values, and pH optima were determined for both activities. Kinetic studies of acetoacetyl-CoA thiolase implicated a ping-pong mechanism. CoA acted as an inhibitor competitive with acetyl-CoA. A millimolar K(i) for a statin drug confirmed that E. faecalis HMG-CoA reductase is a class II enzyme. The oxidoreductant was NADP(H). A role for an active-site histidine during the first redox step of the HMG-CoA, reductase reaction was suggested by the ability of diethylpyrocarbonate to block formation of mevalonate from HMG-CoA, but not from mevaldehyde. Sequence comparisons with other HMG-CoA reductases suggest that the essential active-site histidine is His756. The mvaE gene product represents the first example of an HMG-CoA reductase fused to another enzyme.


Assuntos
Acil Coenzima A/fisiologia , Enterococcus faecalis/enzimologia , Hemiterpenos , Hidroximetilglutaril-CoA Redutases/fisiologia , Compostos Organofosforados/metabolismo , Sequência de Aminoácidos , Dietil Pirocarbonato/farmacologia , Enterococcus faecalis/genética , Concentração de Íons de Hidrogênio , Hidroxilamina/farmacologia , Hidroximetilglutaril-CoA Redutases/química , Cinética , Dados de Sequência Molecular , Especificidade por Substrato , Temperatura
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