How to get Published in Scientific Journals
Presented by Elizabeth Perill, Publisher for Elsevier Ltd.
We will talk about how to write-up and submit your research findings to internationally peer reviewed journals. Find out what it is that distinguishes a very good scientific manuscript from a bad one. We will show you that a well written article cannot make up for poor research whereas a badly written article can diminish good research. The objectives of this workshop are to:
ñ Outline the steps you need to take before you write your paper
ñ Explain how to ensure you are using proper scientific language
ñ Demonstrate how to build up your article properly before submission to a journal for publication
Abstract Rhenovia Pharma and its role in toxicology
Florence Keller, Fabien Pernot, Renaud Greget, Arnaud Legendre, Jean-Marie Bouteiller,
Michel Faupel, Michel Baudry, Serge Bischoff
Rhenovia Pharma, a R&D pharmaceutical and biotechnology company created in 2007, is dedicated to global healthcare in the field of central and peripheral nervous system (CNS&PNS). Rhenovia’s mission consists in the development of innovative solutions based on Modeling and Simulation (M&S) to improve quality of life of patients, their families and caregivers. Biosimulation consists in the use of computational models that provide a dynamic and quantitative description of a number of biological, pathological, and pharmacokinetic processes in order to understand complex brain functions of the brain. Rhenovia’s innovative technology of biosimulation of neuronal functions was initially developed for finding treatments against neurodegenerative diseases such as Alzheimer’s, Huntington’s, rare and orphan diseases. Now, additional domains of application are targeted particularly in the industrial field of neurotoxicity, which is defined as the ability of a drug or an agent to destroy or damage nervous tissue. Today many agents with potential neurotoxic effects are present in a variety of products that are used, consumed and manipulated in daily life (chemicals, pharmaceuticals, cosmetics, food, etc...) by consumers and professional workers (army, farmers, etc...). Some of them, such as insecticides, pesticides and organophosphate agents, are now known to cause important and irreversible brain damages. Biosimulation is a suitable tool to predict and identify neurotoxicological risks and to provide early solutions:
- To IDENTIFY risks factor for brain diseases due to acute and prolonged exposure to chemicals, agrochemicals, or pollutants in the Eco-toxicology environment.
- To PROTECT against identified toxic substances by developing preventive and curative treatment against these affections.
- To TREAT diseases by developing efficient drugs and analytical methods for the
identification of drug efficacy.
Rhenovia’s technology (modeling integrative functions of the CNS&PNS) has the capacity to evaluate and anticipate neurotoxic effects associated with chemical agents present in the daily environment.
Metabolomics of Human Embryonic and Induced Pluripotent Stem Cells to Predict Developmental Toxicity: A Comparison
E.L.R. Donley (CEO, Stemina Biomarker Discovery, Inc., 504 S. Rosa Rd., Suite 150, Madison, WI 53719)
Birth defects are the largest cause of infant morbidity and mortality in the United States. Exposure to developmental disruptors has a significant role in the pathogenesis of defects in human development. Teratogens, defined as substances that cause one or more fetal abnormalities during development, are responsible for 5-10% of all birth defects. More predictive developmental toxicity screens would reduce the prevalence of birth defects and increase pharmaceutical and chemical safety. The majority of preclinical efficacy and toxicity testing of pharmaceuticals are currently performed using animal models, which are costly, time-consuming, and the subject of ongoing ethical debate. Most importantly, rodent models for developmental toxicity testing do not adequately correlate to human response, resulting in only 62% concordance to humans.
Human embryonic stem (hES) cell technology is an innovative and robust alternative to predict developmental toxicity of chemicals during human pregnancy. We have developed the first all-human in vitro developmental toxicity screen that utilizes hES cells and metabolomics to discover metabolite biomarkers of developmental toxicity. Our assay, devTOX, is 88% accurate in blinded studies of known teratogens and non-teratogens.
Induced pluripotent stem (iPS) cells are derived from the genetic manipulation of human somatic cells. These cells are being investigated for use in place of hES cells due to the moral, ethical and political controversies surrounding their use. Human iPS cells are phenotypically and genetically similar to hES cells in many respects (i.e. morphology, proliferation, gene expression). Using Stemina’s metabolomics platform, the metabolic similarity between hES cells and iPS cells has been established. It is vital to understand this information when considering using iPS cells in the same manner as hES cells, such as for human toxicity testing. We measured the secreted metabolites (secretome), across three hES cell lines and two iPS cell lines using liquid chromatography mass spectrometry (LCMS), to determine what differences exist in the secretome between cell types.
Additionally, we exposed all five cell lines to a training set of 23 compounds with known teratogenicity to test the hypothesis that iPS cells exhibit a similar response to that of hES cells when exposed to non-teratogen and teratogens. Our initial comparisons between the three genetically distinct hES cell lines and two iPS cell lines have shown that no metabolites were unique to a single cell line and that few statistical differences in the abundance of secreted features were observed. However, we did uncover a difference in individual cell line responses to treatment. In addition to metabolomics analysis, we evaluated the cytotoxicity of the compound test set using a cell viability assay. The results of these assays have shown a difference between the viability of iPS cells and hES cells following treatment. Many compounds are more cytotoxic to iPS cells than hES cells.
We then tested the iPS based devTOX assay with a set of 9 blinded compounds. There are minimal differences (7 of 227 features) in the secretome of hES and iPS cells. The 2 iPS cell lines examined in this study respond similarly to treatment. Both lines are able to predict the teratogenicity of the compounds, except for methotrexate in line 4.3.7T.A. Features selected for model predictions show similar fold changes in both cell lines. iPS cells can be used as a model to predict teratogenicity of pharmaceutical compounds.
Title: Development of a Mechanism-based Biomarker for Risk Assessment and Screening of Novel Plasticisers.
Simon Plummer PhD, Micromatrices Ltd, UK
Phthalates comprise a class of commercially important industrial chemicals that are used primarily as plasticisers. Phthalates are found ubiquitously in the environment and concerns about the potential health impact of certain phthalates have resulted from the observation of a number of adverse effects in animal studies. In utero exposure of rats to certain phthalates has been shown to cause testicular mal-development (PITMD). These effects are due in part to decreased testosterone synthesis as a result of gene expression changes in pathways that regulate the synthesis of this hormone. To investigate the mechanism(s) of PITMD in more detail we performed transcription profiling on rat fetal testes using Agilent expression arrays. Pathways analysis of phthalate-induced gene expression changes indicated bias towards pathways involved in fatty acid and cholesterol biosynthesis. Detailed examination of these pathways showed that they contained several genes involved in the synthesis, transport and metabolism of the testosterone precursor cholesterol. All of these genes together with other genes involved in testes development and cryptorchidism were repressed by the treatment. As these changes could account for most of the phenotypic features of PITMD we utilised this information to formulate a new hypothesis for the toxic mechanism of action of phthalates in this system. Our bioinformatic analysis revealed a common thread linking these altered genes was that they were all transactivated by the nuclear receptor steroidogenic factor 1 (SF1). SF1, however, was not directly affected by the treatment. We further developed the hypothesis for PITMD based on indirect inhibition of SF1 via another nuclear hormone receptor peroxisome proliferator receptor alpha (PPAR), a known target for phthalates. This hypothesis was tested using Agilent custom designed Chip chip arrays. Our results indicated that the ability of DBP to repress steroidogenic genes such as steroidogenic acute regulator (StAR) were mediated in part by direct DBP-dependent binding of PPARα to the promoter regions of steroidogenic genes. These results have facilitated the development of an array-based in vivo screen centred on genes involved in this hypothesis which has been used in several studies for the risk assessment of novel plasticisers.
Plummer, S., Sharpe, R.M., Hallmark, N., Mahood, I.K., and Elcombe, C. (2007). Time-Dependent and Compartment-Specific Effects of In Utero Exposure to Di(n-butyl) Phthalate on Gene/Protein Expression in the Fetal Rat Testis as Revealed by Transcription Profiling and Laser Capture Microdissection. Toxicol Sci 97, 520-532.
Plummer, S., Dan, D., Quinney, J., Hallmark, N., Phillips, R., and Elcombe, C. (2010). The Effects of dibutylphthalate (DBP) on transcription factor-DNA binding to Fetal Rat testes Genes Relevant to phthalate-induced testicular mal-development (TMD).Journal of the Society of Toxicology 114, Abstract ID1488.
Elcombe, C. R., Dhritiman, D., Farrar, D.G. and Plummer, S. M. (2011). The Effects of Tris (2-ethylhexyl) Trimellitate (TOTM) on Gene Expression Associated with Testicular Mal-development (TMD) in Rat Fetal Testes. The Toxicologist CD – An official Journal of the Society ofToxicology, 120, Number S-2, Abstract ID 1048.
AN 'OMICS' BASED METHOD FOR SENSITIVELY MEASURING GENETIC DAMAGE
Reed, Simon H.1; Bennett, Mark1; Teng, Yumin1; Yu, Shirong1; Evans, Katie1; Waters, Raymond1; Higgs, Andy2
1. Pathology, Cardiff University, Cardiff, United Kingdom.
2. Agilent Technologies UK Limited, 610 Wharfedale Road, Wokingham, Berkshire, United Kingdom.
Simon Reed PhD (Reader, Department of Medical Genetics, Cardiff University, UK)
ABSTRACT: DNA damage can occur via a wide variety of genotoxic agents which can compromise a genome’s integrity. This DNA damage if left unrepaired can cause the generation of genetic mutations that are often associated with diseases including cancer. Being able to sensitively measure the location and the level of DNA damage induced throughout the genome is crucial to being able to determine the mechanism of genotoxicity and the DNA repair pathways that promote genome stability. Using ultraviolet light as a paradigm for DNA damage induction, we’ve developed a novel technique which uses Agilent Technologies' Chip on Chip DNA microarrays that is capable of sensitively measuring the levels and distribution of DNA damage and its repair throughout an entire genome.
Our method involves the affinity capture of damaged DNA and its separation from undamaged parts of the genome. By hybridizing the captured damaged DNA to Agilent's whole genome DNA microarrays, we are able to sensitively measure the levels of DNA damage and their precise location throughout the genome. Repeating this process at various times after the induction of DNA damage permits a sensitive and high-resolution estimation of DNA repair capacity throughout the genome.
In partnership with Agilent Technologies, we are adapting our technique which was originally developed using a model organims for use in the human context. We aim to develop an in-vitro alternative to existing animal-based genetic toxicology assays for use in the chemical, cosmetic and pharmaceutical industries. Our aim is to improve genotoxicity testing in humans, as well as elucidating the underlying mechanisms of genotoxicity.