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Nowadays, Quality Management tools such as failure mode and effect analysis (FMEA) are widely used throughout the aeronautical, automotive, software, food services, health care and many other industries to sustain and improve quality and safety. The increasing complexity of scientific research makes it more difficult to maintain all activities under control, in order to guarantee validity and reproducibility of results. Even in non-regulated research, scientists need to be supported with management tools that maximize study performance and outcomes, while facilitating the research process. Frequently, steps that involve human intervention are the weak links in the process. Risk analysis therefore gives considerable benefit to analytical validation, assessing and avoiding failures due to human error, potential imprecision in applying protocols, uncertainty in equipment function and imperfect control of materials. This paper describes in detail how FMEA methodology can be applied as a performance improvement tool in the field of non-regulated research, specifically on a basic Life Sciences research process. We chose as “pilot process” the selection of oligonucleotide aptamers for therapeutic purposes, as an example of a complex and multi-step process, suitable for technology transfer. We applied FMEA methodology, seeking every opportunity for error and its impact on process output, and then, a set of improvement actions was generated covering most aspects of laboratory practice, such as equipment management and staff training. We also propose a useful tool supporting the risk assessment of research processes and its outputs and that we named “FMEA strip worksheet.” These tools can help scientists working in non-regulated research to approach Quality Management and to perform risk evaluation of key scientific procedures and processes with the final aim to increase and better control efficiency and efficacy of their research.

Rab7 regulates the biogenesis of late endosomes, lysosomes, and autophagosomes. It has been proposed that a functional and physical interaction exists between Rab7 and Rac1 GTPases in CDH1 endocytosis and ruffled border formation. In FRT cells over-expressing Rab7, increased expression and activity of Rac1 was observed, whereas a reduction of Rab7 expression by RNAi resulted in reduced Rac1 activity, as measured by PAK1 phosphorylation. We found that CDH1 endocytosis was extremely reduced only in Rab7 over-expressing cells but was unchanged in Rab7 silenced cells. In Rab7 under or over-expressing cells, Rab7 and LC3B-II co-localized and co-localization in large circular structures occurred only in Rab7 over-expressing cells. These large circular structures occurred in about 10% of the cell population; some of them (61%) showed co-localization of Rab7 with cortactin and f-actin and were identified as circular dorsal ruffles (CDRs), the others as mature autophagosomes. We propose that the over-expression of Rab7 is sufficient to induce CDRs. Furthermore, in FRT cells, we found that the expression of the insoluble/active form of Rab7, rather than Rab5, or Rab8, was inducible by cAMP and that cAMP-stimulated FRT cells showed increased PAK1 phosphorylation and were no longer able to endocytose CDH1. Finally, we demonstrated that Rab7 over-expressing cells are able to endocytose exogenous thyroglobulin via pinocytosis/CDRs more efficiently than control cells. We propose that the major thyroglobulin endocytosis described in thyroid autonomous adenomas due to Rab7 increased expression, occurs via CDRs. J. Cell. Physiol. 231: 1695-1708, 2016. © 2015 Wiley Periodicals, Inc.

The scientific world is facing the "quality revolution": not only results have been led to research and social community attention, but also reliability, safety and efficacy of discoveries and efficiency of fund exploitation. Quality management in scientific R&D has become an essential tool in ensuring that modern scientific development is implemented within a rigorous and robust quality framework. The need for Quality standards in non-regulated research is a matter of considerable current debate inside international research community. The qPMO is a research network involving 5 different Institutes and two Departments of the Italian National Research Council (CNR), aimed at realizing a Total Quality Management (TQM) model for Life Sciences laboratories. This TQM OpenLab model will act as a uniform environment in which strong, innovation-oriented research projects can be designed and developed according to international Quality standards and with the planning of Horizon 2020. qPMO covers four different fields to experiment with a specific Quality approach to scientific research and to generate models for the implementation of Quality methodologies in science. Our experience demonstrated that Quality tools can strongly support the management of scientific research through disseminating knowledge, best practice and interoperability and enhance of the economic value of project and research outcomes.

Pax8 and TTF-1 are transcription factors involved in the morphogenesis of the thyroid gland and in the transcriptional regulation of thyroid-specific genes. Both proteins are expressed in few tissues but their simultaneous presence occurs only in the thyroid where they interact physically and functionally allowing the regulation of genes that are markers of the thyroid differentiated phenotype. TAZ is a transcriptional coactivator that regulates the activity of several transcription factors therefore playing a central role in tissue-specific transcription. The recently demonstrated physical and functional interaction between TAZ and TTF-1 in the lung raised the question of whether TAZ could be an important regulatory molecule also in the thyroid. In this study, we demonstrate the presence of TAZ in thyroid cells and the existence of an important cooperation between TAZ and the transcription factors Pax8 and TTF-1 in the modulation of thyroid gene expression. In addition, we reveal that the three proteins are co-expressed in the nucleus of differentiated thyroid cells and that TAZ interacts with both Pax8 and TTF-1, in vitro and in vivo. More importantly, we show that this interaction leads to a significant enhancement of the transcriptional activity of Pax8 and TTF-1 on the thyroglobulin promoter thus suggesting a role of TAZ in the control of genes involved in thyroid development and differentiation.

Nowadays, the requirement to define adequate standards and to identify and validate general guidelines for scientific activity is becoming increasingly apparent also in non-regulated scientific research. Guidelines are fundamental tools to provide valid indications for proper conduct in a research laboratory, the correct use of equipment and procedures, as well as for aligning and standardizing the procedures used in different scientific contexts. The identification, dissemination and application of common guidelines can improve significantly the reproducibility of the scientific results and the exchange of materials and data in the context of scientific consortia, comprising also industrial partners and meta-analysis projects. A Quality and Project Management OpenLab research network was formed in 2012 to develop and apply Total Quality Management models to Life Sciences research laboratories. One of the main tasks of the network has been the definition of a model for the drafting of guidelines, firmly based on quality principles and documentation management. The outcome is an operational flow describing all the phases of the process, which has been validated by four different drafting groups through the production of 13 guidelines ranging from research activity to equipment and facility management. Different institutes of the National Research Council are currently following these guidelines; some of them have also been used to define the procedures included in a certified Quality Management System for a research laboratory. Our experience shows that the model for guidelines we have developed makes drafting guidelines easier and more immediate, and significantly, it is applicable to different scientific contexts and disciplines, including both non-regulated research and technology transfer-oriented research, and also the Quality Management System of a scientific laboratory.

Rab7 regulates the biogenesis of late endosomes, lysosomes, and autophagosomes. It has been proposed that a functional and physical interaction exists between Rab7 and Rac1 GTPases in CDH1 endocytosis and ruffled border formation. In FRT cells over-expressing Rab7, increased expression and activity of Rac1 was observed, whereas a reduction of Rab7 expression by RNAi resulted in reduced Rac1 activity, as measured by PAK1 phosphorylation. We found that CDH1 endocytosis was extremely reduced only in Rab7 over-expressing cells but was unchanged in Rab7 silenced cells. In Rab7 under or over-expressing cells, Rab7 and LC3B-II co-localized and co-localization in large circular structures occurred only in Rab7 over-expressing cells. These large circular structures occurred in about 10% of the cell population; some of them (61%) showed co-localization of Rab7 with cortactin and f-actin and were identified as circular dorsal ruffles (CDRs), the others as mature autophagosomes. We propose that the over-expression of Rab7 is sufficient to induce CDRs. Furthermore, in FRT cells, we found that the expression of the insoluble/active form of Rab7, rather than Rab5, or Rab8, was inducible by cAMP and that cAMP-stimulated FRT cells showed increased PAK1 phosphorylation and were no longer able to endocytose CDH1. Finally, we demonstrated that Rab7 over-expressing cells are able to endocytose exogenous thyroglobulin via pinocytosis/CDRs more efficiently than control cells. We propose that the major thyroglobulin endocytosis described in thyroid autonomous adenomas due to Rab7 increased expression, occurs via CDRs. J. Cell. Physiol. 231: 1695-1708, 2016. © 2015 Wiley Periodicals, Inc.

Design of Experiments (DoE) statistical methodology permits the simultaneous evaluation of the effects of different factors on experimental performance and the analysis of their interactions in order to identify their optimal combinations. Compared to classical approaches based on changing only one factor at a time (OFAT), DoE facilitates the exploration of a broader range of parameters combinations, as well as providing the possibility to select a limited number of combinations covering the whole frame. The advantage of DoE is to maximise the amount of information provided and to save both time and money. DoE has been primarily used in industry to maximise process robustness, but recently it has also been applied in biomedical research to different types of multivariable analyses, from determination of the best cell media composition to the optimisation of entire multi-step laboratory protocols such as cell transfection.

The Design of Experiment (DoE) is a statistical methodology, very useful in the case of multivariable assays, that permits to evaluate simultaneously the influence of different factors on a specific output and to analyse the interactions among them in order to identify their optimal combinations. Moreover, DoE allows to select from the huge numbers of combinations only a limited number, in order to cover the whole frame, allowing to save both time and money. DoE was mostly used in industrial field in order to maximize robust processes, but recently it has been also applied in biomedical research field. Different studies have demonstrated the advantages of using a DoE approach compared to the classical one (a single parameter is tested in each assay) in the context of automated experiments, determination of cell media [1] compositions or HPLC tuning [2]. In the present study, we utilize for the first time the DoE methodology to optimize the transfection protocol of neural cells, as an example of DoE application to a laboratory procedure. Neural precursor cells are hard to transfect and refractory to lipidic reagents [3], for this reason we choose as transfectant reagent the cationic not-lipidic Poliethylenimmine (PEI). The DoE approach allowed us to identify the main variables (factors) affecting the transfection efficiency and to discover their optimal combinations, developing a protocol that let us to triplicate the transfection efficiency respect to the initial conditions. Moreover, the covariance analysis unmasked significant variable interactions impossible to calculate in one factor-variation tests used in normal laboratory practices. Our results indicate that DoE might be very helpful also in research for the identification of the better experimental conditions and the analysis of interactions between different variables.

Quality principles and methodologies have long been ignored in Non Regulated Scientific Research, even though they have been widely used in industrial and business applications in recent decades, improving management and results as well as reducing costs. A groundbreaking project named Quality and Project Management OpenLab (qPMO) was implemented by a cluster of laboratories belonging to the Italian National Research Council (CNR) with the aim of defining efficient models for the application of Quality methodologies to the Life Sciences. For the first time, CNR researchers are working with Quality consultants to apply Quality methodologies to scientific research. Project management and team building techniques (e.g., decision matrix, project charter, debriefing, Plan-Do-Check-Act) were employed to rapidly define a project with four lines of research based on Quality methodologies. Among them, researchers chose to experiment with the definition of standards and guidelines for research activities, experiment optimization via Design of Experiment (DoE), management of a research lab via an ISO9001 Quality Management System, support to technology transfer via Failure Mode and Effect Analysis (FMEA). All of these aspects converge in a model of Total Quality Management OpenLab which is disseminated through a web platform specifically developed for this project. Further, the acquired habits of acting in organized teams, using group management tools and information technologies, supported the work of each group in their respective research line. The results show better use of time and project consistency: the project was set up in one month, and the four research lines accomplished their planned milestones in advance with respect to the initial timetable. Emphasis was also made on Quality training that created a common management and control culture and brought to researchers' attention tools and methodologies widely used in other fields. Each line of activity also brought innovative and promising Quality approaches to scientific research.

Quality principles and methodologies can strongly support the management of scientific research, in both basic and applied research laboratories, where procedures and results are rapidly changing and can hardly be standardized. In this view, Quality methodologies, such as Failure Mode and Effect Analysis - FMEA, was borrowed from the industrial field, where it is widely used in risk control and process optimization procedures, to validate and support research activities and results, to create a standard and controlled workplace, and to support the interaction between research and industrial application.We applied FMEA analysis on a "pilot" process, developed for the selection of cell-specific aptamers, in agreement with the needs of companies interested in the development of this methodology.

The transcription factor Pax8 is involved in the morphogenesis of the thyroid gland and in the maintenance of the differentiated thyroid phenotype. Despite the critical role played by Pax8 during thyroid development and differentiation, very little is known of its post-translational modifications and how these modifications may regulate its activity. We focused our attention on the study of a specific post-translational modification, i.e., sumoylation. Sumoylation is a dynamic and reversible process regulating gene expression by altering transcription factor stability, protein–protein interaction and subcellular localization of target proteins. The analysis of Pax8 protein sequence revealed the presence of one sumoylation consensus motif (ψKxE), strongly conserved among mammals, amphibians, and fish. We demonstrated that Pax8 is sumoylated by the addition of a single small ubiquitin-like modifier (SUMO) molecule on its lysine residue 309 and that Pax8K309R, a substitution mutant in which the candidate lysine is replaced with an arginine, is no longer modified by SUMO. In addition, we analyzed whether protein inhibitor of activated signal transducers and activators of transcription (PIASy), a member of the PIAS STAT family of proteins, could function as a SUMO ligase and we demonstrated that indeed PIASy is able to increase the fraction of sumoylated Pax8. Interestingly, we show that Pax8 is targeted in the SUMO nuclear bodies, which are structures that regulate the nucleoplasmic concentration of transcription factors by SUMO trapping. Finally, we report here that the steady-state protein level of Pax8 is controlled by sumoylation.

Downstream regulatory element antagonistic modulator (DREAM) was originally identified in neuroendocrine cells as a calcium-binding protein that specifically binds to downstream regulatory elements (DRE) on DNA, and represses transcription of its target genes. To explore the possibility that DREAM may regulate the endocrine activity of the thyroid gland, we analyzed its mRNA expression in undifferentiated and differentiated thyroid cells. We demonstrated that DREAM is expressed in the normal thyroid tissue as well as in differentiated thyroid cells in culture while it is absent in FRT poorly differentiated cells. In the present work, we also show that DREAM specifically binds to DRE sites identified in the 5' untranslated region (UTR) of the thyroid-specific transcription factors Pax8 and TTF-2/FoxE1 in a calcium-dependent manner. By gel retardation assays we demonstrated that thapsigargin treatment increases the binding of DREAM to the DRE sequences present in Pax8 and TTF-2/Foxe1 5' UTRs, and this correlates with a significant reduction of the expression of these genes. Interestingly, in poorly differentiated thyroid cells overexpression of exogenous DREAM strongly inhibits Pax8 expression. Moreover, we provide evidence that a mutated form of DREAM unable to bind Ca(2+) interferes with thyroid cell proliferation. Therefore, we propose that in thyroid cells DREAM is a mediator of the calcium-signaling pathway and it is involved in the regulation of thyroid cell function.

The Pax gene family encodes transcription factors that are essential in organogenesis and in the differentiation of various organs in higher eukaryotes. Pax proteins have a DNA binding domain at the N-terminus, and a transcriptional activation domain at the C-terminus. How these domains interact with the transcriptional machinery of the cell is still unclear. In the present paper, we describe the identification by means of immunological screening of the WW domain binding protein WBP-2 as a biochemical interactor of Pax8 (a WW domain is a protein-interaction domain containing two conserved tryptophan residues). Pax8 is required for the morphogenesis of the thyroid gland and for the maintenance of the thyroid differentiated cellular phenotype. WBP-2 was identified originally as a WW domain binding protein, and its function is still unknown. WBP-2 binds to Pax8 in vitro in pulldown assays, and in vivo in tissue culture cells in co-immunoprecipitation assays. Interestingly, Pax8 does not contain a WW domain. Our results point to the identification of a new protein-interacting domain that is present in the C-terminal portion of Pax8 and that is required for protein–protein interaction with WBP-2. Our results demonstrate that WBP-2 is not a transcriptional co-activator of Pax8, but rather behaves as an adaptor molecule, as suggested in other studies.

Pax genes encode for transcription factors essential for tissue development in many species. Pax8, the only member of the family expressed in the thyroid tissue, is involved in the morphogenesis of the gland and in the transcriptional regulation of thyroid-specific genes. TTF-1, a homeodomain-containing factor, is also expressed in the thyroid tissue and has been demonstrated to play a role in thyroid-specific gene expression. Despite the presence of Pax8 and TTF-1 also in a few other tissues, the simultaneous expression of the two transcription factors occurs only in the thyroid, supporting the idea that Pax8 and TTF-1 might cooperate to influence thyroid-specific gene expression. In this report, we describe a physical and functional interaction between these two factors. The fusion protein GST-Pax8 is able to bind TTF-1 present in thyroid or in non-thyroid cell extracts, and by using bacterial purified TTF-1 we demonstrate that the interaction is direct. By co-immunoprecipitation, we also show that the interaction between the two proteins occurs in vivo in thyroid cells. Moreover, Pax8 and TTF-1 when co-expressed in HeLa cells synergistically activate Tg gene transcription. The synergism requires the N-terminal activation domain of TTF-1, and deletions of Pax8 indicate that the C-terminal domain of the protein is involved. Our results demonstrate a functional cooperation and a physical interaction between transcription factors of the homeodomain-containing and of the paired domain-containing gene families in the regulation of tissue-specific gene expression.

The transcription factor Pax8 plays an important role in the expression of the differentiated phenotype of thyroid follicular cells. It has recently been shown that Pax8 is necessary for thyroglobulin (Tg) gene expression in the fully differentiated rat thyroid cell line PC. We have used the PC model system to investigate the role of Pax8 as a mediator of TSH regulation of Tg gene expression. We have demonstrated that Pax8 expression, as well as Tg expression, is severely reduced in cells grown in the absence of hormones and serum. The re-addition of TSH or forskolin to the culture medium is able to restore to wild-type levels the expression of both Pax8 and Tg. We have determined that the action of TSH/forskolin on Pax8 is at the transcriptional level. However, the re-expression of Pax8 can be observed several hours before that of Tg, suggesting that either another factor is needed or that Pax8 itself must be post-translationally modified by a newly synthesized protein to become active. To distinguish between these two possibilities we have stably transfected into PC cells an exogenous Pax8 that is expressed independently of TSH. Our results indicate that in these cells the Tg promoter is still dependent on TSH despite the constitutive presence of Pax8. Furthermore, we also show that in this condition Tg gene transcription requires de novo protein synthesis. In conclusion, TSH regulates the expression of Pax8 at a transcriptional level and also regulates the activity of Pax8 by controlling the expression of one or more as yet unknown factors.

The thyroglobulin gene, the substrate for thyroid hormone biosynthesis, is not expressed in the FRT cell line, which, even though it manifests the polarised epithelial phenotype, does not express any of the thyroid functional properties. Two transcription factors, TTF-1 and Pax-8, have been implicated in thyroid specific expression of the thyroglobulin gene. FRT cells contain Pax-8 but they lack TTF-1. In this paper, we show that transfection of TTF-1 expression vectors in FRT cells results in activation of thyroglobulin gene expression. If the expression vector encoded for TTF-1-ER, a fusion gene coding for the entire TTF-1 protein fused to the hormone-binding domain of the steroid receptor, under the control of the RSV promoter, thyroglobulin gene expression was controlled by estrogen. These data provide a direct demonstration that TTF-1 activates the chromosomal thyroglobulin promoter. Since transfection of TTF-1 expression vectors in non-thyroid cell types did not result in thyroglobulin gene expression, it is suggested that Pax-8, in addition, perhaps, to a specific cellular environment, might be required for thyroid specific expression of the thyroglobulin gene. (C) 1997 Elsevier Science B.V.