Differentiation and functioning of the lateral line organ in zebrafish require Smpx activity

The small muscle protein, X-linked (SMPX) gene encodes a cytoskeleton-associated protein, highly expressed in the inner ear hair cells (HCs), possibly regulating auditory function. In the last decade, several mutations in SMPX have been associated with X-chromosomal progressive non syndromic hearing loss in humans and, in line with this, Smpx-deficient animal models, namely zebrafish and mouse, showed significant impairment of inner ear HCs development, maintenance, and functioning. In this work, we uncovered smpx expression in the neuromast mechanosensory HCs of both Anterior and Posterior Lateral Line (ALL and PLL, respectively) of zebrafish larvae and focused our attention on the PLL. Smpx was subcellularly localized throughout the cytoplasm of the HCs, as well as in their primary cilium. Loss-of-function experiments, via both morpholino-mediated gene knockdown and CRISPR/Cas9 F0 gene knockout, revealed that the lack of Smpx led to fewer properly differentiated and functional neuromasts, as well as to a smaller PLL primordium (PLLp), the latter also Smpx-positive. In addition, the kinocilia of Smpx-deficient neuromast HCs appeared structurally and numerically altered. Such phenotypes were associated with a significant reduction in the mechanotransduction activity of the neuromast HCs, in line with their positivity for Smpx. In summary, this work highlights the importance of Smpx in lateral line development and, specifically, in proper HCs differentiation and/or maintenance, and in the mechanotransduction process carried out by the neuromast HCs. Because lateral line HCs are both functionally and structurally analogous to the cochlear HCs, the neuromasts might represent an invaluable-and easily accessible-tool to dissect the role of Smpx in HCs development/functioning and shed light on the underlying mechanisms involved in hearing loss.

NF-YAl drives EMT in Claudinlow tumours

NF-Y is a trimeric transcription factor whose binding site -the CCAAT box- is enriched in cancer-promoting genes. The regulatory subunit, the sequence-specificity conferring NF-YA, comes in two major isoforms, NF-YA long (NF-YAl) and short (NF-YAs). Extensive expression analysis in epithelial cancers determined two features: widespread overexpression and changes in NF-YAl/NF-YAs ratios (NF-YAr) in tumours with EMT features. We performed wet and in silico experiments to explore the role of the isoforms in breast -BRCA- and gastric -STAD- cancers. We generated clones of two Claudin^low BRCA lines SUM159PT and BT549 ablated of exon-3, thus shifting expression from NF-YAl to NF-YAs. Edited clones show normal growth but reduced migratory capacities in vitro and ability to metastatize in vivo. Using TCGA, including upon deconvolution of scRNA-seq data, we formalize the clinical importance of high NF-YAr, associated to EMT genes and cell populations. We derive a novel, prognostic 158 genes signature common to BRCA and STAD Claudin^low tumours. Finally, we identify splicing factors associated to high NF-YAr, validating RBFOX2 as promoting expression of NF-YAl. These data bring three relevant results: (i) the definition and clinical implications of NF-YAr and the 158 genes signature in Claudin^low tumours; (ii) genetic evidence of 28 amino acids in NF-YAl with EMT-promoting capacity; (iii) the definition of selected splicing factors associated to NF-YA isoforms.

The zebrafish (Danio rerio) embryo-larval contact assay combined with biochemical biomarkers and swimming performance in sewage sludge and hydrochar hazard assessment

Hydrothermal carbonization is considered a powerful technology to convert sewage sludge (SS) into a valuable carbonaceous solid known as hydrochar (HC). Up to now criteria for landfill application of SS and HC are based only on physicochemical properties and levels of pollutant residues. Nevertheless, to ensure their safe environmental applications it is mandatory to develop biosensors which can provide relevant information on their toxic potential for natural ecosystems. Therefore, this study aimed to assess the suitability of a contact assay using zebrafish embryo/larvae combined with sub-lethal end-points to evaluate the hazard associated with SS and related HC exposure. A suite of biomarkers was also applied on larvae, related to detoxification and oxidative stress as the activity of Ethoxyresorufin-O-deethylase, glutathione-S-transferase, and catalase, the content of reactive oxygen species and the behavioral assay using the DanioVision™ chamber. Legacy priority pollutants were also measured either in SS and HC tested samples and in contact waters. The exposure to SS caused higher lethality compared to HC. No significant changes in the activity of oxidative stress markers was observed upon exposure to both matrices. The behavioral test showed a hypoactivity condition in larvae exposed to both SS and HC with the effects of SS stronger than HC. Chemical analysis revealed the presence of trace elements and halogenated compounds in either SS, HC. Heavy metals were also released in contact waters, while volatile hydrocarbons (C6-C10) and halogenated compounds resulted below LOD (<0.05 μ L^-1). Our study highlights the suitability of zebrafish embryotoxicity test, coupled with behavioral traits, as screening tool for assessing potential risks, associated with the landfill application of both SS and HC, for aquatic wildlife.

The Pick-and-Roll in Basketball From Deep Interviews of Elite Coaches: A Mixed Method Approach From Polar Coordinate Analysis

Pick-and-roll is the most widespread cooperative action among high-level basketball teams and the most applied strategy by coaches to gain an advantage over the rival team. During pick-and-roll, opposing teams perform antagonistic actions based on goals that are expressed in offensive and defensive tactics. The aim of this study is to examine the approaches of high-level coaches on the offensive and defensive dynamics emerging in matches of a basketball elite team during an entire season of the Spanish Asociación de Clubes de Baloncesto (ACB) league. To this end, we used a mixed-methods approach based on systematic observation of verbatim transcripts of interviews conducted with six high-level coaches about the pick-and-roll dynamics that emerged in matches of the Unicaja Málaga team during an entire season of the ACB league. The observational design was nomothetic, punctual, and multidimensional. The choice of this methodology is justified since we developed an ad hoc indirect observation tool to evaluate the coaches’ perspective on this dynamic. Once the intra-observer reliability of the instrument was confirmed, we performed a polar coordinate analysis to identify the significant relationships between the coaches’ evaluations and the offensive and defensive pick-and-roll elements that supported such verbal behaviors. The results highlight the presence of various offensive and defensive aspects of pick-and-roll (n = 2224) emerging in the Unicaja team that were significantly associated with positive and negative evaluations of the coaches. The interview confirms that coach 1 and his staff were less confident in options that pick-and-roll offer, which is also reflected in the record of screens made and simulated, than coach 3. This study shows that the application of mixed methods, by analysis of the polar coordinate of the coding carried out on responses of a systematized interview, has proven to be an effective strategy in obtaining relevant information on the expert knowledge of the elite coaches on the influence of pick-and-roll on tactical actions in basketball.

Inner Ear and Muscle Developmental Defects in Smpx-Deficient Zebrafish Embryos

The last decade has witnessed the identification of several families affected by hereditary non-syndromic hearing loss (NSHL) caused by mutations in the SMPX gene and the loss of function has been suggested as the underlying mechanism. In the attempt to confirm this hypothesis we generated an Smpx-deficient zebrafish model, pointing out its crucial role in proper inner ear development. Indeed, a marked decrease in the number of kinocilia together with structural alterations of the stereocilia and the kinocilium itself in the hair cells of the inner ear were observed. We also report the impairment of the mechanotransduction by the hair cells, making SMPX a potential key player in the construction of the machinery necessary for sound detection. This wealth of evidence provides the first possible explanation for hearing loss in SMPX-mutated patients. Additionally, we observed a clear muscular phenotype consisting of the defective organization and functioning of muscle fibers, strongly suggesting a potential role for the protein in the development of muscle fibers. This piece of evidence highlights the need for more in-depth analyses in search for possible correlations between SMPX mutations and muscular disorders in humans, thus potentially turning this non-syndromic hearing loss-associated gene into the genetic cause of dysfunctions characterized by more than one symptom, making SMPX a novel syndromic gene.

The Action of Verbal and Non-verbal Communication in the Therapeutic Alliance Construction: A Mixed Methods Approach to Assess the Initial Interactions With Depressed Patients

In psychodynamic psychotherapy, verbal (structures and intents) and non-verbal (voice and interruptions) dimensions of communication intertwine conveying information and determining the mutual regulation between therapist and patient through conversational sequences. The communication components interplay is the foundation for building the therapeutic alliance, a relational dimension that predicts a psychotherapy outcome and change, influenced by patient-therapist exchanges from the initial stages of their encounter. Depressed patients present specific verbal and non-verbal communication and show difficulties in developing and maintaining the therapeutic alliance. Based on the reviewed literature, the main aim of this study was to analyze how the action of specific communicative modes, implemented by the therapist and depressed patients, affect the reciprocal construction of the early therapeutic alliance by each participant during the mutual regulation processes. We employed a mixed methods approach based on a systematic observation of communication and alliance ruptures and repairs within the audio recordings and verbatim transcripts of 20 psychotherapy sessions (6,232 speaking turns) with seven depressed patients. The observational design was nomothetic, follow-up, and multidimensional. The choice of methodology is justified because we developed a comprehensive procedure that integrates an ad hoc indirect observation system (the Communicative Modes Analysis System in Psychotherapy), analyzing verbal and non-verbal communication, and an observational tool with deductive categories (the Collaborative Interactions Scale-Revised), assessing the therapeutic alliance construction. Once we confirmed the intra-and inter-observer reliability for the ad hoc system and the inter-rater reliability for the tool with deductive (or theoretical) categories, we performed descriptive statistics (to describe quantitatively communicative modes and alliance ruptures and repairs), lag sequential analysis (to detect stable patterns in communication-alliance interactions), and polar coordinate analysis (to identify significant relationships between communicative modes and alliance ruptures and repairs). Results confirm that the therapist's verbal (asking and exploring) and non-verbal (elaborating and cooperatively interrupting) modes and the depressed patients' verbal (asserting and exploring) and non-verbal (expressing emotions and cooperatively interrupting) modes determine stable patterns and significant associations with collaborative behaviors connected to the reciprocal construction of alliance by each participant. All this may provide professionals with useful information to increase the psychotherapy effectiveness with depressed patients.

Environmental concentration of fluoxetine disturbs larvae behavior and increases the defense response at molecular level in zebrafish (Danio rerio)

Fluoxetine (FLX) is one of the main antidepressants used worldwide. After human use, FLX enters the aquatic ecosystems, where it has commonly detected in the high ng/L concentration range. Several investigations have shown that exposure to different concentrations of FLX caused different adverse effects towards a number of aquatic species. However, the information on the onset and the relationship between molecular and behavioral FLX-induced effects remains scant. The aim of this study was to assess the effects induced by two FLX concentrations, namely 50 ng/L and 500 ng/L, on swimming activity of zebrafish (Danio rerio) larvae at 96-h post-fertilization (hpf) and to investigate if such behavioral effects were related to modulation of the expression of oxidative stress-related (sod1, sod2, cat, gpxa, and gst), stress- and anxiety-related (oxtl, prl2, npy, and ucn3l) genes, and genes encoding for the transporters of the main neurotransmitters (slc6a3, slc6a4a, slc6a4b, slc6a11). Fluoxetine exposure altered the swimming behavior of larvae, as shown by the reduction of the distance traveled by treated larvae in response to an external stimulus. Such behavioral change was related, at molecular level, to an enhanced expression of sod1, cat, and gpxa, suggesting an overproduction of pro-oxidant molecules. In addition, FLX modulated the expression of oxtl, slc6a4a, slc6a4b, and slc6a11, suggesting its capability to affect anxiety- and neurotransmitter-related genes.

Evaluation of the infiltration of polystyrene nanobeads in zebrafish embryo tissues after short-term exposure and the related biochemical and behavioural effects

One of the current main challenges faced by the scientific community is concerning the fate and toxicity of plastics, due to both the well-known threats made by larger plastic items spreading in ecosystems and their fragmentation into micro- and nanoparticles. Since the chemical and physical characteristics of these smaller plastic fragments are markedly different with respect to their bulk product, the potential toxicological effects in the environment need to be deeply investigated. To partially fill this gap of knowledge, the aim of this study was to evaluate the polystyrene nanobead intake in the tissues of zebrafish (Danio rerio) embryos and their related toxicity. Embryos at 72 h post fertilization (hpf) were exposed for 48 h to 0.5 μm fluorescent polystyrene nanobeads at a concentration of 1 mg L^-1. Confocal microscopy was employed to investigate nanoplastic ingestion and tissue infiltration, while potential sub-lethal effects were evaluated by measuring several endpoints, which covered the adverse effects at the molecular (protein carbonylation), cellular (P-glycoprotein, activity of several antioxidant/detoxifying enzymes) and organism levels by evaluating of possible changes in the embryos' swimming behaviour. Imaging observations clearly highlighted the nanoplastics' uptake, showing nanobeads not only in the digestive tract, but also migrating to other tissues through the gut epithelium. Biomarker analyses revealed a significant decrease in cyclooxygenase activity and an induction of superoxide dismutase. The behavioural test highlighted a significant (p < 0.05) variation in the turn angle between the control and exposed embryos. This study points out the capability of nanoplastics to infiltrate zebrafish embryo tissues, even after a short exposure, thus suggesting the need for deeper investigations following longer exposure times, and highlighting the potential of nanoplastics to cause toxicological effects on freshwater organisms, at the organism level.

The Communicative Modes Analysis System in Psychotherapy From Mixed Methods Framework: Introducing a New Observation System for Classifying Verbal and Non-verbal Communication

Communication represents the core of psychotherapy. The dynamic interaction between verbal and non-verbal components during patient-therapist exchanges, indeed, promotes the co-construction of meanings bringing about change within a process of reciprocal influence of participants. Our paper aims to illustrate the building of a new observational instrument of the therapeutic discourse, the Communicative Modes Analysis System in Psychotherapy (CMASP), and its reliability study from Mixed Methods framework. The CMASP is a single classification system analyzing the communication features within therapeutic exchanges. Born to overcome the limits of traditional psychotherapy research which considers verbal and non-verbal dimensions of communication as in polar opposition, the CMASP building was based on the performative function derived from the Speech Act Theory. We used this function as a comprehensive theorization to interpret the communication components in psychotherapy as an integrated and interacting system. In fact, the instrument detects and classifies, at the overall and dimension level, the verbal and extra-linguistic components of psychotherapeutic communication implemented by the therapist and patients in the form of communicative modes. From the observational methodology framework, it was built an instrument able to record and analyze verbal, vocal and interruption behaviors by combining elements of qualitative and quantitative research approaches. The sample consisted of 30 psychotherapy audio recordings and verbatim transcripts of psychotherapy sessions (for a total of 8327 speaking turns). Four main dimensions were elaborated (Verbal Mode-Structural Form, Verbal Mode-Communicative Intent, Vocal Mode, and Interruption Mode) according to the agency role of communication components. The instrument is a field format combined with category systems. For each dimension, we built a category system that is exhaustive and mutually exclusive. From all dimensions, we have a total of 33 categories. Intra-and inter-judge reliability among four independent judges was computed on a total of 503 speaking turns coded through Cohen's κ and Krippendorff's canonical agreement coefficients (Cc), respectively. The CMASP showed high intra-and inter-judge agreement at the global, dimensional, and categorical level providing researchers and professionals with a single and flexible classification system, able to give multiple and concurrent information about the psychotherapy process.

Environmental concentrations of triclosan activate cellular defence mechanism and generate cytotoxicity on zebrafish (Danio rerio) embryos

Triclosan (TCS, 5‑chloro‑2‑(2,4‑dichlorophenoxy) phenol) is becoming a major surface waters pollutant worldwide at concentrations ranging from ng L^-1 to μg L^-1. Up to now, the adverse effects on aquatic organisms have been investigated at concentrations higher than the environmental ones, and the pathways underlying the observed toxicity are still not completely understood. Therefore, the aim of this study was to investigate the toxic effects of TCS at environmental concentrations on zebrafish embryos up to 120 hours post fertilization (hpf). The experimental design was planned considering both the quantity and the exposure time for the effects on the embryos, exposing them to two different concentrations (0.1 μg L^-1, 1 μg L^-1) of TCS, for 24 h (from 96 to 120 hpf) and for 120 h (from 0 to 120 hpf). A suite of biomarkers was applied to measure the induction of embryos defence system, the possible increase of oxidative stress and the DNA damage. We measured the activity of glutathione‑S‑transferase (GST), P‑glycoprotein efflux and ethoxyresorufin‑o‑deethylase (EROD), the level of ROS, the oxidative damage through the Protein Carbonyl Content (PCC) and the activity of antioxidant enzymes. The genetic damage was evaluated through DNA Diffusion Assay, Micronucleus test (MN test), and Comet test. The results showed a clear response of embryos defence mechanism, through the induction of P-gp efflux functionality and the activity of detoxifying/antioxidant enzymes, preventing the onset of oxidative damage. Moreover, the significant increase of cell necrosis highlighted a strong cytotoxic potential for TCS. The overall results obtained with environmental concentrations and both exposure time, underline the critical risk associated to the presence of TCS in the aquatic environment.

The interactions of fullerene C60 and Benzo(α)pyrene influence their bioavailability and toxicity to zebrafish embryos

This study aimed to assess the toxicological consequences related to the interaction of fullerene nanoparticles (C₆₀) and Benzo(α)pyrene (B(α)P) on zebrafish embryos, which were exposed to C₆₀ and B(α)P alone and to C₆₀ doped with B(α)P. The uptake of pollutants into their tissues and intra-cellular localization were investigated by immunofluorescence and electron microscopy. A set of biomarkers of genotoxicity and oxidative stress, as well as functional proteomics analysis were applied to assess the toxic effects due to C₆₀ interaction with B(α)P. The carrier role of C₆₀ for B(α)P was observed, however adsorption on C₆₀ did not affect the accumulation and localization of B(α)P in the embryos. Instead, C₆₀ doped with B(α)P resulted more prone to sedimentation and less bioavailable for the embryos compared to C₆₀ alone. As for toxicity, our results suggested that C₆₀ alone elicited oxidative stress in embryos and a down-regulation of proteins involved in energetic metabolism. The C₆₀ + B(α)P induced cellular response mechanisms similar to B(α)P alone, but generating greater cellular damages in the exposed embryos.

Exposure to cocaine and its main metabolites altered the protein profile of zebrafish embryos

Illicit drugs have been identified as emerging aquatic pollutants because of their widespread presence in freshwaters and potential toxicity towards aquatic organisms. Among illicit drug residues, cocaine (COC) and its main metabolites, namely benzoylecgonine (BE) and ecgonine methyl ester (EME), are commonly detected in freshwaters worldwide at concentration that can induce diverse adverse effects to non-target organisms. However, the information of toxicity and mechanisms of action (MoA) of these drugs, mainly of COC metabolites, to aquatic species is still fragmentary and inadequate. Thus, this study was aimed at investigating the toxicity of two concentrations (0.3 and 1.0 μg/L) of COC, BE and EME similar to those found in aquatic ecosystems on zebrafish (Danio rerio) embryos at 96 h post fertilization through a functional proteomics approach. Exposure to COC and both its metabolites significantly altered the protein profile of zebrafish embryos, modulating the expression of diverse proteins belonging to different functional classes, including cytoskeleton, eye constituents, lipid transport, lipid and energy metabolism, and stress response. Expression of vitellogenins and crystallins was modulated by COC and both its main metabolites, while only BE and EME altered proteins related to lipid and energy metabolism, as well as to oxidative stress response. Our data confirmed the potential toxicity of low concentrations of COC, BE and EME, and helped to shed light on their MoA on an aquatic vertebrate during early developmental period.

Environmental concentrations of cocaine and its main metabolites modulated antioxidant response and caused cyto-genotoxic effects in zebrafish embryo cells

Illicit drugs have been recently identified as a serious environmental problem because of the growing evidence regarding their occurrence in aquatic environment and potential toxicity towards non-target organisms. Among them, cocaine (COC) and its main metabolites, namely benzoylecgonine (BE) and ecgonine methyl ester (EME), are commonly measured in freshwaters worldwide at levels that might cause diverse sub-lethal effects to aquatic organisms. Thus, the present study was aimed at investigating the potential adverse effects induced by the exposure to environmental concentrations (0.04, 0.4, 4 and 40 nM) of COC, BE, and EME on zebrafish (Danio rerio) embryos at 96 h post fertilization. Cytotoxicity was assessed by the Trypan Blue exclusion method, while primary and fixed genetic damages were evaluated by the Single Cell Gel Electrophoresis (SCGE) assay, and the DNA diffusion assay together with the Micronucleus test, respectively. The involvement of oxidative stress in the mechanism of action (MoA) of all tested drugs was assessed by measuring the activity of defense enzymes (SOD, CAT, GPx, and GST) and the expression of their encoding genes. Exposure to COC and both metabolites significantly reduced cell viability, increased DNA fragmentation and promoted the onset of apoptotic cells and micronuclei in zebrafish embryos. Results from oxidative stress-related endpoints and gene expression suggested that the observed genotoxicity may be caused by an overproduction of free radicals that imbalanced the oxidative status of embryos. The integration of biomarker responses into a synthetic index showed that at each tested concentration, BE and EME had a similar toxicity and were both more toxic than COC. Our data confirmed the potential toxicity of environmental concentrations of COC, BE, and EME, suggesting the need of further in-depth studies to shed light on their MoA and long-term toxicity towards non-target aquatic species.

Biosensing Motor Neuron Membrane Potential in Live Zebrafish Embryos

The protocols described here are designed to allow researchers to study cell communication without altering the integrity of the environment in which the cells are located. Specifically, they have been developed to analyze the electrical activity of excitable cells, such as spinal neurons. In such a scenario, it is crucial to preserve the integrity of the spinal cell, but it is also important to preserve the anatomy and physiological shape of the systems involved. Indeed, the comprehension of the manner in which the nervous system-and other complex systems-works must be based on a systemic approach. For this reason, the live zebrafish embryo was chosen as a model system, and the spinal neuron membrane voltage changes were evaluated without interfering with the physiological conditions of the embryos. Here, an approach combining the employment of zebrafish embryos with a FRET-based biosensor is described. Zebrafish embryos are characterized by a very simplified nervous system and are particularly suited for imaging applications thanks to their transparency, allowing for the employment of fluorescence-based voltage indicators at the plasma membrane during zebrafish development. The synergy between these two components makes it possible to analyze the electrical activity of the cells in intact living organisms, without perturbing the physiological state. Finally, this non-invasive approach can co-exist with other analyses (e.g., spontaneous movement recordings, as shown here).

Corrigendum: Intronless WNT10B-short variant underlies new recurrent allele-specific rearrangement in acute myeloid leukaemia

Scientific Reports 6: Article number: 37201; published online: 17 November 2016; updated: 26 April 2017 This Article contains typographical errors in the Methods section under subheading ‘WNT10B/WNT10B IVS1 Gene expression analysis’. “The WNT10B (P4-P2 primers) amplification was performed with following thermal conditions: 94 °C for 1 min, 33 cycles at 94° for 30 s, 58 °C for 30 s, 72 °C for 30 s and 72 °C for 5 min.

Intronless WNT10B-short variant underlies new recurrent allele-specific rearrangement in acute myeloid leukaemia

Defects in the control of Wnt signaling have emerged as a recurrent mechanism involved in cancer pathogenesis and acute myeloid leukaemia (AML), including the hematopoietic regeneration-associated WNT10B in AC133bright leukaemia cells, although the existence of a specific mechanism remains unproven. We have obtained evidences for a recurrent rearrangement, which involved the WNT10B locus (WNT10BR) within intron 1 (IVS1) and flanked at the 5' by non-human sequences whose origin remains to be elucidated; it also expressed a transcript variant (WNT10BIVS1) which was mainly detected in a cohort of patients with intermediate/unfavorable risk AML. We also identified in two separate cases, affected by AML and breast cancer respectively, a genomic transposable short form of human WNT10B (ht-WNT10B). The intronless ht-WNT10B resembles a long non-coding RNA (lncRNA), which suggests its involvement in a non-random microhomology-mediated recombination generating the rearranged WNT10BR. Furthermore, our studies supports an autocrine activation primed by the formation of WNT10B-FZD4/5 complexes in the breast cancer MCF7 cells that express the WNT10BIVS1. Chemical interference of WNT-ligands production by the porcupine inhibitor IWP-2 achieved a dose-dependent suppression of the WNT10B-FZD4/5 interactions. These results present the first evidence for a recurrent rearrangement promoted by a mobile ht-WNT10B oncogene, as a relevant mechanism for Wnt involvement in human cancer.

INaP selective inhibition reverts precocious inter- and motorneurons hyperexcitability in the Sod1-G93R zebrafish ALS model

The pathogenic role of SOD1 mutations in amyotrophic lateral sclerosis (ALS) was investigated using a zebrafish disease model stably expressing the ALS-linked G93R mutation. In addition to the main pathological features of ALS shown by adult fish, we found remarkably precocious alterations in the development of motor nerve circuitry and embryo behavior, and suggest that these alterations are prompted by interneuron and motor neuron hyperexcitability triggered by anomalies in the persistent pacemaker sodium current I_NaP. The riluzole-induced modulation of I_NaP reduced spinal neuron excitability, reverted the behavioral phenotypes and improved the deficits in motor nerve circuitry development, thus shedding new light on the use of riluzole in the management of ALS. Our findings provide a valid phenotype-based tool for unbiased in vivo drug screening that can be used to develop new therapies.

Mechanical properties of the compass depressors of the sea-urchin Paracentrotus lividus (Echinodermata, Echinoidea) and the effects of enzymes, neurotransmitters and synthetic tensilin-like protein

The compass depressors (CDs) of the sea-urchin lantern are ligaments consisting mainly of discontinuous collagen fibrils associated with a small population of myocytes. They are mutable collagenous structures, which can change their mechanical properties rapidly and reversibly under nervous control. The aims of this investigation were to characterise the baseline (i.e. unmanipulated) static mechanical properties of the CDs of Paracentrotus lividus by means of creep tests and incremental force-extension tests, and to determine the effects on their mechanical behaviour of a range of agents. Under constant load the CDs exhibited a three-phase creep curve, the mean coefficient of viscosity being 561±365 MPa.s. The stress-strain curve showed toe, linear and yield regions; the mean strain at the toe-linear inflection was 0.86±0.61; the mean Young's modulus was 18.62±10.30 MPa; and the mean tensile strength was 8.14±5.73 MPa. Hyaluronidase from Streptomyces hyalurolyticus had no effect on creep behaviour, whilst chondroitinase ABC prolonged primary creep but had no effect on secondary creep or on any force-extension parameters; it thus appears that neither hyaluronic acid nor sulphated glycosaminoglycans have an interfibrillar load transfer function in the CD. Acetylcholine, the muscarinic agonists arecoline and methacholine, and the nicotinic agonists nicotine and 1-[1-(3,4-dimethyl-phenyl)-ethyl]-piperazine produced an abrupt increase in CD viscosity; the CDs were not differentially sensitive to muscarinic or nicotinic agonists. CDs showed either no, or no consistent, response to adrenaline, L-glutamic acid, 5-hydroxytryptamine and γ-aminobutyric acid. Synthetic echinoid tensilin-like protein had a weak and inconsistent stiffening effect, indicating that, in contrast to holothurian tensilins, the echinoid molecule may not be involved in the regulation of collagenous tissue tensility. We compare in detail the mechanical behaviour of the CD with that of mammalian tendon and highlight its potential as a model system for investigating poorly understood aspects of the ontogeny and phylogeny of vertebrate collagenous tissues.

Introduction to genomics

The science of genomes: only within the past few decades have scientists progressed from the analysis of a single or a small number of genes at once to the investigation of thousands of genes, going from the study of the units of inheritance to the investigation of the whole genome of an organism. The science of the genomes, or "genomics," initially dedicated to the determination of DNA sequences (the nucleotide order on a given fragment of DNA), has promptly expanded toward a more functional level--studying the expression profiles and the roles of both genes and proteins. The aim of the chapter is to review some basic assumptions and definitions that are the fabric of genomics, and to elucidate key concepts and approaches on which genomics rely.

prox1b Activity is essential in zebrafish lymphangiogenesis

Background

The lymphatic vascular system, draining interstitial fluids from most tissues and organs, exerts crucial functions in several physiological and pathological processes. Lymphatic system development depends on Prox1, the first marker to be expressed in the endothelial cells of the cardinal vein from where lymph vessels originate. Prox1 ortholog in the optically clear, easily manipulated zebrafish model has been previously isolated and its contribution to lymphangiogenesis has been clarified. Because of a round of genome duplication occurred at the base of teleosts radiation, several zebrafish genes have been retained in duplicate through evolution. We investigated for the presence of additional prox1 genes and determined their role in zebrafish lymphangiogenesis.

Methodology/Principal Findings

We isolated a second ortholog, named prox1b, and analyzed its expression during development by whole mount in situ hybridization (WISH). We detected strong prox1b expression in the endothelium of the posterior cardinal vein (PCV) from where lymphatic precursors originate. To analyze prox1b involvement in lymphangiogenesis we utilized the fli1:GFP transgenics and followed the formation of the toracic duct (TD), the primary lymph vessel in fish, after prox1b knockdown. Our findings clearly demonstrated that the absence of prox1b activity severely hampers the formation of the TD.

Conclusions/Significance

This work provides substantial progress toward the understanding of zebrafish lymphangiogenesis. In light of the features shared by the lymphatic systems of zebrafish and higher vertebrates, the establishment of such lymphatic model will provide a powerful tool to study, for instance, disorders of body fluid homeostasis, inflammation and cancer metastasis, and may ultimately contribute to novel therapies.

Mutational screening and zebrafish functional analysis of GIGYF2 as a Parkinson-disease gene

The Grb10-Interacting GYF Protein-2 (GIGYF2) gene has been proposed as the Parkinson-disease (PD) gene underlying the PARK11 locus. However, association of GIGYF2 with PD has been challenged and a functional validation of GIGYF2 mutations is lacking. In this frame, we performed a mutational screening of GIGYF2 in an Italian PD cohort. Exons containing known mutations were analyzed in 552 cases and 552 controls. Thereafter, a subset of 184 familial PD cases and controls were subjected to a full coding-exon screening. These analyses identified 8 missense variations in 9 individuals (4 cases, 5 controls). Furthermore, we developed a zebrafish model of gigyf2 deficiency. Abrogation of gigyf2 function in zebrafish embryos did not lead to a drastic cell loss in diencephalic dopaminergic (DA) neuron clusters, suggesting that gigyf2 is not required for DA neuron differentiation. Notably, gigyf2 functional abrogation did not increase diencephalic DA neurons susceptibility to the PD-inducing drug MPP+. These data, together with those recently reported by other groups, suggest that GIGYF2 is unlikely to be the PARK11 gene.

Identification and expression pattern of zebrafish prox2 during embryonic development

Prox2, together with the previously isolated Prox1, is the vertebrate homolog of the Drosophila homeobox-containing gene prospero, the founder member of a family of transcription factors which have been shown to play critical roles in many developmental events. We have isolated a cDNA which encodes a putative protein that shares a high degree of homology with mammalian Prox1, Prox2, and zebrafish Prox1. Comparative genomic analysis revealed that this protein corresponds to the zebrafish Prox2 homolog being the gene syntenic with the chromosome region hosting mouse Prox2. Whole-mount in situ experiments demonstrated that prox2 is expressed, during zebrafish embryonic development, in defined structures of the central nervous system and the eye, as previously reported in mouse. Additionally, reverse transcriptase-polymerase chain reaction analysis disclosed prox2 expression in several adult organs. Finally, prox1 loss- and gain-of-function assays have been carried out to search for regulative effects on prox2 expression.

Crucial role of zebrafish prox1 in hypothalamic catecholaminergic neurons development

Background

Prox1, the vertebrate homolog of prospero in Drosophila melanogaster, is a divergent homeogene that regulates cell proliferation, fate determination and differentiation during vertebrate embryonic development.

Results

Here we report that, in zebrafish, prox1 is widely expressed in several districts of the Central Nervous System (CNS). Specifically, we evidenced prox1 expression in a group of neurons, already positive for otp1, located in the hypothalamus at the level of the posterior tuberculum (PT). Prox1 knock-down determines the severe loss of hypothalamic catecholaminergic (CA) neurons, identified by tyrosine hydroxylase (TH) expression, and the synergistic prox1/otp1 overexpression induces the appearance of hypothalamic supernumerary TH-positive neurons and ectopic TH-positive cells on the yolk epitelium.

Conclusion

Our findings indicate that prox1 activity is crucial for the proper development of the otp1-positive hypothalamic neuronal precursors to their terminal CA phenotype.

Differential regulation of the zebrafish orthopedia 1 gene during fate determination of diencephalic neurons

BACKGROUND

The homeodomain transcription factor Orthopedia (Otp) is essential in restricting the fate of multiple classes of secreting neurons in the neuroendocrine hypothalamus of vertebrates. However, there is little information on the intercellular factors that regulate Otp expression during development.

RESULTS

Here, we identified two otp orthologues in zebrafish (otp1 and otp2) and explored otp1 in the context of the morphogenetic pathways that specify neuroectodermal regions. During forebrain development, otp1 is expressed in anterior groups of diencephalic cells, positioned in the preoptic area (PO) (anterior alar plate) and the posterior tuberculum (PT) (posterior basal plate). The latter structure is characterized by Tyrosine Hydroxylase (TH)-positive cells, suggesting a role for otp1 in the lineage restriction of catecholaminergic (CA) neurons. Disruptions of Hedgehog (HH) and Fibroblast Growth Factor (FGF) pathways point to the ability of SHH protein to trigger otp1 expression in PO presumptive neuroblasts, with the attenuating effect of Dzip1 and FGF8. In addition, our data disclose otp1 as a determinant of CA neurons in the PT, where otp1 activity is strictly dependent on Nodal signaling and it is not responsive to SHH and FGF.

CONCLUSION

In this study, we pinpoint the evolutionary importance of otp1 transcription factor in cell states of the diencephalon anlage and early neuronal progenitors. Furthermore, our data indicate that morphogenetic mechanisms differentially regulate otp1 expression in alar and basal plates.

Identification of thioredoxin reductase 1-regulated genes using small interference RNA and cDNA microarray

Thioredoxin reductase 1 (TrxR1) is a cytosolic enzyme that plays a central role in controlling cellular redox homeostasis. TrxR1 can transduce regulatory redox signals through NADPH-dependent reduction of thioredoxin (Trx), which is able to reduce a broad spectrum of target enzymes and regulate the activity of several transcription factors (e.g., p53 and NF-kappaB). The TrxR1/Trx system is involved in every step of cancer biology, ranging from transformation and progression to invasion, metastasis and resistance to therapy. TrxR1 was also recently identified as one key enzyme involved in cell death induced by interferon-beta (IFN-beta)/all-trans retinoic acid (ATRA) anti-cancer treatment. Our study employed small interference RNA (siRNA) and microarray techniques to investigate the effect of TrxR1 silencing on gene expression in HepG2 cells. We also investigated TrxR1-mediated cell response to IFN-beta/ATRA treatment. We identified TrxR1-dependent genes with functions related to several cellular processes such as apoptosis (SOX4), ubiquitination (Ubiquitin D, F-box protein 25), organization of cytoskeletal/extracellular matrix (Keratin 19, Fibronectin 1) and transport (Cystine/Glutamate transporter). We also investigated the effect of TrxR1 siRNA on the protein profile using surface enhanced laser desorption ionization time-of-flight (SELDI-TOF) technology. Profiles confirmed significant involvement of TrxR1 in cell response to IFN-beta/ATRA.

A genomic and proteomic study of the spectrum of nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease, and some of its forms are progressive. This study describes the profiling of hepatic gene expression and serum protein content in patients with different subtypes of NAFLD. Liver biopsy specimens from 98 bariatric surgery patients were classified as normal, steatosis alone, steatosis with nonspecific inflammation, and nonalcoholic steatohepatitis (NASH). Microarray hybridizations were performed in triplicate and the microarray expression levels of a selected group of genes were confirmed using real-time quantitative reverse-transcriptase polymerase chain reaction. Serum protein profiles of the same patients were determined by SELDI-TOF mass spectrometry. Of 98 obese patients, 91 were diagnosed with NAFLD (12 steatosis alone, 52 steatosis with nonspecific inflammation, and 27 NASH), and 7 patients without NAFLD served as obese controls. Each group of NAFLD patients was compared with the obese controls, and 22 genes with more than twofold differences in expression levels were revealed. Proteomics analyses were performed for the same group comparisons and revealed twelve significantly different protein peaks. In conclusion, this genomic/proteomic analysis suggests differential expression of several genes and protein peaks in patients within and across the forms of NAFLD. These findings may help clarify the pathogenesis of NAFLD and identify potential targets for therapeutic intervention.

Hepatic gene expression in patients with obesity-related non-alcoholic steatohepatitis

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is among the most common causes of chronic liver disease. NAFLD includes a spectrum of clinicopathologic syndromes that includes non-alcoholic steatohepatitis (NASH) that has potential for progression. The pathogenesis of NASH is poorly characterized.

AIM

This study was designed to identify differences in hepatic gene expression in patients with NASH and to relate such differences to their clinical characteristics.

DESIGN

Consecutive patients undergoing bariatric surgery were prospectively recruited. Extensive clinical data and two liver biopsy specimens were obtained at the time of enrollment. A single hepatopathologist reviewed and classified the liver biopsies. Patients with excessive alcohol use and other causes of liver disease were excluded. A group of 29 NASH patients, 12 with steatosis alone, seven obese controls and six non-obese controls were selected for further investigation. Customized cDNA microarrays containing 5220 relevant genes were designed specifically for this study. Microarray experiments were run in triplicate for each sample and a selected group of genes were confirmed using real-time PCR.

OUTCOME MEASURE

Differential hepatic gene expressions in patients with NASH as compared with controls.

RESULTS

Thirty-four genes with significant differential expression were identified in patients with NASH when compared with non-obese controls. Moreover, 19 of these genes showed no significant expression differences in obese vs. non-obese controls, suggesting a stronger association of these genes to NASH.

CONCLUSIONS

Several differentially expressed genes in patients with NASH are related to lipid metabolism and extracellular matrix remodeling. Additionally, genes related to liver regeneration, apoptosis, and the detoxification process were differentially expressed. These findings may help clarify the molecular pathogenesis of NASH and identify potential targets for therapeutic intervention.

Development of a new reference standard for microarray experiments

Often microarray studies require a reference to indirectly compare the samples under observation. References based on pooled RNA from different cell lines have already been described (here referred to as RNA-R), but they usually do not exhaustively represent the set of genes printed on a chip, thus requiring many adjustments during the analyses. A reference could also be generated in vitro transcribing the collection of cDNA clones printed on the microarray in use (here referred to as T3-R). Here we describe an alternative and simpler PCR-based methodology to construct a similar reference (Chip-R), and we extensively test and compare it to both RNA-R and T3-R. The use of both Chip-R and T3-R dramatically increases the number of signals on the slides and gives more reproducible results than RNA-R. Each reference preparation is also evaluated in a simple microarray experiment comparing two different RNA populations. Our results show that the introduction of a reference always interferes with the analysis. Indeed, the direct comparison is able to identify more up- or down-regulated genes than any reference-mediated analysis. However, if a reference has to be used, Chip-R and T3-R are able to guarantee more reliable results than RNA-R.

Microarrays in cancer research

Microarray technology has presented the scientific community with a compelling approach that allows for simultaneous evaluation of all cellular processes at once. Cancer, being one of the most challenging diseases due to its polygenic nature, presents itself as a perfect candidate for evaluation by this approach. Several recent articles have provided significant insight into the strengths and limitations of microarrays. Nevertheless, there are strong indications that this approach will provide new molecular markers that could be used in diagnosis and prognosis of cancers. To achieve these goals it is essential that there is a seamless integration of clinical and molecular biological data that allows us to elucidate genes and pathways involved in various cancers. To this effect we are currently evaluating gene expression profiles in human brain, ovarian, breast and hematopoetic, lung, colorectal, head and neck and biliary tract cancers. To address the issues we have a joint team of scientists, doctors and computer scientists from two Virginia Universities and a major healthcare provider. The study has been divided into several focus groups that include; Tissue Bank Clinical & Pathology Laboratory Data, Chip Fabrication, QA/QC, Tissue Devitalization, Database Design and Data Analysis, using multiple microarray platforms. Currently over 300 consenting patients have been enrolled in the study with the largest number being that of breast cancer patients. Clinical data on each patient is being compiled into a secure and interactive relational database and integration of these data elements will be accomplished by a common programming interface. This clinical database contains several key parameters on each patient including demographic (risk factors, nutrition, co-morbidity, familial history), histopathology (non genetic predictors), tumor, treatment and follow-up information. Gene expression data derived from the tissue samples will be linked to this database, which allows us to query the data at multiple levels. The challenge of tissue acquisition and processing is of paramount importance to the success of this venture. A tissue devitalization timeline protocol was devised to ensure sample and RNA integrity. Stringent protocols are being employed to ascertain accurate tumor homogeneity, by serial dissection of each tumor sample at 10 microM frozen sections followed by histopathological evaluation. The multiple platforms being utilized in this study include Affimetrix, Oligo-Chips and custom-designed cDNA arrays. Selected RNA samples will be evaluated on each platform between the groups. Analysis steps will involve normalization and standardization of gene expression data followed by hierarchical clustering to determine co-regulation profiles. The aim of this conjoint effort is to elucidate pathways and genes involved in various cancers, resistance mechanisms, molecular markers for diagnosis and prognosis.