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Spanish Ministry of Economy and Competitiveness, Grant/Award Number: DEP2013--47540, DEP2016-79512--R and DEP2017--91544--EXP; Spanish Ministry of Economy, Industry and Competitiveness (MINECO); European Regional Development Fund (FEDER), Grant/Award Number: RYC--2016--21199 and ENDORE SAF2017--87526--R; Junta de Andalucia, Grant/Award Number: BIO--302 and US--1254251; University of Jaen, Grant/Award Number: PAIUJA--EI_CTS02; Spanish Ministry of Education, Culture and Sport, Grant/Award Number: FPU 16/02760; NIH, Grant/Award Number:UO1 TR002004; PERC Systems Biology Fund; Unit of Excellence on EXERNET Research Network on Exercise and Health in Special Populations; Alicia Koplowitz Foundation; Henning Och Johan Throne--Holsts Stiftelse Grant; University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES); Junta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European Regional Development Fund (ERDF), Grant/Award Number: SOMM17/6107/UGR; European Regional Development Funds, Grant/Award Number: B--CTS-355--UGR18 and B--CTS--500--UGR18; Funding for open access charge: Universidad de Granada/CBUA, Objectives: High cardiorespiratory fitness (CRF) levels reduce the risk of developing cardiovascular disease (CVD) during adulthood. However, little is known about the molecular mechanisms underlying the health benefits of high CRF levels at the early stage of life. This study aimed to analyze the whole-blood transcriptome profile of fit children with overweight/obesity (OW/OB) compared to unfit children with OW/OB. Design: 27 children with OW/OB (10.14 ± 1.3 years, 59% boys) from the ActiveBrains project were evaluated. VO2peak was assessed using a gas analyzer, and participants were categorized into fit or unfit according to the CVD risk-related cut-points. Whole-blood transcriptome profile (RNA sequencing) was analyzed. Differential gene expression analysis was performed using the limma R/Bioconductor software package (analyses adjusted by sex and maturational status), and pathways’ enrichment analysis was performed with DAVID. In addition, in silico validation data mining was performed using the PHENOPEDIA database. Results: 256 genes were differentially expressed in fit children with OW/OB compared to unfit children with OW/OB after adjusting by sex and maturational status (FDR < 0.05). Enriched pathway analysis identified gene pathways related to inflammation (eg, dopaminergic and GABAergic synapse pathways). Interestingly, in silico validation data mining detected a set of the differentially expressed genes to be related to CVD, metabolic syndrome, hypertension, inflammation, and asthma. Conclusion: The distinct pattern of whole-blood gene expression in fit children with OW/OB reveals genes and gene pathways that might play a role in reducing CVD risk factors later in life., Spanish Ministry of Economy and Competitiveness DEP2013-47540 DEP2016-79512-R DEP2017-91544-EXP, Spanish Ministry of Economy, Industry and Competitiveness (MINECO), European Commission RYC-2016-21199, ENDORE SAF2017-87526-R, Junta de Andalucia BIO-302 US-1254251, University of Jaen PAIUJA-EI_CTS02, Spanish Ministry of Education, Culture and Sport FPU 16/02760, United States Department of Health & Human Services, National Institutes of Health (NIH) - USA UO1 TR002004, PERC Systems Biology Fund, Unit of Excellence on EXERNET Research Network on Exercise and Health in Special Populations, Alicia Koplowitz Foundation, Henning Och Johan Throne-Holsts Stiftelse Grant, University of Granada, Unit of Excellence on Exercise and Health (UCEES), Junta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European Regional, Development Fund (ERDF) SOMM17/6107/UGR European Commission B-CTS-355-UGR18 B-CTS-500-UGR18, Universidad de Granada/CBUA

Background Youth populations with overweight/obesity (OW/OB) exhibit heterogeneity in cardiometabolic health phenotypes. The underlying mechanisms for those differences are still unclear. This study aimed to analyze the whole-blood transcriptome profile (RNA-seq) of children with metabolic healthy overweight/obesity (MHO) and metabolic unhealthy overweight/obesity (MUO) phenotypes. Methods Twenty-seven children with OW/OB (10.1 ± 1.3 years, 59% boys) from the ActiveBrains project were included. MHO was defined as having none of the following criteria for metabolic syndrome: elevated fasting glucose, high serum triglycerides, low high-density lipoprotein-cholesterol, and high systolic or diastolic blood pressure, while MUO was defined as presenting one or more of these criteria. Inflammatory markers were additionally determined. Total blood RNA was analyzed by 5'-end RNA-sequencing. Results Whole-blood transcriptome analysis revealed a distinct pattern of gene expression in children with MHO compared to MUO children. Thirty-two genes differentially expressed were linked to metabolism, mitochondrial, and immune functions. Conclusions The identified gene expression patterns related to metabolism, mitochondrial, and immune functions contribute to a better understanding of why a subset of the population remains metabolically healthy despite having overweight/obesity. Impact A distinct pattern of whole-blood transcriptome profile (RNA-seq) was identified in children with metabolic healthy overweight/obesity (MHO) compared to metabolic unhealthy overweight/obesity (MUO) phenotype. The most relevant genes in understanding the molecular basis underlying the MHO/MUO phenotypes in children could be: RREB1, FAM83E, SLC44A1, NRG1, TMC5, CYP3A5, TRIM11, and ADAMTSL2. The identified whole-blood transcriptome profile related to metabolism, mitochondrial, and immune functions contribute to a better understanding of why a subset of the population remains metabolically healthy despite having overweight/obesity.

Research question Women with endometriosis are considered to be at higher risk of several chronic diseases, such as autoimmune disorders, gynaecological cancers, asthma/atopic diseases and cardiovascular and inflammatory bowel diseases. Could the study of endometriosis-associated comorbidities help to identify potential biomarkers and target pathways of endometriosis? Design A systematic review was performed to identify all possible endometriosis-associated comorbid conditions. Next, this list of disorders was coded into MeSH terms, and the gene expression profiles were downloaded from the Phenopedia database and subsequently analysed following a systems biology approach. Results The results identified a group of 127 candidate genes that were recurrently expressed in endometriosis and its closest comorbidities and that were defined as ‘endometriosis sibling disorders' (ESD). The enrichment analysis showed that these candidate genes are principally involved in immune and drug responses, hormone metabolism and cell proliferation, which are well-known hallmarks of endometriosis. The expression of ESD genes was then validated on independent sample cohorts (n = 207 samples), in which the involvement of 16 genes (AGTR1, BDNF, C3, CCL2, CD40, CYP17A1, ESR1, IGF1, IGF2, IL10, MMP1, MMP7, MMP9, PGR, SERPINE1 and TIMP2) in endometriosis was confirmed. Several of these genes harbour polymorphisms that associate to either endometriosis or its comorbid conditions. Conclusions The study results highlight the molecular processes underlying the aetiopathogenesis of endometriosis and its comorbid conditions, and identify putative endometriosis biomarkers.

Background and objective Knowing whether a subject is conscious or not is a current challenge with a deep potential clinical impact. Recent theoretical considerations suggest that consciousness is linked to the complexity of distributed interactions within the corticothalamic system. The fractal dimension (FD) is a quantitative parameter that has been extensively used to analyse the complexity of structural and functional patterns of the human brain. In this study we investigate FD to assess whether it can discriminate between consciousness and different states of unconsciousness in healthy individuals. Methods We study 69 high-density electroencephalogram (hd-EEG) measurements after transcranial magnetic stimulation (TMS) in 18 healthy subjects progressing from wakefulness to non-rapid eye movement (NREM) sleep and sedation induced by different anaesthetic agents (xenon and propofol). We quantify the integration of thalamocortical networks by calculating the FD of a spatiotemporal voxelization obtained from the locations of all sources that are significantly activated by the perturbation (4DFD). Moreover, we study the temporal evolution of the evoked spatial distributions and compute a measure of the differentiation of the response by means of the Higuchi FD (HFD). Finally, a Fractal Dimension Index (FDI) of perturbational complexity is computed as the product of both quantities: integration FD (4DFD) and differentiation FD (HFD). Results We found that FDI is significantly lower in sleep and sedation when compared to wakefulness and provides an almost perfect intra-subject discrimination between conscious and unconscious states. Conclusions These results support the combination of FD measures of cortical integration and cortical differentiation as a novel paradigm of tracking complex spatiotemporal dynamics in the brain that could provide further insights into the link between complexity and the brain's capacity to sustain consciousness.

The genetic heterogeneity of autism has stymied the search for causes and cures. Whole-genomic studies on large numbers of families have helped identify combinations of inherited and de novo signal. In the present work, we re-analyze DNA microarrays using a novel strategy that takes prior knowledge of genetic relationships into account and that was designed to boost signal important to our understanding of the molecular basis of autism. Our strategy was designed to identify significant genomic variation within a priori defined biological concepts and improves signal detection while lessening the severity of multiple test correction seen in standard analysis of genome-wide association data. Upon application of our approach using 3,244 biological concepts, we detected genomic variation in 68 biological concepts with significant association to autism in comparison to family-based controls. These concepts clustered naturally into a total of 19 classes, principally including cell adhesion, cancer, and immune response. The top-ranking concepts contained high percentages of genes already suspected to play roles in autism or in a related neurological disorder. In addition, many of the sets associated with autism at the DNA level also proved to be predictive of changes in gene expression within a separate population of autistic cases, suggesting that the signature of genomic variation may also be detectable in blood-based transcriptional profiles. This cross-validation with gene expression data from individuals with autism coupled with the enrichment within autism-related neurological disorders supported the possibility that the mutations play important roles in the onset of autism and should be given priority for further study. Our work provides new leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of complex disease using prior knowledge of genetic organization.

The genetic heterogeneity of autism has stymied the search for causes and cures. Even whole-genomic studies on large numbers of families have yielded results of relatively little impact. In the present work, we analyze two genomic databases using a novel strategy that takes prior knowledge of genetic relationships into account and that was designed to boost signal important to our understanding of the molecular basis of autism. Our strategy was designed to identify significant genomic variation within a priori defined biological concepts and improves signal detection while lessening the severity of multiple test correction seen in standard analysis of genome-wide association data. Upon application of our approach using 3,244 biological concepts, we detected genomic variation in 68 biological concepts with significant association to autism in comparison to family-based controls. These concepts clustered naturally into a total of 19 classes, principally including cell adhesion, cancer, and immune response. The top-ranking concepts contained high percentages of genes already suspected to play roles in autism or in a related neurological disorder. In addition, many of the sets associated with autism at the DNA level also proved to be predictive of changes in gene expression within a separate population of autistic cases, suggesting that the signature of genomic variation may also be detectable in blood-based transcriptional profiles. This robust cross-validation with gene expression data from individuals with autism coupled with the enrichment within autism-related neurological disorders supported the possibility that the mutations play important roles in the onset of autism and should be given priority for further study. In sum, our work provides new leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of complex disease using prior knowledge of genetic organization.Author SummaryThe genetic heterogeneity of autism has stymied the search for causes and cures. Even whole-genomic studies on large numbers of families have yielded results of relatively little impact. In the present work, we reanalyze two of the most influential whole-genomic studies using a novel strategy that takes prior knowledge of genetic relationships into account in an effort to boost signal important to our understanding of the molecular structure of autism. Our approach demonstrates that these genome wide association studies contain more information relevant to autism than previously realized. We detected 68 highly significant collections of mutations that map to genes with measurable and significant changes in gene expression in autistic individuals, and that have been implicated in other neurological disorders believed to be closely related, and genetically linked, to autism. Our work provides leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of disease using prior knowledge of genetic organization.

Background CLN3 disease is caused by mutations in the CLN3 gene. The purpose of this study is to discern global expression patterns reflecting therapeutic targets in CLN3 disease. Methods Differential gene expression in vehicle-exposed mouse brain was determined after intraperitoneal vehicle/Galactosylceramide (GalCer) injections for 40 weeks with GeneChip Mouse Genome 430 2.0 arrays. Results Analysis identified 66 genes in male and 30 in female brains differentially expressed in GalCer-treated versus vehicle-exposed Cln3Δex7/8 mice. Gene ontology revealed aberrations of biological function including developmental, cellular, and behavioral processes. GalCer treatment altered pathways of long-term potentiation/depression, estrogen signaling, synaptic vesicle cycle, ErbB signaling, and prion diseases in males, but prolactin signaling, selenium compound metabolism and steroid biosynthesis in females. Gene-gene network analysis highlighted networks functionally pertinent to GalCer treatment encompassing motor dysfunction, neurodegeneration, memory disorder, inflammation and astrogliosis in males, and, cataracts, inflammation, astrogliosis, and anxiety in females. Conclusions This study sheds light on global expression patterns following GalCer treatment of Cln3Δex7/8 mice. Understanding molecular effects of GalCer on mouse brain gene expression, paves the way for personalized strategies for treating this debilitating disease in humans.

High altitude (HA) conditions induce several physiological and molecular changes, prevalent in individuals who are unexposed to this environment. Individuals exposed towards HA hypoxia yields physiological and molecular orchestration to maintain adequate tissue oxygen delivery and supply at altitude. This study aimed to understand the temporal changes at altitude of 4,111m. Physiological parameters and transcriptome study was conducted at high altitude day 3, 7, 14 and 21. We observed changes in differentially expressed gene (DEG) at high altitude time points along with altered BP, HR, SpO2, mPAP. Physiological changes and unsupervised learning of DEG’s discloses high altitude day 3 as distinct time point. Gene enrichment analysis of ontologies and pathways indicate cellular dynamics and immune response involvement in early day exposure and later stable response. Major clustering of genes involved in cellular dynamics deployed into broad categories: cell-cell interaction, blood signaling, coagulation system, and cellular process. Our data reveals genes and pathways perturbed for conditions like vascular remodeling, cellular homeostasis. In this study we found the nodal point of the gene interactive network and candidate gene controlling many cellular interactive pathways VIM, CORO1A, CD37, STMN1, RHOC, PDE7B, NELL1, NRP1 and TAGLN and the most significant among them i.e. VIM gene was identified as top hub gene. This study suggests a unique physiological and molecular perturbation likely to play a critical role in high altitude associated pathophysiological condition during early exposure compared to later time points.

Biologically data-driven networks have become powerful analytical tools that handle massive, heterogeneous datasets generated from biomedical fields. Protein-protein interaction networks can identify the most relevant structures directly tied to biological functions. Functional enrichments can then be performed based on these structural aspects of gene relationships for the study of channelopathies. Channelopathies refer to a complex group of disorders resulting from dysfunctional ion channels with distinct polygenic manifestations. This study presents a semi-automatic workflow using protein-protein interaction networks that can identify the most relevant genes and their biological processes and pathways in channelopathies to better understand their etiopathogenesis. In addition, the clinical manifestations that are strongly associated with these genes are also identified as the most characteristic in this complex group of diseases. This research provides a systems biology approach to extract information from interaction networks of gene expression. We show how large-scale computational integration of heterogeneous datasets, PPI network analyses, functional databases and published literature may support the detection and assessment of possible potential therapeutic targets in the disease. Applying our workflow makes it feasible to spot the most relevant genes and unknown relationships in channelopathies and shows its potential as a first-step approach to identify both genes and functional interactions in clinical-knowledge scenarios of target diseases., This work was supported by funds from MINECO-FEDER (TIN2016–81041-R to E.R.), European Human Brain Project SGA2 (H2020-RIA 785907 to M.J.S.), Junta de Andalucía (BIO-302 to F.J.E.) and MEIC (Systems Medicine Excellence Network, SAF2015–70270-REDT to F.J.E.).

Fractal analysis represents a promising new approach to structural neuroimaging data, yet systematic evaluation of the fractal dimension (FD) as a marker of structural brain complexity is scarce. Here we present in-depth methodological assessment of FD estimation in structural brain MRI. On the computational side, we show that spatial scale optimization can significantly improve FD estimation accuracy, as suggested by simulation studies with known FD values. For empirical evaluation, we analyzed two recent open-access neuroimaging data sets (MASSIVE and Midnight Scan Club), stratified by fundamental image characteristics including registration, sequence weighting, spatial resolution, segmentation procedures, tissue type, and image complexity. Deviation analyses showed high repeated-acquisition stability of the FD estimates across both data sets, with differential deviation susceptibility according to image characteristics. While less frequently studied in the literature, FD estimation in T2-weighted images yielded robust outcomes. Importantly, we observed a significant impact of image registration on absolute FD estimates. Applying different registration schemes, we found that unbalanced registration induced i) repeated-measurement deviation clusters around the registration target, ii) strong bidirectional correlations among image analysis groups, and iii) spurious associations between the FD and an index of structural similarity, and these effects were strongly attenuated by reregistration in both data sets. Indeed, differences in FD between scans did not simply track differences in structure per se, suggesting that structural complexity and structural similarity represent distinct aspects of structural brain MRI. In conclusion, scale optimization can improve FD estimation accuracy, and empirical FD estimates are reliable yet sensitive to image characteristics.

Little consensus has been reached on the best protocol for endometrial preparation for frozen embryo transfer (FET). It is not known how, and to what extent, hormone supplementation in artificial cycles influences endometrial preparation for embryo implantation at a molecular level, especially in patients who have experienced recurrent implantation failure. Transcriptome analysis of 15 endometrial biopsy samples at the time of embryo implantation was used to compare two different endometrial preparation protocols, natural versus artificial cycles, for FET in women who have experienced recurrent implantation failure compared with fertile women. IPA and DAVID were used for functional analyses of differentially expressed genes. The TRANSFAC database was used to identify oestrogen and progesterone response elements upstream of differentially expressed genes. Cluster analysis demonstrated that natural cycles are associated with a better endometrial receptivity transcriptome than artificial cycles. Artificial cycles seemed to have a stronger negative effect on expression of genes and pathways crucial for endometrial receptivity, including ESR2, FSHR, LEP, and several interleukins and matrix metalloproteinases. Significant overrepresentation of oestrogen response elements among the genes with deteriorated expression in artificial cycles (P < 0.001) was found; progesterone response elements predominated in genes with amended expression with artificial cycles (P = 0.0052).

We modelled the population biology of Oestrus sp. parasitising the Iberian ibex (Capra pyrenaica), using a system dynamics approach. Levels included in the model were as follows: first-instar larvae, third-instar larvae, pupae and resilient pupae. The values used for flows and auxiliary variables were obtained from the scientific literature, including research on both Oestrus ovis and O. sp.; we assumed that these two species are closely related, both morphologically and from a biological point of view. Simulations provided by our model allowed us to estimate the minimum monthly production of first-instar larvae and thus to establish periodic population dynamics, together with predictions for the number of larval generations. The model predicted 3–4 larval generations per year. The model proved to be very sensitive to minimal changes in a number of variables, especially the first-instar larval production rate. Despite its limitations, this methodology could be a versatile tool for studying the pop...

Integrated Information Theory (IIT) has become nowadays the most sensible general theory of consciousness. In addition to very important statements, it opens the door for an abstract (mathematical) formulation of the theory. Given a mechanism in a particular state, IIT identifies a conscious experience with a conceptual structure, an informational object which exists, is composed of identified parts, is informative, integrated and maximally irreducible. This paper introduces a space-time continuous version of the concept of integrated information. To this aim, a graph and a dynamical systems treatment is used to define, for a given mechanism in a state for which a dynamics is settled, an Informational Structure, which is associated to the global attractor at each time of the system. By definition, the informational structure determines all the past and future behavior of the system, possesses an informational nature and, moreover, enriches all the points of the phase space with cause-effect power by means of its associated Informational Field. A detailed description of its inner structure by invariants and connections between them allows to associate a transition probability matrix to each informational structure and to develop a measure for the level of integrated information of the system., Author summary In this paper we introduce a space-time continuous version for the level of integrated information of a network on which a dynamics is defined. The concept of integrated information comes from the IIT of consciousness. By a strict mathematical formulation, we complement the existing IIT theoretical framework from a dynamical systems perspective. In other words, we develop the bases for a continuous mathematical approach to IIT introducing a dynamical system as the driving rule of a given mechanism. We also introduce and define the concepts of Informational Structure and Informational Field as the complex network with the power to ascertain the dynamics (past and future scenarios) of the studied phenomena. The detailed description of an informational structure is showing the cause-effect power of a mechanism in a state and thus, a characterization of the quantity and quality of information, and the way this is integrated. We firstly introduce how network patterns arise from dynamic phenomena on networks, leading to the concept of informational structure. Then, we formally introduce the mathematical objects supporting the theory, from graphs to informational structures, throughout the integration of dynamics on graphs with a global model of differential equations. After this, we formally present some of the IIT’s postulates associated to a given mechanism. Finally, we provide the quantitative and qualitative characterization of the integrated information, and how it depends on the geometry of the mechanism.

In the last years, the use of floating concrete caissons in coastal infrastructures has been generalized: docking structures, vertical breakwater and special floating structures. In this field, one of the most important and less analyzed stages of the marine works is the sinking process of the floating caissons. The test campaign presented in this work is innovative in scale (1:12) and includes an analysis of the different stages of a floating caisson during its life cycle: detached concrete caisson, caisson positioning and sinking and berthed floating caisson, resulting in more than 130 tests performed. Movements and tensions have been analyzed for a wide array of sea states and different configurations of mooring systems and horizontal layouts. A new tool for dynamic positioning control was designed and developed as part of the test campaign. The design of this tool has led to the development of a specific numerical model that reproduced the dynamic behavior during sinking. The dynamic positioning control was implemented in the physical model campaign, which has meant an important advance in the construction process of maritime infrastructures. Moreover, the campaign carried out has allowed the validation and calibration of the tools developed, allowing all the work to reduce costs and increase the safety of these types of marine operations.

Genome-wide association studies (GWAS) have identified genetic risk variant adjacent to the homeobox transcription factor PITX2 in atrial fibrillation (AF) patients. Experimental studies demonstrated that Pitx2 insufficiency leads to cellular and molecular substrates that increased atrial arrhythmias susceptibility. Pitx2 expression is present not only in the atrial but also in the ventricular myocytes. This study aims to investigate if insufficiency ofPitx2in the developing and adult ventricular chambers increased susceptibility to ventricular arrhythmias. ConditionalPitx2loss-offunction ventricular chamber-specific (Mlc2v-Cre) mouse mutants were generated using Cre/loxP technology.Pitx2insufficiency in the ventricular myocardium leads interventricular septal thickening during cardiogenesis but else mice are viable until adulthood. Adult Mlc2vCre+Pitx2-/-hearts display hypertrophic and dilated ventricular chambers. ECG recordings demonstrated that Mlc2vCre+Pitx2-/-mice display increased QT and QRS intervals. Molecular analyses demonstrate that repolarization but not depolarization is severely impaired in these mutants. Microarrays analysis identified mRNAs and microRNAs altered in Pitx2 ventricular-specific mutants and provide evidences for miR-1 and miR-148 deregulation which in turn modulate Klf4 and distinct ion channel expression linked to cardiac hypertrophy and long QT-like defects. Our data demonstrate that Pitx2 insufficiency play leads to cellular and molecular ventricular remodeling which results in hypertrophic and dilated ventricular chambers and electrophysiological defects resembling long QT syndrome.

The development of the omics high-throughput technologies has led to a better understanding of the molecular basis underlying many physiological and pathological processes. However, the large amount of information derived from its application needs to be carefully analyzed in order to extract as much biological meaningful information as possible. For this purpose, several computational tools and methods have been designed to adequately manage the analysis of complex high-throughput omics data. In the current chapter, we provide an overview of the different computational approaches/options for analyzing the generated omics data, present developed databases and analysis tools in the field, and finalize the chapter with an example of analysis application in reproductomics.

We have previously reported that tyrosol (TYR) promotes lifespan extension in the nematode Caenorhabditis elegans, also inducing a stronger resistance to thermal and oxidative stress in vivo. In this study, we performed a whole-genome DNA microarray in order to narrow down the search for candidate genes or signaling pathways potentially involved in TYR effects on C. elegans longevity. Nematodes were treated with 0 or 250 μM TYR, total RNA was isolated at the adult stage, and derived cDNA probes were hybridized to Affymetrix C. elegans expression arrays. Microarray data analysis was performed, and relative mRNA expression of selected genes was validated using qPCR. Microarray analysis identified 208 differentially expressed genes (206 over-expressed and two under-expressed) when comparing TYR-treated nematodes with vehicle-treated controls. Many of these genes are linked to processes such as regulation of growth, transcription, reproduction, lipid metabolism and body morphogenesis. Moreover, we detected an interesting overlap between the expression pattern elicited by TYR and those induced by other dietary polyphenols known to extend lifespan in C. elegans, such as quercetin and tannic acid. Our results suggest that important cellular mechanisms directly related to longevity are influenced by TYR treatment in C. elegans, supporting our previous notion that this phenol might act on conserved genetic pathways to increase lifespan in a whole organism.

We present 3dfd.ujaen.es, a Web platform for computing and analyzing the 3D fractal dimension (3DFD).The first Web platform that allows the users to calculate, visualize, analyze and compare the 3DFD from 3D images (i.e. MRI).Novel technologies are used: CUDA for high-performance computing, and interactive 3D visualization of the images with WebGL. This study presents a Web platform (http://3dfd.ujaen.es) for computing and analyzing the 3D fractal dimension (3DFD) from volumetric data in an efficient, visual and interactive way. The Web platform is specially designed for working with magnetic resonance images (MRIs) of the brain. The program estimates the 3DFD by calculating the 3D box-counting of the entire volume of the brain, and also of its 3D skeleton. All of this is done in a graphical, fast and optimized way by using novel technologies like CUDA and WebGL. The usefulness of the Web platform presented is demonstrated by its application in a case study where an analysis and characterization of groups of 3D MR images is performed for three neurodegenerative diseases: Multiple Sclerosis, Intrauterine Growth Restriction and Alzheimer's disease. To the best of our knowledge, this is the first Web platform that allows the users to calculate, visualize, analyze and compare the 3DFD from MRI images in the cloud.

Background Numerous studies have highlighted the elevated degree of comorbidity associated with autism spectrum disorder (ASD). These comorbid conditions may add further impairments to individuals with autism and are substantially more prevalent compared to neurotypical populations. These high rates of comorbidity are not surprising taking into account the overlap of symptoms that ASD shares with other pathologies. From a research perspective, this suggests common molecular mechanisms involved in these conditions. Therefore, identifying crucial genes in the overlap between ASD and these comorbid disorders may help unravel the common biological processes involved and, ultimately, shed some light in the understanding of autism etiology. Results In this work, we used a two-fold systems biology approach specially focused on biological processes and gene networks to conduct a comparative analysis of autism with 31 frequently comorbid disorders in order to define a multi-disorder subcomponent of ASD and predict new genes of potential relevance to ASD etiology. We validated our predictions by determining the significance of our candidate genes in high throughput transcriptome expression profiling studies. Using prior knowledge of disease-related biological processes and the interaction networks of the disorders related to autism, we identified a set of 19 genes not previously linked to ASD that were significantly differentially regulated in individuals with autism. In addition, these genes were of potential etiologic relevance to autism, given their enriched roles in neurological processes crucial for optimal brain development and function, learning and memory, cognition and social behavior. Conclusions Taken together, our approach represents a novel perspective of autism from the point of view of related comorbid disorders and proposes a model by which prior knowledge of interaction networks may enlighten and focus the genome-wide search for autism candidate genes to better define the genetic heterogeneity of ASD. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3667-9) contains supplementary material, which is available to authorized users.

The inner uterine lining (endometrium) is a unique tissue going through remarkable changes each menstrual cycle. Endometrium has its characteristic DNA methylation profile, although not much is known about the endometrial methylome changes throughout the menstrual cycle. The impact of methylome changes on gene expression and thereby on the function of the tissue, including establishing receptivity to implanting embryo, is also unclear. Therefore, this study used genome-wide technologies to characterize the methylome and the correlation between DNA methylation and gene expression in endometrial biopsies collected from 17 healthy fertile-aged women from pre-receptive and receptive phase within one menstrual cycle. Our study showed that the overall methylome remains relatively stable during this stage of the menstrual cycle, with small-scale changes affecting 5% of the studied CpG sites (22,272 out of studied 437,022 CpGs, FDR

Two recent microarray and qRT-PCR studies showed that inbred Roman high- (RHA-I, low anxiety and frustration vulnerability) and low-avoidance (RLA-I, high anxiety and frustration vulnerability) rats, psychogenetically selected on the basis of their divergence in two-way avoidance performance, differed in basal whole-brain and hippocampal expression of genes related to neurotransmission, emotion, stress, aversive learning, and drug seeking behavior. We have extended these studies by analyzing strain differences in hippocampal gene expression following a frustrative experience involving reward downshift, i.e. instrumental successive negative contrast (iSNC), a phenomenon in which the sudden reduction of an expected reward induces frustration/anxiety. Food-deprived male Roman rats were exposed to a reduction in the amount of solid food presented in the goal of a straight alley (from 12 pellets in “training” trials – i.e. preshift trials- to 2 pellets in “frustration testing” trials – i.e. postshift trials-). The iSNC effect, as measured by response latencies in the “postshift” trials, appeared only in RLA-I rats (i.e. higher response latencies in the 12-2 RLA-I group as compared to the 2-2 RLA-I control group in postshift trials). Two and a half hours after the “postshift” behavioral test, hippocampi were removed and stored (−80 °C) until analysis. Microarray analysis of these hippocampi showed that four differentially-expressed, and qRT-PCR-validated genes (TAAR2, THAP1, PKD2L1, NANOS), have relevance for brain function and behavior, including schizophrenia, depression, anxiety, and drug addiction, thus showing the usefulness of Roman strains as a genetic model for research on the neurogenetic basis of frustration.

Systems biology interdisciplinary approaches have become an essential analytical tool that may yield novel and powerful insights about the nature of human health and disease. Complex disorders are known to be caused by the combination of genetic, environmental, immunological or neurological factors. Thus, to understand such disorders, it becomes necessary to address the study of this complexity from a novel perspective. Here, we present a review of integrative approaches that help to understand the underlying biological processes involved in the etiopathogenesis of neurological diseases, for example, those related to autism and autism spectrum disorders (ASD) endophenotypes. Furthermore, we highlight the role of systems biology in the discovery of new biomarkers or therapeutic targets in complex disorders, a key step in the development of personalized medicine, and we demonstrate the role of systems approaches in the design of classifiers that can shorten the time for behavioral diagnosis of autism.

Cardiovascular development is a complex process in which several transcriptional pathways are operative, providing instructions to the developing cardiomyocytes, while coping with contraction and morphogenetic movements to shape the mature heart. The discovery of microRNAs has added a new layer of complexity to the molecular mechanisms governing the formation of the heart. Discrete genetic ablation of the microRNAs processing enzymes, such as Dicer and Drosha, has highlighted the functional roles of microRNAs during heart development. Importantly, selective deletion of a single microRNA, miR-1-2, results in an embryonic lethal phenotype in which both morphogenetic, as well as impaired conduction, phenotypes can be observed. In an effort to grasp the variability of microRNA expression during cardiac morphogenesis, we recently reported the dynamic expression profile during ventricular development, highlighting the importance of miR-27 on the regulation of a key cardiac transcription factor, Mef2c. In this review, we compare the microRNA expression profile in distinct models of cardiogenesis, such as ventricular chamber development, induced pluripotent stem cell (iPS)-derived cardiomyocytes and the aging heart. Importantly, out of 486 microRNAs assessed in the developing heart, 11% (55) displayed increased expression, many of which are also differentially expressed in distinct cardiogenetic experimental models, including iPS-derived cardiomyocytes. A review on the functional analyses of these differentially expressed microRNAs will be provided in the context of cardiac development, highlighting the resolution and power of microarrays analyses on the quest to decipher the most relevant microRNAs in the developing, aging and diseased heart.

El objetivo del presente trabajo es describir brevemente conceptos de la genómica de los cordados así como de la genómica comparada y sus aspectos éticos. El genoma de los cordados cambió ligeramente dando lugar al genoma de los vertebrados, entre ellos el de los mamíferos, entre los que se incluye el ser humano. La genómica comparada estudia las semejanzas y diferencias entre genomas de diferentes organismos; trata de explicar la información proporcionada por la selección natural para entender la función y los procesos evolutivos que actúan sobre los genomas. La complejidad de los procesos evolutivos constituye todo un desafío a la hora de analizar e interpretar la información biológica generada; en este sentido, la Bioinformática y la Biología Computacional proporcionan un amplio abanico de técnicas estadísticas, matemáticas y algorítmicas para el análisis de datos biológicos. Un reto clave es analizar el caudal de datos de secuencias de ADN con el fin de comprender la información almacenada en términos de estructura, función y evolución proteicas. En Biología computacional BLAST y ClustalW2 son las herramientas más empleadas para el análisis de alineamientos múltiples de secuencias. La Genómica está resultando clave también en el campo de la medicina; conocer la cartografía del genoma humano proporciona una valiosa información a tener en cuenta a la hora de detectar genes implicados en ciertas enfermedades. Esto conlleva que en la actualidad nos centremos más en la predicción de patologías que en la prevención, por lo que la tendencia es que en el futuro la Medicina Genómica acabe desbancando a la Medicina Preventiva. El Proyecto Genoma Humano presenta diversas aplicaciones que, al no tener una clara cobertura legal, traen consigo un nuevo paradigma con problemas éticos, sociales y legales que la comunidad científica trata de resolver para compaginar los aspectos morales con el progreso en la investigación.

Over the last decades, fractal analysis has been applied to the study of the spatial and temporal complexity of a wide range of objects in biology and medicine, including the irregular and complex patterns of the nervous system. In clinical neurosciences, fractal geometry has emerged as a powerful tool to objectively analyze and quantify the intricate structures comprising the topological and functional complexity of the human brain, shedding light on the understanding of the brain function at a systems level. The fractal approach has the potential to allow physicians and scientists to predict clinical outcomes, classification between normal and pathological states, and, ultimately, the identification and diagnosis of certain neurological conditions. In this chapter, the main applications of fractal analysis into clinical neurosciences are reviewed, with special emphasis on the diagnostic precision of the fractal dimension value in different neurological diseases.

The success of assisted reproduction technology is highly dependent on a precise selection of gametes and embryos and determining the best endometrial window for embryo implantation. For many years, morphological criteria have constituted the only way to assess spermatozoon, oocytes, embryos and endometrial samples in order to improve outcomes. However, this approach has reached a ceiling of success and has been related to unacceptably high rates of multiple pregnancies. New technologies have been developed in order to improve the results and reduce risks via better selection of those gametes and embryos with the highest pregnancy potential, and of more favorable endometrial environments for embryo implantation. In addition, these technologies should ideally be objective, accurate, fast and affordable. Lately, the global strategies that are being employed in reproductive medicine include genomic, transcriptomic, proteomic, metabolomic profiling of oocytes, cummulus cells, granulosa cells, embryos, endomet...

background: The use of ovarian stimulation, to stimulate a multi-follicular response for assisted reproduction treatments, may force the production of oocytes from follicles that do not reach optimal maturation, possibly yielding oocytes that are not fully competent. The present study aimed to define the follicular environment and oocyte competence of unstimulated pre-ovulatory follicles, to compare it with that of similar-sized stimulated follicles. For this purpose, we analyzed the follicular hormonal milieu, the oocyte meiotic spindle, the embryo development and the cumulus cells gene expression (GE) profiles. methods and results: The study population was divided in two groups: (i) 42 oocyte donors undergoing unstimulated cycles and (ii) 18 oocyte donors undergoing controlled ovarian stimulation cycles (COS). Follicular fluid was analyzed to quantify the concentrations of estradiol (E2), progesterone (P), FSH, LH, testosterone (T) and androstendione (D4). T was higher in the COS group, while D4, E2 and LH were significantly higher in unstimulated cycles. The cumulus oophorus cells (CC) surrounding the oocyte were removed and their GE profiles were analyzed with microarrays. There were 18 differentially expressed genes in CC: 7 were up-regulated and 11 were down-regulated in the COS cycles. The microarray was validated by qRT –PCR. The analysis of spindle structure revealed no significant differences between the groups, except for the parameter of length which presented differences. The fertilization ability and embryo morphology on Days 2, 3 and 4 did not show any significant differences between groups. conclusions: The use of ovarian stimulation induces changes in the follicular fluid and in CC GE that may affect immune processes, meiosis and ovulation pathways. Although these differences do not seem to relate to early-stage embryo morphology, the implications of some of the molecules, especially ALDH1A2, CTSL and ZNF33B at the CC level, deserve to be addressed in future studies.

Differences in gene expression and imprinting have been reported, comparing in vivo versus in vitro generated preimplantation embryos. Furthermore, mouse studies have shown that placenta development is altered following in vitro culture. However, the molecular mechanisms underlying these findings are unknown. We therefore isolated trophectoderm (TE) and inner cell mass (ICM) cells from in vivo and in vitro fertilization (IVF) embryos and evaluated their transcriptome using microarrays. We found that the transcriptomes of in vitro produced ICM and TE cells showed remarkably few differences compared to ICM and TE cells of in vivo generated embryos. In vitro fertilization embryos showed a reduced number of TE cells compared to in vivo embryos. In addition, TE of IVF embryos showed significant downregulation of solute transporter genes and of genes involved in placenta formation (Eomesodermin, Socs3) or implantation (Hbegf). In summary, IVF and embryo culture significantly affects the transcriptome of ICM and TE cells.

This work presents a computer program for computing the 3D fractal dimension (3DFD) from magnetic-resonance images of the brain. The program is based on an algorithm that calculates the 3D box counting of the entire volume of the brain, and also of its 3D skeletonization. The validity and accuracy of the software has been confirmed using solids with well-known 3DFD values. The usefulness of the program developed is demonstrated by its successful characterization of several neurodegenerative diseases.

Microarray technology was used to explore differences in brain gene expression under basal conditions in two strains of psychogenetically selected rats which differ in anxiety/stress responses, the inbred Roman High-(RHA-I) and Roman Low-(RLA-I) Avoidance rats. Microarray analysis detected 14 up-regulated and 24 down-regulated genes in RLA-I vs. RHA-I rats functionally related to neurobiological processes. The differentially expressed genes CAMKK2, CRHBP, EPHX2, HOMER3, NDN, PRL and RPL6 were selected for microarray validation using qRT-PCR. EPHX2, CAMKK2 (both up-regulated in RLA-I vs. RHA-I rats) and HOMER3 (down-regulated in RLA-I vs. RHA-I rats) showed a similar tendency and fold-change both in microarray and RT-PCR analyses; PRL (up-regulated in RLA-I vs. RHA-I rats), CRHBP and RPL6 (both down-regulated in RLA-I vs. RHA-I animals) showed a similar tendency but a different order of magnitude of change among experiments; finally, NDN was validated neither in tendency nor in magnitude of change.

Identification of genes involved in trophoblast differentiation is of great interest in understanding cellular and molecular mechanisms involved in placental development and is relevant clinically to fetal development, fertility, and maternal health. Herein, we investigated differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage by culture with bone morphogenetic protein 4 (BMP4) over a 10-day period. Within 2 days, the stemness markers POU5F1 and NANOG were markedly down-regulated, followed temporally by up-regulation of the CDX2, KRT7, HLA-G, ID2, CGA, and CGB trophoblast markers. To understand, on a global scale, changes in the transcriptome during the differentiation of hESCs down the trophoblast lineage, a large-scale microarray analysis was performed. Through whole-genome analysis, more than 3800 genes displayed statistically significant and 2-fold or greater changes in expression during the time course. Of those genes that showed the largest increases, many were involved in processes associated with trophoblast biology; however, novel genes were also identified. Some of them are hypothesized to be associated mainly with extracellular matrix remodeling (e.g., NID2) and cell migration and invasion (e.g., RAB25). Using Ingenuity pathways analysis software to identify signaling pathways involved in trophoblast differentiation or function, we discovered that many genes are involved in WNT/beta-catenin, ERK/MAPK, NFKB, and calcium signaling pathways, suggesting potential roles for these families in trophoblast development. This work provides an in vitro functional genomic model with which to identify genes involved in trophoblast development.

Checa, A.G., Esteban-Delgado, F.J. and Salas, C. 2010. Crenulations of the hinge plate of pectinoideans. —Acta Zoologica (Stockholm) 92: 344–354. Crenulations are a succession of micron-sized elongated ridges and troughs with a general dorsoventral pseudo-labyrinthine pattern that are present on the hinge plate of most pectinoideans. The crenulations of opposing valves are complementary and interpenetrate in a hinge-like fashion. They are also imprinted in the dorsal mantle, although there is evidence that the mantle adheres only at the ridges, but not at the troughs. Those mantle areas that secrete the ridges contain cells that are richer in structures, indicating an active metabolism than those facing the troughs. Crenulations are formed because the dorsal mantle expands allometrically along the anteroposterior direction. The excess length is accommodated by creasing. Crenulations initiate at the anterior and posterior ends of the hinge plate as shallow spheruliths, which increase in height with time until the mantle on both sides detaches from the shell areas forming the neighbouring troughs. A contact differentiation of the mantle into actively and passively secreting bands follows. This genetic model explains the general pattern as well as the changes in the morphology of crenulations that occur during growth. Crenulations are secondary postlarval structures unrelated to the provinculum. Their presence in the earliest pectinoideans makes crenulations a plesiomorphic character of the group.

Aims Non-coding RNA has been recently demonstrated to be a novel mechanism for modulation of gene expression at the post-transcriptional level. The importance of microRNAs in the cardiovascular system is now apparent. Mutations of distinct microRNAs have provided evidence for fundamental roles of microRNAs during cardiovascular development. However, there is limited information about global microRNA profiles during mouse heart development. In this study, we have gained insight from the expression profiles of microRNAs during mouse ventricular development by microarray and qRT-PCR analysis. Methods and results Our microarray analysis reveals that relatively few microRNAs display either increasing or decreasing expression profiles during ventricular chamber formation. Interestingly, most of the differentially expressed microRNAs display a rather discrete peak of expression at particular developmental stages. Furthermore, we demonstrate that microRNA-27b (miR-27b) displays an overt myocardial expression during heart development and that the transcription factor-encoding gene Mef2c is an miR-27b target. Conclusion Our data present a comprehensive profile of microRNA expression during ventricular maturation, providing an entry point for investigation of the functional roles of the most abundantly and differentially expressed microRNAs during cardiogenesis.

Intrinsic abnormalities in transplanted eutopic endometrium are believed to contribute to the pathogenesis of pelvic endometriosis. Herein we investigated transcriptomic differences in human endometrial stromal fibroblasts (hESFs) from women with (hESF(endo)) vs. without (hESF(nonendo)) endometriosis, in response to activation of the protein kinase A (PKA) pathway with 8-bromoadenosine-cAMP (8-Br-cAMP). hESF(nonendo) (n = 4) and hESF(endo) (n = 4) were isolated from eutopic endometrium and treated +/- 0.5 mm 8-Br-cAMP for 96 h. Purified total RNA was subjected to microarray analysis using the whole-genome Gene 1.0 ST Affymetrix platform. A total of 691 genes were regulated in cAMP-treated hESF(nonendo) vs. 158 genes in hESF(endo), suggesting a blunted response to cAMP/PKA pathway activation in women with disease. Real-time PCR and ELISA validated the decreased expression of decidualization markers in hESF(endo) compared with hESF(nonendo). In the absence of disease, 8-Br-cAMP down-regulated progression through the cell cycle via a decrease in cyclin D1, cyclin-dependent kinase 6, and cell division cycle 2 and an increase in cyclin-dependent kinase inhibitor 1A. However, cell cycle components in hESF(endo) were not responsive to 8-Br-cAMP, resulting in persistence of a proliferative phenotype. hESF(endo) treated with 8-Br-cAMP exhibited altered expression of immune response, extracellular matrix, cytoskeleton, and apoptosis genes. Changes in phosphodiesterase expression and activity were not different among experimental groups. These data support that eutopic hESF(endo) with increased proliferative potential can seed the pelvic cavity via retrograde menstruation and promote establishment, survival, and proliferation of endometriosis lesions, independent of hydrolysis of cAMP and likely due to an inherent abnormality in the PKA pathway.

The calcitic columnar prisms of pteriomorphian bivalves have the crystallographic c-axis oriented perpendicular to the shell surface and the a-axes rotated without any preferential orientation. In oysters, SEM, XRD and EBSD analyses show that individual prisms initially have their a-axes randomly oriented but are able to progressively orient them parallel to those of their neighbors. This ability is apparently confined to groups, such as oysters and scallops, in which prisms are internally constituted by smaller lath-like crystal units. We have developed a competition model - not between prisms, but between the lath-like secondary units of prisms - which is based on differences in the inclination of laths relative to the shell growth surface. Units having a growth component which coincides with the growth direction protrude faster from the growth surface and out-compete those which are not favorably oriented, which reduces the overall dispersion of the a-axes of the prismatic lamella. The extent of re-alignment increases with the relative inclination of the growth surface and the length attained by the prisms. Oysters are the only group in which these two characters are pronounced enough to provide a measurable re-alignment. The proposed competition model is unprecedented in biomaterials and reveals how important crystal growth processes are in microstructure organization.

Microarray technology is a current approach for detecting alterations in the expression of thousands of genes simultaneously between two different biological conditions. Genes of interest are selected on the basis of an obtained p-value, and, thus, the list of candidates may vary depending on the data processing steps taken and statistical tests applied. Using standard approaches to the statistical analysis of microarray data from individuals with Autism Spectrum Disorder (ASD), several genes have been proposed as candidates. However, the lists of genes detected as differentially regulated in published mRNA expression analyses of Autism often do not overlap, owed at least in part to (i) the multifactorial nature of ASD, (ii) the high inter-individual variability of the gene expression in ASD cases, and (iii) differences in the statistical analysis approaches applied. Game theory recently has been proposed as a new method to detect the relevance of gene expression in different conditions. In this work, we test the ability of Game theory, specifically the Shapley value, to detect candidate ASD genes using a microarray experiment in which only a few genes can be detected as dysregulated using conventional statistical approaches. Our results showed that coalitional games significantly increased the power to identify candidates. A further functional analysis demonstrated that groups of these genes were associated with biological functions and disorders previously shown to be related to ASD.

We have studied the geological history of Central America, particularly the Caribbean, in order to discover the impact of other areas on the islands in the Caribbean Sea. The study of the distribution of 675 Melastomataceae species led us to establish the biogeographical ranks of Subregion, Superprovince, Province and Subprovince. We also suggest a biogeographical typology for the Caribbean Islands. In order to discover the relationships between the 16 territories under study, we collected the endemic Melastomataceae taxa occurring in each of them and applied the Jaccard index. Finally, we establish the Caribbean Subregion, with the Western Antilles Superprovince, which in turn includes the Provinces of Florida and Cuba. In this latter, we define two subprovinces, Cuba and Jamaica. The Central—Eastern Antilles Superprovince includes the provinces of Eastern Antilles and Hispaniola. The research involved the implementation of a floristic and distributional study of the Melastomataceae endemic taxa...

The paper deals with the nitrophilous Hordeum leporinum pasture- lands peculiar to the olive groves of Jaen, Spain. The study first selects physio- gnomically homogeneous land plots and subsequently samples are taken where the relevant species is dominant. Simultaneously, an edaphic sample is taken and the different edaphic parameters are analysed. By means of phytosociologi- cal and statistical methods (cluster analysis) and co—location networks, we describe a new association, namely Anacyclo clavati—Hordeetum leporinum. With the aid of advanced statistical techniques and Bayesian networks, we carry out different analyses in order to find out plant—soil correlations, in particular, for Filago lutescens and Hordeum leporinum. The paper also provides a decision tree for Hordeum leporinum. In this decision tree the values of the different eda- phic parameters are checked against the values of the abundance—dominance index.

This paper deals with the biodiversity of the Hordeum leporinum communities in Portugal. The sampling of the communities was carried out in a region which extends from the Alentejo to Castelo-Branco. In this region the Hordeum leporinum communities grow on the neutro—basic substrates of decarbonated soils with pH—values close to 7. Our research concentrates on three associations of the Hordeion leporini: Anacyclo radiati—Hordeetum leporini, Ancyclo radiati—Chrysanthemetum coronarii and Anacyclo radiati—Papaveretum rhoeadis. The survey studies their respective floristic composition, structure and ecology. The results of the phytosociological study, as shown in a synthetic table and analysed by means of a statistical cluster analysis, have not only revealed the status novo character of the Anacyclo-Chrysanthemetum, but also led us to suggest the new Anacyclo-Papaveretum rhoeadis association. The research also included an edaphic analysis of the sampled plots. However, these results revealed that th...

BACKGROUND: New approaches for non-invasive embryo-quality assessment are among the major goals in Reproductive Medicine. We hypothesize that the detection of changes in the protein profile of the culture media in which blastocysts are cultured could be a potential indicator of the viability of the embryo and, thus, a useful tool for selecting the more appropriate blastocysts to be transferred. METHODS: Using protein-array technology, we analysed the protein profile corresponding to 24 h conditioned media of blastocysts that implanted versus those that did not implant. A statistical approach was followed to compare each of these media versus a medium in the absence of blastocysts (control medium). In addition, a gene ontology functional analysis—including those proteins showing a statistical difference among conditions—was performed, and a network with the predicted functional partners and corresponding relationships was obtained. RESULTS: The soluble TNF receptor 1 and IL-10 increased significantly and MSP-a, SCF, CXCL13, TRAILR3 and MIP-1b decreased significantly when the protein profile of the blastocyst culture medium was compared with the control medium. CXCL13 (BLC) and granulocyte-macrophage colonystimulating factor was also decreased significantly in the implanted blastocyst media compared with that in media from the non-implanted counterparts with a similar morphology. None of the proteins included in the array was increased significantly in the implanted blastocyst-conditioned media. CONCLUSIONS: The differences identified in the protein profile of the culture media in the presence of implanted versus non-implanted blastocysts can be considered a new non-invasive approach in the search for new tools to diagnose blastocyst viability.