Micro-analytical Evidence of Copper-Based Pigment and Fungal Contamination of Medieval Mural Paintings in Beram, Croatia.

The aim of the present study was to map the painting materials, degradation processes, and biological features present on the mural painting in the church of St. Mary in Beram (Croatia) to study their possible interaction and produce information helping the preservation of this valuable painting. The research was conducted on micro samples of painting materials taken from different sites along the painting and the characterization of the present fungal species was carried out. The painting samples, together with observable patinas and degradation products, were studied by optical microscopy (OM), scanning electron microscopy, energy-dispersive spectroscopy (SEM/EDS), Fourier-Transform Infrared spectroscopy, and powder X-ray diffraction. Fungal diversity was studied using cultivation methods followed by OM and SEM analyses in addition to molecular analysis. The results contribute to the characterization of the original painting materials, successively added materials and occurred interventions, to the understanding of degradation progressions and fungal biotransformation processes. A mineral, cumengite, a copper-based pigment extremely rarely used in art, was found. Its occurrence together with barium sulfate, gypsum, and calcium oxalate possibly produced by microbiological activity was studied and information was added regarding the composition of painting materials in St. Mary church mural cycle.

Mechanisms of inactivation of the tumour suppressor gene RHOA in colorectal cancer.

BACKGROUND: Reduced RHOA signalling has been shown to increase the growth/metastatic potential of colorectal tumours. However, the mechanisms of inactivation of RHOA signalling in colon cancer have not been characterised. METHODS: A panel of colorectal cancer cell lines and large cohorts of primary tumours were used to investigate the expression and activity of RHOA, as well as the presence of RHOA mutations/deletions and promoter methylation affecting RHOA. Changes in RHOA expression were assessed by western blotting and qPCR after modulation of microRNAs, SMAD4 and c-MYC. RESULTS: We show here that RHOA point mutations and promoter hypermethylation do not significantly contribute to the large variability of RHOA expression observed among colorectal tumours. However, RHOA copy number loss was observed in 16% of colorectal tumours and this was associated with reduced RHOA expression. Moreover, we show that miR-200a/b/429 downregulates RHOA in colorectal cancer cells. In addition, we found that TGF-ß/SMAD4 upregulates the RHOA promoter. Conversely, RHOA expression is transcriptionally downregulated by canonical Wnt signalling through the Wnt target gene c-MYC that interferes with the binding of SP1 to the RHOA promoter in colon cancer cells. CONCLUSIONS: We demonstrate a complex pattern of inactivation of the tumour suppressor gene RHOA in colon cancer cells through genetic, transcriptional and post-transcriptional mechanisms.

MicroRNAs contribute to induced pluripotent stem cell somatic donor memory.

Induced pluripotent stem cells (iPSCs) maintain during the first few culture passages a set of epigenetic marks and metabolites characteristic of their somatic cell of origin, a concept defined as epigenetic donor memory. These residual somatic features are lost over time after extensive culture passaging. Therefore, epigenetic donor memory may be responsible for the higher differentiation efficiency toward the tissue of origin observed in low passage iPSCs versus high passage iPSC or iPSCs derived from a different tissue source. Remarkably, there are no studies on the relevance of microRNA (miRNA) memory following reprogramming, despite the established role of these molecules in the context of pluripotency and differentiation. Using hematopoietic progenitors cells as a model, we demonstrated that miRNAs play a central role in somatic memory retention in iPSCs. Moreover, the comparison of the miRNA expression profiles among iPSCs from different sources allowed for the detection of a set of candidate miRNAs responsible for the higher differentiation efficiency rates toward blood progenitors observed in low passage iPSCs. Combining bioinformatic predictive algorithms with biological target validation, we identified miR-155 as a key player for the in vitro differentiation of iPSC toward hematopoietic progenitors. In summary, this study reveals that during the initial passages following reprogramming, iPSCs maintained the expression of a miRNA set exclusive to the original somatic population. Hence the use of these miRNAs might hold a direct application toward our understanding of the differentiation process of iPSCs toward hematopoietic progenitor cells.

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells.

Generation of human induced pluripotent stem cells (hiPSCs) by the expression of specific transcription factors depends on successful epigenetic reprogramming to a pluripotent state. Although hiPSCs and human embryonic stem cells (hESCs) display a similar epigenome, recent reports demonstrated the persistence of specific epigenetic marks from the somatic cell type of origin and aberrant methylation patterns in hiPSCs. However, it remains unknown whether the use of different somatic cell sources, encompassing variable levels of selection pressure during reprogramming, influences the level of epigenetic aberrations in hiPSCs. In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Interestingly, we observe that the reprogramming efficiency of somatic cell lines inversely correlates with the amount of methylation change needed to acquire pluripotency. Additionally, we determine that both shared and line-specific epigenetic aberrations in hiPSCs can directly translate into changes in gene expression in both the pluripotent and differentiated states. Significantly, our analysis of different hiPSC lines from multiple cell types of origin allow us to identify a reprogramming-specific epigenetic signature comprised of nine aberrantly methylated genes that is able to segregate hESC and hiPSC lines regardless of the somatic cell source or differentiation state.

RhoA downregulation in the murine intestinal epithelium results in chronic Wnt activation and increased tumorigenesis.

Rho GTPases are molecular switches regulating multiple cellular processes. To investigate the role of RhoA in normal intestinal physiology, we used a conditional mouse model overexpressing a dominant negative RhoA mutant (RhoAT19N) in the intestinal epithelium. Although RhoA inhibition did not cause an overt phenotype, increased levels of nuclear ß-catenin were observed in the small intestinal epithelium of RhoAT19N mice, and the overexpression of multiple Wnt target genes revealed a chronic activation of Wnt signaling. Elevated Wnt signaling in RhoAT19N mice and intestinal organoids did not affect the proliferation of intestinal epithelial cells but significantly interfered with their differentiation. Importantly, 17-month-old RhoAT19N mice showed a significant increase in the number of spontaneous intestinal tumors. Altogether, our results indicate that RhoA regulates the differentiation of intestinal epithelial cells and inhibits tumor initiation, likely through the control of Wnt signaling, a key regulator of proliferation and differentiation in the intestine.

Concise review: Induced pluripotent stem cells versus embryonic stem cells: close enough or yet too far apart?

The state of a cell is defined by the genes it transcribes and the epigenetic landscape that regulates their expression. Pluripotent cells have markedly different epigenetic signatures when compared with differentiated cells. Permissive chromatin, high occurrence of bivalent domains, and low levels of heterochromatin allow pluripotent cells to react to distinctive stimuli and undergo changes of cell state by differentiating into various tissues. Differentiated cells can be reprogrammed by a set of transcription factors to induced pluripotent stem cells (iPSC) that convert their transcriptional and epigenetic state to pluripotency and thus closely resemble embryonic stem cells (ESC). However, questions remain on whether the epigenetic reprogramming is complete or if there are some recurring iPSC specific aberrations that impede their full pluripotency potential. For this reason, iPSC need to be closely compared with ESC, which is used as a golden standard for in vitro pluripotency. Transcribed genes, epigenetic landscape, differentiation potential, and mutational load show small but distinctive dissimilarities between these two cell types.

DNA hypermethylation in somatic cells correlates with higher reprogramming efficiency.

The efficiency of somatic cell reprogramming to pluripotency using defined factors is dramatically affected by the cell type of origin. Here, we show that human keratinocytes, which can be reprogrammed at a higher efficiency than fibroblast [Nat Biotechnol 2008;26:1276-1284], share more genes hypermethylated at CpGs with human embryonic stem cells (ESCs) than other somatic cells frequently used for reprogramming. Moreover, pluripotent cells reprogrammed from keratinocytes (KiPS) are more similar to ESCs than those reprogrammed from fibroblasts (FiPS) in regard to DNA methylation levels, mostly due to the presence of genes that fail to acquire high levels of DNA methylation in FiPS cells. We propose that higher reprogramming efficiency correlates with the hypermethylation of tissue-specific genes rather than with a more permissive pluripotency gene network.

The Effect of Lactiplantibacillus plantarum I-Enriched Diet on the Phenolic Content and Antioxidant Capacity of Queen Scallop (Aequipecten opercularis Linnaeus, 1758) Extracts.

The use of probiotics in the diet of bivalves poses a great potential in aquaculture as an alternative to antibiotics. The aim of this study was to assess the effect of Lactiplantibacillus plantarum I on the phenolic content and antioxidant capacity (AC) of queen scallop extracts after one month of feeding. Total phenols (TP) ranged from 28.17 ± 3.11 to 58.58 ± 8.57 mg GAE/100 g, total non-flavonoids (TNF) from 23.33 ± 3.66 to 36.56 ± 9.91 mg GAE/100 g, and total flavonoids (TF) from 10.56 ± 5.57 to 30.16 ± 1.69 mg CE/100 g. AC was assessed via three different methods: the ferric-reducing ability of plasma assay (FRAP), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic) acid assay (ABTS), and 2,2-diphenyl-1-picryhydrazyl assay (DPPH). FRAP values ranged from 0.13 ± 0.03 to 0.17 ± 0.02 µM AA/g, ABTS from 0.68 ± 0.11 to 2.79 ± 0.34 µM AA/g, and DPPH from 1.75 ± 0.17 to 2.98 ± 0.53 µM AA/g. Among all extracts, the best phenolic content and AC were observed in water extracts from queen scallops. The bivalves treated with the Lactiplantibacillus plantarum I-enriched diet showed higher AC according to the FRAP assay in all extracts. A significant correlation was observed between AC and TP and TNF in control and Lactiplantibacillus plantarum I-treated scallops.

Invasive Alien Species as a Potential Source of Phytopharmaceuticals: Phenolic Composition and Antimicrobial and Cytotoxic Activity of Robinia pseudoacacia L. Leaf and Flower Extracts.

Black locust (Robinia pseudoacacia L.), an invasive tree in Europe, commonly known for its negative impact on biodiversity, is a rich source of phenolic compounds recognized in traditional medicine. Since the metabolite profile depends on the environment and climate, this study aimed to provide the first LC-MS phytochemical screening of the black locust from the Istria region (Croatia). The compounds were extracted from leaves and flowers with 70% ethanol and 80% methanol. Total phenolics (TP) and flavonoids (TF), as well as antioxidant capacity (AC) measured by ABTS (17.49-146.41 mg TE/g DW), DPPH (24.67-118.49 mg TE/g DW), and FRAP (7.38-77.53 mg TE/g DW) assays, were higher in leaf than in flower extracts. Higher TP and total non-flavonoid (TNF) values were displayed in ethanolic than in methanolic extracts. In total, 64 compounds were identified, of which flavonols (20) and hydroxycinnamic acid derivatives (15) were the most represented. Flavanols such as catechin dominated in leaf extracts, followed by flavonols, with kaempferol glucuronyl rhamnosyl hexosides as the main compound, respectively. Flower extracts had the highest share of flavones, followed by ellagitannins, with luteolin dirhamnosyl hexosides and vescalagin, respectively, being predominant. The extracts had good quorum sensing, biofilm formation prevention, and eradicating capacity. The results provided new insights into the phytochemical properties of R. pseudoacacia as the first step toward its potential pharmaceutical use.

Fecal bacteria contamination in the Adriatic Sea: Investigating environmental factors and modeling to manage recreational coastal waters.

This study is based on assessing fecal indicator bacteria contamination along meteorological, hydrological and physical-chemical variables after high rainy events during the summer period. The study focused on four different coastal sites in the western and eastern Adriatic coast characterized by various geomorphological and hydrological features, levels of urbanization and anthropogenic pressures, with the aim of finding appropriate and effective solutions to ensure the safety and sustainability of tourism and public health. Detailed in-situ survey revealed a wide range of fecal indicator bacterial (FIB) across the different river mouths with concentrations of E. coli ranging from 165 to 6700 CFU 100 mL-1. It was found that nitrogen compounds track microbial load and acted as tracers for fecal contaminants. Further, a modelling tool was also used to analyze the spatial and temporal distribution of fecal pollution at these coastal sites. The integrated monitoring through high frequent survey in river waters and modeling framework allowed for the estimation of fecal indicator bacterial load at the river mouth and examination of fecal pollutant dispersion in recreational waters, considering different scenarios of fecal dispersion along the coast. This study formed the basis of a robust decision support system aimed at improving the management of recreational areas and ensuring the protection of water bodies through efficient management of bathing areas.

Biopotential of Underutilized Rosaceae Inflorescences: LC-DAD-MS Phytochemical Profiles Associated with Antioxidant, Antidiabetic, Anti-Inflammatory and Antiproliferative Activity In Vitro.

The aim of this work was to assess the biopotential of the young inflorescence tissues of Prunus, Malus and Chaenomeles in order to evaluate the possibility of their application in the food industry, and to provide a polyphenolic fingerprint for their quality control. The contents of different bioactive compounds and their antioxidant capacities were spectrophotometrically measured, the main phenolic compounds were identified and quantified using LC-DAD-MS, the antidiabetic potential was determined using α-amylase and α-glucosidase inhibition assays, the anti-inflammatory potential was determined using a 5-lipoxygenase inhibition assay, and the cytotoxicity was determined by MTT assay. Using one-way ANOVA, principal component analysis, hierarchical clustering and Pearson's correlation coefficient, the relations between the samples, and between the samples and the measured parameters, were revealed. In total, 77 compounds were identified. The concentration of sugars was low in M. purpurea, at 1.56 ± 0.08 mg/g DW. The most effective sample in the inhibition of antidiabetic enzymes and anti-inflammatory 5-lipoxygenase was C. japonica. The inhibition of α-glucosidase was strongly positively correlated with the total and condensed tannins, procyanidin dimers and procyanidin tetramer, and was very strongly correlated with chlorogenic acid. In α-amylase inhibition, C. japonica and P. serrulata 'Kiku Shidare Zakura' were equally efficient to the standard inhibitor, maltose. The most effective in the growth and proliferation inhibition of HepG2, HCT116 and HaCaT cells was P. avium. The results suggest Prunus, Malus and Chaenomeles inflorescences as functional food ingredients.

Casein kinase 1 gamma couples Wnt receptor activation to cytoplasmic signal transduction.

Signalling by Wnt proteins (Wingless in Drosophila) has diverse roles during embryonic development and in adults, and is implicated in human diseases, including cancer. LDL-receptor-related proteins 5 and 6 (LRP5 and LRP6; Arrow in Drosophila) are key receptors required for transmission of Wnt/beta-catenin signalling in metazoa. Although the role of these receptors in Wnt signalling is well established, their coupling with the cytoplasmic signalling apparatus remains poorly defined. Using a protein modification screen for regulators of LRP6, we describe the identification of Xenopus Casein kinase 1 gamma (CK1gamma), a membrane-bound member of the CK1 family. Gain-of-function and loss-of-function experiments show that CK1gamma is both necessary and sufficient to transduce LRP6 signalling in vertebrates and Drosophila cells. In Xenopus embryos, CK1gamma is required during anterio-posterior patterning to promote posteriorizing Wnt/beta-catenin signalling. CK1gamma is associated with LRP6, which has multiple, modular CK1 phosphorylation sites. Wnt treatment induces the rapid CK1gamma-mediated phosphorylation of these sites within LRP6, which, in turn, promotes the recruitment of the scaffold protein Axin. Our results reveal an evolutionarily conserved mechanism that couples Wnt receptor activation to the cytoplasmic signal transduction apparatus.

Investigation of the role of tyrosine kinase receptor EPHA3 in colorectal cancer.

EPH signaling deregulation has been shown to be important for colorectal carcinogenesis and genome-wide sequencing efforts have identified EPHA3 as one of the most frequently mutated genes in these tumors. However, the role of EPHA3 in colorectal cancer has not been thoroughly investigated. We show here that ectopic expression of wild type EPHA3 in colon cancer cells did not affect their growth, motility/invasion or metastatic potential in vivo. Moreover, overexpression of mutant EPHA3 or deletion of the endogenous mutant EPHA3 in colon cancer cells did not affect their growth or motility. EPHA3 inactivation in mice did not initiate the tumorigenic process in their intestine, and had no effects on tumor size/multiplicity after tumor initiation either genetically or pharmacologically. In addition, immunohistochemical analysis of EPHA3 tumor levels did not reveal associations with survival or clinicopathological features of colorectal cancer patients. In conclusion, we show that EPHA3 does not play a major role in colorectal tumorigenesis. These results significantly contribute to our understanding of the role of EPH signaling during colorectal carcinogenesis, and highlighting the need for detailed functional studies to confirm the relevance of putative cancer driver genes identified in sequencing efforts of the cancer genome.

Loss of the EPH receptor B6 contributes to colorectal cancer metastasis.

Although deregulation of EPHB signaling has been shown to be an important step in colorectal tumorigenesis, the role of EPHB6 in this process has not been investigated. We found here that manipulation of EPHB6 levels in colon cancer cell lines has no effect on their motility and growth on a solid substrate, soft agar or in a xenograft mouse model. We then used an EphB6 knockout mouse model to show that EphB6 inactivation does not efficiently initiate tumorigenesis in the intestinal tract. In addition, when intestinal tumors are initiated genetically or pharmacologically in EphB6+/+ and EphB6-/- mice, no differences were observed in animal survival, tumor multiplicity, size or histology, and proliferation of intestinal epithelial cells or tumor cells. However, reintroduction of EPHB6 into colon cancer cells significantly reduced the number of lung metastasis after tail-vein injection in immunodeficient mice, while EPHB6 knockdown in EPHB6-expressing cells increased their metastatic spread. Consistently, although EPHB6 protein expression in a series of 130 primary colorectal tumors was not associated with patient survival, EPHB6 expression was significantly lower in lymph node metastases compared to primary tumors. Our results indicate that the loss of EPHB6 contributes to the metastatic process of colorectal cancer.

Highly Expressed Genes in Rapidly Proliferating Tumor Cells as New Targets for Colorectal Cancer Treatment.

PURPOSE: The clinical management of colorectal cancer patients has significantly improved because of the identification of novel therapeutic targets such as EGFR and VEGF. Because rapid tumor proliferation is associated with poor patient prognosis, here we characterized the transcriptional signature of rapidly proliferating colorectal cancer cells in an attempt to identify novel candidate therapeutic targets. EXPERIMENTAL DESIGN: The doubling time of 52 colorectal cancer cell lines was determined and genome-wide expression profiling of a subset of these lines was assessed by microarray analysis. We then investigated the potential of genes highly expressed in cancer cells with faster growth as new therapeutic targets. RESULTS: Faster proliferation rates were associated with microsatellite instability and poorly differentiated histology. The expression of 1,290 genes was significantly correlated with the growth rates of colorectal cancer cells. These included genes involved in cell cycle, RNA processing/splicing, and protein transport. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protoporphyrinogen oxidase (PPOX) were shown to have higher expression in faster growing cell lines and primary tumors. Pharmacologic or siRNA-based inhibition of GAPDH or PPOX reduced the growth of colon cancer cells in vitro. Moreover, using a mouse xenograft model, we show that treatment with the specific PPOX inhibitor acifluorfen significantly reduced the growth of three of the seven (42.8%) colon cancer lines investigated. CONCLUSIONS: We have characterized at the transcriptomic level the differences between colorectal cancer cells that vary in their growth rates, and identified novel candidate chemotherapeutic targets for the treatment of colorectal cancer.

Myo5b knockout mice as a model of microvillus inclusion disease.

Inherited MYO5B mutations have recently been associated with microvillus inclusion disease (MVID), an autosomal recessive syndrome characterized by intractable, life-threatening, watery diarrhea appearing shortly after birth. Characterization of the molecular mechanisms underlying this disease and development of novel therapeutic approaches is hampered by the lack of animal models. In this study we describe the phenotype of a novel mouse model with targeted inactivation of Myo5b. Myo5b knockout mice show perinatal mortality, diarrhea and the characteristic mislocalization of apical and basolateral plasma membrane markers in enterocytes. Moreover, in transmission electron preparations, we observed microvillus atrophy and the presence of microvillus inclusion bodies. Importantly, Myo5b knockout embryos at day 20 of gestation already display all these structural defects, indicating that they are tissue autonomous rather than secondary to environmental cues, such as the long-term absence of nutrients in the intestine. Myo5b knockout mice closely resemble the phenotype of MVID patients and constitute a useful model to further investigate the underlying molecular mechanism of this disease and to preclinically assess the efficacy of novel therapeutic approaches.

RHOA inactivation enhances Wnt signalling and promotes colorectal cancer.

Activation of the small GTPase RHOA has strong oncogenic effects in many tumour types, although its role in colorectal cancer remains unclear. Here we show that RHOA inactivation contributes to colorectal cancer progression/metastasis, largely through the activation of Wnt/ß-catenin signalling. RhoA inactivation in the murine intestine accelerates the tumorigenic process and in human colon cancer cells leads to the redistribution of ß-catenin from the membrane to the nucleus and enhanced Wnt/ß-catenin signalling, resulting in increased proliferation, invasion and de-differentiation. In mice, RHOA inactivation contributes to colon cancer metastasis and reduced RHOA levels were observed at metastatic sites compared with primary human colon tumours. Therefore, we have identified a new mechanism of activation of Wnt/ß-catenin signalling and characterized the role of RHOA as a novel tumour suppressor in colorectal cancer. These results constitute a shift from the current paradigm and demonstrate that RHO GTPases can suppress tumour progression and metastasis.

Macrohistone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming to pluripotency.

Transcription-factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserving cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macrohistone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knockdown of macrohistone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, whereas overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes, macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators. The presence of macroH2A.1 at these genes prevents the regain of H3K4me2 during reprogramming, imposing an additional layer of repression that preserves cell identity.

Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming.

Recent studies indicate that human-induced pluripotent stem cells contain genomic structural variations and point mutations in coding regions. However, these studies have focused on fibroblast-derived human induced pluripotent stem cells, and it is currently unknown whether the use of alternative somatic cell sources with varying reprogramming efficiencies would result in different levels of genetic alterations. Here we characterize the genomic integrity of eight human induced pluripotent stem cell lines derived from five different non-fibroblast somatic cell types. We show that protein-coding mutations are a general feature of the human induced pluripotent stem cell state and are independent of somatic cell source. Furthermore, we analyse a total of 17 point mutations found in human induced pluripotent stem cells and demonstrate that they do not generally facilitate the acquisition of pluripotency and thus are not likely to provide a selective advantage for reprogramming.

Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes.

The utility of induced pluripotent stem (iPS) cells for investigating the molecular logic of pluripotency and for eventual clinical application is limited by the low efficiency of current methods for reprogramming. Here we show that reprogramming of juvenile human primary keratinocytes by retroviral transduction with OCT4, SOX2, KLF4 and c-MYC is at least 100-fold more efficient and twofold faster compared with reprogramming of human fibroblasts. Keratinocyte-derived iPS (KiPS) cells appear indistinguishable from human embryonic stem cells in colony morphology, growth properties, expression of pluripotency-associated transcription factors and surface markers, global gene expression profiles and differentiation potential in vitro and in vivo. To underscore the efficiency and practicability of this technology, we generated KiPS cells from single adult human hairs. Our findings provide an experimental model for investigating the bases of cellular reprogramming and highlight potential advantages of using keratinocytes to generate patient-specific iPS cells.