Impact of Early-Life Exposure to Bisphenol A on Survival and Histopathology of Liver and Kidney of Zebrafish (Danio rerio)

Bisphenol A (BPA) is a highly used chemical and an ubiquitous environmental contaminant in urban aquatic ecosystems. BPA disrupts hormonal and metabolic pathways of living organisms through its endocrine disrupting activity. Early-life BPA exposure could perturb key developmental processes, thus affecting the survival of living organisms. BPA is known to accumulate in water bodies, therefore it is important to understand the impact of BPA on aquatic organisms and ecosystem health. The objective of this study was to investigate the impact of early-life BPA exposure on survival and histology of kidney and liver of zebrafish. Zebrafish model is widely used in environmental monitoring and BPA-related studies. During the study zebrafish were treated for 60 days with two environmentally prevalent concentrations of BPA (1 μg/L and10 μg/L) and with a treatment control. Twenty wild-type juvenile zebrafish of age 35 dpf (days post fertilisation) were assigned to triplicate tanks and were treated until maturity in 95 dpf. Water of the tanks were changed once per three days. Survival percentage of the fish were calculated weekly. The kidney and liver of a sample of five fish from control treatment and 10 μg/L of BPA were obtained at 95 dpf for histopathological study. Kidney and liver sections were stained using heamatoxylin/eosin and examined under light microscope for structural pathology. The highest mean survival of 90% was observed in the control group at the end of the treatment period while, 56.57% and 41.67 % of survival were observed at 1 μg/L and 10 μg/L of BPA treatments respectively. This observation led to the conclusion that BPA has a significant impact on fish survival where high BPA concentrations resulted in significantly low survival. Histopathological analysis of the kidneys of fish treated with 10 μg/L of BPA revealed damaged renal tubules, shrinkage of tubules or tubule lumen, degeneration of tubules and hematopoietic tissue when compared with the control group. The liver histopathology of BPA-treated fish revealed lipid accumulation in hepatocytes. The reduced survival and structural distortion of liver and kidney of zebrafish in BPA-treated tanks could be due to chronic early-life BPA exposure as the quality of water significantlyaffects the fish survival, growth and development. It can be concluded that early-life exposure to environmentally prevalent doses of BPA can result in increased mortality in zebrafish model. This study calls for more comprehensive studies to understand the physiological impact of early-life BPA exposure on aquatic organisms.Keywords: Bisphenol A, Zebrafish, Survival, Histology, Liver, Kidne

A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia echini A3(T)

Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less-abundant GH96 a-agarases harbored in the agar-specific polysaccharide utilization locus (PUL) of Colwellia echini strain A3(T) facilitate the versatility of the agarolytic pathway. The cellular and molecular functions of the a-agarases examined by genomic, transcriptomic, and biochemical analyses revealed that alpha-agarases of C. echini A3(T) create a novel auxiliary pathway. alpha-Agarases convert even-numbered neoagarooligo-saccharides to odd-numbered agaro- and neoagarooligosaccharides, providing an alternative route for the depolymerization process in the agarolytic pathway. Comparative genomic analysis of agarolytic bacteria implied that the agarolytic gene repertoire in marine bacteria has been diversified during evolution, while the essential core agarolytic gene set has been conserved. The expansion of the agarolytic gene repertoire and novel hydrolytic functions, including the elucidated molecular functionality of alpha-agarase, promote metabolic versatility by channeling agar metabolism through different routes. IMPORTANCE Colwellia echini A3(T) is an example of how the gain of gene(s) can lead to the evolutionary expansion of agar-specific polysaccharide utilization loci (PUL). C. echini A3(T) encodes two a-agarases in addition to the core beta-agarolytic enzymes in its agarolytic PUL. Among the agar-degrading CAZymes identified so far, only a few alpha-agarases have been biochemically characterized. The molecular and biological functions of two alpha-agarases revealed that their unique hydrolytic pattern leads to the emergence of auxiliary agarolytic pathways. Through the combination of transcriptomic, genomic, and biochemical evidence, we elucidate the complete alpha-agarolytic pathway in C. echini A3(T). The addition of alpha-agarases to the agarolytic enzyme repertoire might allow marine agarolytic bacteria to increase competitive abilities through metabolic versatility

The use of high-throughput sequencing to investigate an outbreak of glycopeptide-resistant Enterococcus faecium with a novel quinupristin-dalfopristin resistance mechanism.

High-throughput sequencing (HTS) has successfully identified novel resistance genes in enterococci and determined clonal relatedness in outbreak analysis. We report the use of HTS to investigate two concurrent outbreaks of glycopeptide-resistant Enterococcus faecium (GRE) with an uncharacterised resistance mechanism to quinupristin-dalfopristin (QD).Seven QD-resistant and five QD-susceptible GRE isolates from a two-centre outbreak were studied. HTS was performed to identify genes or predicted proteins that were associated with the QD-resistant phenotype. MLST and SNP typing on HTS data was used to determine clonal relatedness.Comparative genomic analysis confirmed this GRE outbreak involved two distinct clones (ST80 and ST192). HTS confirmed the absence of known QD resistance genes, suggesting a novel mechanism was conferring resistance. Genomic analysis identified two significant genetic determinants with explanatory power for the high level of QD resistance in the ST80 QD-resistant clone: an additional 56aa leader sequence at the N-terminus of the lsaE gene and a transposon containing seven genes encoding proteins with possible drug or drug-target modification activities. However, HTS was unable to conclusively determine the QD resistance mechanism and did not reveal any genetic basis for QD resistance in the ST192 clone. This study highlights the usefulness of HTS in deciphering the degree of relatedness in two concurrent GRE outbreaks. Although HTS was able to reveal some genetic candidates for uncharacterised QD resistance, this study demonstrates the limitations of HTS as a tool for identifying putative determinants of resistance to QD

Isolation of human monoclonal autoantibodies derived from pancreatic lymph node and peripheral blood B cells of islet autoantibody-positive patients

Aims/hypothesis Autoantibodies against pancreatic islets and infections by enteroviruses are associated with type 1 diabetes, but the specificity of immune responses within the type 1 diabetic pancreas is poorly characterised. We investigated whether pancreatic lymph nodes could provide a source of antigen-specific B cells for analysis of immune responses within the (pre)diabetic pancreas. Methods Human IgG antibodies were cloned from single B lymphocytes sorted from pancreatic lymph node cells of three organ donors positive for islet autoantibodies, and from the peripheral blood of a patient with type 1 diabetes. Antibodies to insulinoma-associated antigen 2 (IA-2), GAD65, zinc trans- porter 8 (ZnT8) and Coxsackie B virus proteins were assayed by immunoprecipitation and by immunofluorescence on pan- creatic sections. Results Human IgG antibodies (863) were successfully cloned and produced from 4,092 single B cells from lymph nodes and peripheral blood. Reactivity to the protein tyrosine phosphatase domain of the IA-2 autoantigen was detected in two cloned antibodies: one derived from a pancreatic lymph node and one from peripheral blood. Epitopes for these two antibodies were similar to each other and to those for circulat- ing antibodies in type 1 diabetes. The remaining 861 antibod- ies were negative for reactivity to IA-2, GAD65 or ZnT8 by both assays tested. Reactivity to a Coxsackie viral protein 2 was detected in one antibody derived from a peripheral blood B cell, but not from lymph nodes. Conclusions/interpretation We show evidence for the infre- quent presence of autoantigen-specific IgG+ B lymphocytes in the pancreatic-draining lymph nodes of islet autoantibody- positive individuals

Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.

Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26 displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26 mediates epithelial disintegration, possibly leading to stomach H(+) leakage, and the fusion might contribute to invasiveness once a cell is transformed. Cell Rep 2015 Jul 14; 12(2):272-285

Epigenetic Changes of CXCR4 and Its Ligand CXCL12 as Prognostic Factors for Sporadic Breast Cancer

Chemokines and their receptors are involved in the development and cancer progression. The chemokine CXCL12 interacts with its receptor, CXCR4, to promote cellular adhesion, survival, proliferation and migration. The CXCR4 gene is upregulated in several types of cancers, including skin, lung, pancreas, brain and breast tumors. In pancreatic cancer and melanoma, CXCR4 expression is regulated by DNA methylation within its promoter region. In this study we examined the role of cytosine methylation in the regulation of CXCR4 expression in breast cancer cell lines and also correlated the methylation pattern with the clinicopathological aspects of sixty-nine primary breast tumors from a cohort of Brazilian women. RT-PCR showed that the PMC-42, MCF7 and MDA-MB-436 breast tumor cell lines expressed high levels of CXCR4. Conversely, the MDA-MB-435 cell line only expressed CXCR4 after treatment with 5-Aza-CdR, which suggests that CXCR4 expression is regulated by DNA methylation. To confirm this hypothesis, a 184 bp fragment of the CXCR4 gene promoter region was cloned after sodium bisulfite DNA treatment. Sequencing data showed that cell lines that expressed CXCR4 had only 15% of methylated CpG dinucleotides, while the cell line that not have CXCR4 expression, had a high density of methylation (91%). Loss of DNA methylation in the CXCR4 promoter was detected in 67% of the breast cancer analyzed. The absence of CXCR4 methylation was associated with the tumor stage, size, histological grade, lymph node status, ESR1 methylation and CXCL12 methylation, metastasis and patient death. Kaplan-Meier curves demonstrated that patients with an unmethylated CXCR4 promoter had a poorer overall survival and disease-free survival. Furthermore, patients with both CXCL12 methylation and unmethylated CXCR4 had a shorter overall survival and disease-free survival. These findings suggest that the DNA methylation status of both CXCR4 and CXCL12 genes could be used as a biomarker for prognosis in breast cancer

DNA methylation epigenotypes in breast cancer molecular subtypes

12 páginas, 3 figuras, 3 tablas.-- et al.[Introduction]: Identification of gene expression-based breast cancer subtypes is considered a critical means of prognostication. Genetic mutations along with epigenetic alterations contribute to gene-expression changes occurring in breast cancer. So far, these epigenetic contributions to sporadic breast cancer subtypes have not been well characterized, and only a limited understanding exists of the epigenetic mechanisms affected in those particular breast cancer subtypes. The present study was undertaken to dissect the breast cancer methylome and to deliver specific epigenotypes associated with particular breast cancer subtypes. [Methods]: By using a microarray approach, we analyzed DNA methylation in regulatory regions of 806 cancer-related genes in 28 breast cancer paired samples. We subsequently performed substantial technical and biologic validation by pyrosequencing, investigating the top qualifying 19 CpG regions in independent cohorts encompassing 47 basal-like, 44 ERBB2+ overexpressing, 48 luminal A, and 48 luminal B paired breast cancer/adjacent tissues. With the all-subset selection method, we identified the most subtype-predictive methylation profiles in multivariable logistic regression analysis. [Results]: The approach efficiently recognized 15 individual CpG loci differentially methylated in breast cancer tumor subtypes. We further identified novel subtype-specific epigenotypes that clearly demonstrate the differences in the methylation profiles of basal-like and human epidermal growth factor 2 (HER2)-overexpressing tumors. [Conclusions]: Our results provide evidence that well-defined DNA methylation profiles enable breast cancer subtype prediction and support the utilization of this biomarker for prognostication and therapeutic stratification of patients with breast cancer.This work was supported by grants from project CGL2008-01131 (Departamento de Sanidad del Gobierno Vasco), S-PE08UN45 and PE09BF02 (Departamento de Ciencia y Tecnologia del Gobierno Vasco), BIO2008-04212, and RD06/0020/1019 (Red Tematica de Investigacion Cooperativa en Cancer, RTICC) from the MICINN. The CIBER de Enfermedades Raras is an initiative of the ISCIII. NGB had a doctoral fellowship from the Basque Government (Departamento de Educacion, Universidades e Investigacion).Peer reviewe

The Cost of Climate Change to Agricultural Industries: Coconuts in Sri Lanka

Agriculture in low latitude countries such as Sri Lanka is already operating at the maximum temperature limits for crop growth and faces increased production risk from expected climate change. Sri Lanka is a developing country with limited economic and technological capacity to develop adaptation strategies; hence more vulnerable to climate change than developed countries. Coconut (Cocos nucifera L) is a rain fed perennial crop important in Sri Lankan culture, food consumption and the economy. It is the second most important food in the Sri Lankan diet after rice. Several studies have examined the impact of climate change on Sri Lankan agriculture, but none were conducted to simulate the impact of future climate change and future adaptation strategies on coconut production, or to calculate the economic welfare effects for different stakeholders in the coconut value chain. In this paper we report the development of an economic model of the coconut value chain that allows prediction of welfare impacts, and a quantitative representation of coconut yield that allows prediction of the impact of changing climatic conditions. The average outcome of 16 climate models was used to generate future climatic conditions, with two future climatic scenarios for 2020, 2030 and 2050 considered for three production regions. The most important yield estimate was a yield decline of more than 10 percent in the wet climatic zone due to the expected increase of maximum temperature. Without extra adaptation measures this is predicted to result in a loss to the industry of 4,795 Rs. Million annually by 2020, which is nearly 4.7 percent of the total value of the industry at equilibrium prices and quantities. The negative impact of climate change has the potential to be reduced with the implementation of additional adaptation practices. However, the cost effectiveness of these practices needs to be considered. Wider adoption of fertilizer application at specific times and moisture conservation practices are estimated to be economically beneficial

RepoZip : a technique for lossless compression of document collections

Many computer systems; especially in corporations, contain large amount of documents such as letters, reports and presentations. Many such documents are present in several versions. Such data needs to be synchronized with branch offices and mobile devices, often over slow and expensive connections. However, as many documents are stored in an already compressed format, it is difficult to compress them further by exploiting the hidden redundancies. We present a novel approach named RepoZip which improves the compression of an existing compression algorithm over a document collection, by exploiting the inter-document meta-data and content-level redundancies. It concentrates on compressing OOXML documents that have been constructed through the archival of a hierarchy of meta-data files and PDF documents which include deflated content streams. Therefore, the RepoZip approach achieves larger compression gains over OOXML document collections or PDF document collections by exploiting usually undetected meta-data level similarities

Biodegradable polyurethane for fused deposition modelling

Fused Deposition Modelling (FDM) is used to build prototypes from a CAD model using thermoplastic polymer filament. At present, bioresorbable filaments are not commercially available, however, some work has been reported in the literature (Hutmacher et al., 1999), where poly-(e-caprolactone), (PCL) was used as a filament and scaffolds were made for tissue engineering. CSIRO has recently developed a versatile range of biodegradable polyurethanes2 for tissue engineering applications. This work has been extended in order to optimise materials with properties suitable for FDM technologies