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International audience; Heparan sulfate (HS) proteoglycan chains are key components of the breast tumor microenvironment that critically influence the behavior of cancer cells. It is established that abnormal synthesis and processing of HS play a prominent role in tumorigenesis, albeit mechanisms remain mostly obscure. HS function is mainly controlled by sulfotransferases, and here we report a novel cellular and pathophysiological significance for the 3-O-sulfotransferase 3-OST3A (HS3ST3A), catalyzing the final maturation step of HS, in breast cancer. We show that 3-OST3A is epigenetically repressed in all breast cancer cell lines of a panel representative of distinct molecular subgroups, except in human epidermal growth factor receptor 2-positive (HER2+) sloan-kettering breast cancer (SKBR3) cells. Epigenetic mechanisms involved both DNA methylation and histone modifications, producing different repressive chromatin environments depending on the cell molecular signature. Gain and loss of function experiments by cDNA and siRNA transfection revealed profound effects of 3-OST3A expression on cell behavior including apoptosis, proliferation, response to trastuzumab in vitro and tumor growth in xenografted mice. 3-OST3A exerted dual activities acting as tumor-suppressor in lumA-michigan cancer foundation (MCF)-7 and triple negative-MD Anderson (MDA) metastatic breast (MB)-231 cells, or as an oncogenic factor in HER2+-SKBR3 cells. Mechanistically, fluorescence-resonance energy transfer-fluorescence-lifetime imaging microscopy experiments indicated that the effects of 3-OST3A in MCF-7 cells were mediated by altered interactions between HS and fibroblast growth factor-7 (FGF-7). Further, this interplay between HS and FGF-7 modulated downstream ERK, AKT and p38 cascades, suggesting that altering 3-O-sulfation affects FGFR2IIIb-mediated signaling. Corroborating our cellular data, a clinical study conducted in a cohort of breast cancer patients uncovered that, in HER2+ patients, high level expression of 3-OST3A in tumors was associated with reduced relapse-free survival. Our findings define 3-OST3A as a novel regulator of breast cancer pathogenicity, displaying tumor-suppressive or oncogenic activities in a cell-and tumor-dependent context, and demonstrate the clinical value of the HS-O-sulfotransferase 3-OST3A as a prognostic marker in HER2+ patients.

Isolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplification-based resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.

In sharp contrast to birds and mammals most cold blooded vertebrates have homomorphic (morphologically undifferentiated) sex chromosomes. This might result either from recurrent X Y recombination (occurring e.g. during occasional events of sex reversal) or from frequent turnovers (during which sex determining genes are overthrown by new autosomal mutations). Evidence for turnovers is indeed mounting in fish but very few have so far been documented in amphibians possibly because of practical difficulties in identifying sex chromosomes. Female heterogamety (ZW) has long been established in Bufo bufo based on sex reversal and crossing experiments. Here we investigate a sex linked marker identified from a laboratory cross between Palearctic green toads (Bufo viridis subgroup). The F(1) offspring produced by a female Bufo balearicus and a male Bufo siculus were phenotypically sexed displaying an even sex ratio. A sex specific marker detected in highly reproducible AFLP genotypes was cloned. Sequencing revealed a noncoding microsatellite containing fragment. Reamplification and genotyping of families of this and a reciprocal cross showed B. siculus to be male heterogametic (XY) and suggested the same system for B. balearicus. Our results thus reveal a cryptic heterogametic transition within bufonid frogs and help explain patterns of hybrid fitness within the B. viridis subgroup. Turnovers of genetic sex determination systems may be more frequent in amphibians than previously thought and thus contribute to the prevalence of homomorphic sex chromosomes in this group.

Desulfovibrio are sulfate-reducing anaerobic gram-negative rods that have been proposed as potential periodontopathogens. We investigated the capacity of Desulfovibrio to invade epithelial cells and induce cytokine secretion from these cells. Desulfovibrio strains were co-cultured with KB cells and counts of intracellular bacteria evaluated up to 3 days after infection. Desulfovibrio desulfuricans and Desulfovibrio fairfieldensis were able to survive within epithelial cells. Intracytoplasmic location of both bacterial species was confirmed by confocal laser scanning microscopy and transmission electron microscopy. Invasion was sensitive to nocodazole, an inhibitor of microtubule polymerization, but not to cytochalasin D, a microfilament inhibitor, suggesting that microtubule rearrangements were involved in the internalization of Desulfovibrio strains by KB cells. Infection by Desulfovibrio resulted in increased production of IL-6 and IL-8 by KB cells. The ability of D. desulfuricans and D. fairfieldensis to survive within oral epithelial cells and to modulate the epithelial immune response may contribute to the initiation and progression of periodontal diseases.

We present a new method for calibrating a classified 3D seismic volume. The classification process employs a Kohonen self-organizing map, a type of unsupervised artificial neural network; the subsequent calibration is performed using one or more suites of well logs. Kohonen self-organizing maps and other unsupervised clustering methods generate classes of data based on the identification of various discriminating features. These methods seek an organization in a dataset and form relational organized clusters. However, these clusters may or may not have any physical analogues in the real world. In order to relate them to the real world, we must develop a calibration method that not only defines the relationship between the clusters and real physical properties, but also provides an estimate of the validity of these relationships. With the development of this relationship, the whole dataset can then be calibrated. The clustering step reduces the multi-dimensional data into logically smaller groups. Each original data point defined by multiple attributes is reduced to a one- or two-dimensional relational group. This establishes some logical clustering and reduces the complexity of the classification problem. Furthermore, calibration should be more successful since it will have to consider less variability in the data. In this paper, we present a simple calibration method that employs Bayesian logic to provide the relationship between cluster centres and the real world. The output will give the most probable calibration between each self-organized map node and wellboremeasured parameters such as lithology, porosity and fluid saturation. The second part of the output comprises the calibration probability. The method is described in detail, and a case study is briefly presented using data acquired in the Orange River Basin, South Africa. The method shows promise as an alternative to current techniques for integrating seismic and log data during reservoir characterization.

Existing solid waste management (SWM) planning software provides only limited assistance to decision makers struggling to find strategies that address their multifarious concerns. The combinatorial nature (many waste items and many management options) and multiple objectives of the SWM problem severely constrain the effectiveness of a manual search process using these tools. Recognizing this, researchers have proposed several optimization-based search procedures. These methods, however, enjoy limited use due to the substantial expertise required for their application. This paper presents a new computer-based decision support framework that addresses these limitations. The new framework integrates process models that quantify the life-cycle inventory of a range of pollutants and costs for an extensive municipal solid waste system, an optimization search procedure that identifies strategies that meet cost and environmental objectives and site-specific restrictions, and a user-friendly interface that facilitates utilization of these components by practitioners. After describing the software design, the use and value of the tool in typical waste management scenarios is demonstrated through a hypothetical, but realistic, case study in which several alternative SWM strategies are generated and examined.

The reaction of sodium with an anthracite sample is studied at 700°C for various sodium relative pressures and is compared to the simple case of intercalation in a pitch coke. The behaviour of the anthracite sample is similar to that observed with non graphitizing carbon: intercalation and capillary condensation take place simultaneously. The sodium intercalation is found to be very sensitive to the previous heat treatment temperature of the sample, which determines the extent of order, and perfection of the carbon layers.

This paper discusses the approach adopted by the authors for teaching an undergraduate course (lecture and laboratory) in digital controls. Theoretical material is developed in the lecture concerning the application of direct digital control (DDC) to an analog bench-scale system consisting of a DC motor and tachometer. A simulation of the closed-loop control system with embedded digital controller is developed and run by the students using the TUTSIM dynamic simulation language. Finally, students perform a laboratory experiment in which they write a program to control the actual system using a personal computer and inexpensive interface card. The combination of hands-on experience and computer simulation with the more traditional, theoretical lecture material provides a well-rounded learning experience that better prepares the students to implement digital control systems in the real world. >

Desulfovibrio are sulfate-reducing anaerobic gram-negative rods that have been proposed as potential periodontopathogens. We investigated the capacity of Desulfovibrio to invade epithelial cells and induce cytokine secretion from these cells. Desulfovibrio strains were co-cultured with KB cells and counts of intracellular bacteria evaluated up to 3 days after infection. Desulfovibrio desulfuricans and Desulfovibrio fairfieldensis were able to survive within epithelial cells. Intracytoplasmic location of both bacterial species was confirmed by confocal laser scanning microscopy and transmission electron microscopy. Invasion was sensitive to nocodazole, an inhibitor of microtubule polymerization, but not to cytochalasin D, a microfilament inhibitor, suggesting that microtubule rearrangements were involved in the internalization of Desulfovibrio strains by KB cells. Infection by Desulfovibrio resulted in increased production of IL-6 and IL-8 by KB cells. The ability of D. desulfuricans and D. fairfieldensis to survive within oral epithelial cells and to modulate the epithelial immune response may contribute to the initiation and progression of periodontal diseases.

Study of the osmotic resistance to hypotonic medium of platelets has often been suggested as a global test to assess the viability of these cells in transfusion or to study modification during haematological pathologies. A number of authors have analysed the behaviour of platelets in hypotonic media by a variety of methods (cell count, determinations of substances released, morphology, etc.), but most studies are currently based on the so-called "Hypotonic Shock Response" test (HSR). In this study, the authors describe a new automated and reproducible apparatus, called fragilimeter, using slow dialysis to assess platelet osmotic resistance. The variations in light transmission through a platelet suspension according to ionic strength are linked to the change in cellular volume and lysis and characterise the osmotic behaviour of the cells. The results revealed the good reproducibility and sensibility of the technique. This apparatus allows also the realisation of the "HSR" test.

To harness the energy contained in such unconventional sources as winds, tides, and sunlight, a power system must incorporate an energy storage device to act as a buffer between the source and the load. Since the size of the energy storage device depends upon the relative timing of the availability of energy and the load demand, a system simulation is a logical approach to the study and design of power systems using these unconventional en ergy sources. GPSS is presented as an excellent simula tion vehicle. The physical properties to be simulated are discussed and the resulting GPSS programs are presented. Some proposed applications for these power systems are presented.