Proteomics in uveal melanoma research: opportunities and challenges in biomarker discovery

Uveal melanoma (UM) is the most frequent primary intraocular tumor in adult humans. Despite the significant advances in diagnosis and treatment of UM in the last decades, the prognosis of UM sufferers is still poor. Metastatic liver disease is the leading cause of death in UM and can develop after a long disease-free interval, suggesting the presence of occult micrometastasis. Proteomics technology has opened new opportunities for elucidating the molecular mechanism of complex diseases, such as cancer. This article will review the recent developments in biomarker discovery for UM research by proteomics. In the last few years, the first UM proteomics-based analyses have been launched, yielding promising results. An update on recent developments on this field is presented.     

Towards a Dynamic Approach to Urban Metabolism: Tracing the Temporal Evolution of Brussels’ Urban Metabolism from 1970 to 2010

Urban metabolism (UM) is a way of characterizing the flows of materials and energy through and within cities. It is based on a comparison of cities to living organisms, which, like cities, require energy and matter flows to function and which generate waste during the mobilization of matter. Over the last 40 years, this approach has been applied in numerous case studies. Because of the data‐intensive nature of a UM study, however, this methodology still faces some challenges. One such challenge is that most UM studies only present macroscopic results on either energy, water, or material flows at a particular point in time. This snapshot of a particular flow does not allow the tracing back of the flow's evolution caused by a city's temporal dynamics. To better understand the temporal dynamics of a UM, this article first presents the UM for Brussels Capital Region for 2010, including energy, water, material, and pollution flows. A temporal evaluation of these metabolic flows, as well as some urban characteristics starting from the seminal study of Duvigneaud and Denayer‐De Smet in the early 1970s to 2010, is then carried out. This evolution shows that Brussels electricity, natural gas, and water use increased by 160%, 400%, and 15%, respectively, over a period of 40 years, whereas population only increased by 1%. The effect of some urban characteristics on the UM is then briefly explored. Finally, this article succinctly compares the evolution of Brussels’ UM with those of Paris, Vienna, Barcelona, and Hong Kong and concludes by describing further research pathways that enable a better understanding of the complex functioniong of UM over time.     

Recent Progress in the Development of Anode Materials for Solid Oxide Fuel Cells

The field of research into solid oxide fuel cell (SOFC) anode materials has been rapidly moving forward. In the four years since the last in‐depth review significant advancements have been made in the reduction of the operating temperature and improvement of the performance of SOFCs. This progress report examines the developments in the field and looks to draw conclusions and inspiration from this research. A brief introduction is given to the field, followed by an overview of the principal previous materials. A detailed analysis of the developments of the last 4 years is given using a selection of the available literature, concentrating on metal‐fluorite cermets and perovskite‐based materials. This is followed by a consideration of alternate fuels for use in SOFCs and their associated problems and a short discussion on the effect of synthesis method on anode performance. The concluding remarks compile the significant developments in the field along with a consideration of the promise of future research. The recent progress in the development of anode materials for SOFCs based on oxygen ion conducting electrolytes is reviewed.     

Application of lipases in kinetic resolution of racemates

Lipases have been well established as valuable catalysts in organic synthesis. This review article focuses on some of the recent developments in the rapidly growing field of lipase-catalyzed kinetic resolution of racemates as a versatile method for the separation of enantiomers. The literature search dates back to the last five years and covers some comprehensive examples. The main emphasis is on the use of lipases in organic solvents.     

Expression and function of the UM4D4 antigen in human thymus

UM4D4 is a newly identified T cell surface molecule, distinct from the Ag receptor and CD2, which is expressed on 25% of peripheral blood T cells, resting or activated. Monoclonal anti-UM4D4 is mitogenic for T cells and T cell clones. Since alternative activation pathways independent of Ag/MHC recognition may be important in thymic differentiation, the expression and function of UM4D4 was examined in human thymus. UM4D4 was found on the surface of 6% of thymocytes. All thymocyte subsets contained UM4D4+ cells but expression was greatest on thymocytes that were CD1- (12%), CD3+ (11%) and especially CD4-CD8- (18%). CD3+CD4- CD8- cells, most of which bear the gamma delta-receptor, were greater than or equal to 50% + for UM4D4. Moreover, anti-UM4D4 was comitogenic for thymocytes together with PMA or IL-2. Anti-UM4D4 also reacted strongly with a subset of thymic epithelial cells in both cortex and medulla. Dual color fluorescence microscopy, with anti-UM4D4 and antibodies to other thymic epithelial Ag, showed UM4D4 expression on neuroendocrine thymic epithelium but not on thymic fibrous stroma. Thus, UM4D4 is expressed on, and represents an activation pathway for, a subset of thymic T cells. In addition, this determinant, initially identified as a novel T cell activating molecule, is broadly expressed by neuroendocrine thymic epithelium. Although the function of UM4D4 on the thymic epithelial cells is not yet clear, it is possible that UM4D4 represents a pathway for the functional activation of a subset of the thymic epithelium as well as a subset of thymocytes, thus playing a dual role in T cell differentiation.     

Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins

In the last 15 years substantial advances have been made to place isotope labels in native and glycosylated proteins for NMR studies and structure determination. Key developments include segmental isotope labeling using Native Chemical Ligation, Expressed Protein Ligation and Protein Trans-Splicing. These advances are pushing the size limit of NMR spectroscopy further making larger proteins accessible for this technique. It is just emerging that segmental isotope labeling can be used to define inter-domain interactions in NMR structure determination. Labeling of post-translational modified proteins like glycoproteins remains difficult but some promising developments were recently achieved. Key achievements are segmental and site-specific labeling schemes that improve resonance assignment and structure determination of the glycan moiety. We adjusted the focus of this perspective article to concentrate on the NMR applications based on recent developments rather than on labeling methods themselves to illustrate the considerable potential for biomolecular NMR.     

Overexpression of uvomorulin in a compaction-negative F9 mutant cell line

The mutant F9 cell line F9att-5.51 synthesizes reduced amounts of uvomorulin (UM) protein and we hypothesized earlier (Adamson, Baribault, and Kemler, Dev. Biol. (1990), 138, 338) that this may account for its inability to compact into tightly aggregated balls of cells. Subsequently, when 5.51 cells are treated with retinoic acid to stimulate their differentiation, they are unable to form embryoid bodies as do wild-type cells which form an outer epithelial layer of visceral endoderm cells. We have now examined the possibility that the UM protein made in the mutant line is defective, but find that it is normal in structure and stability. The gene coding for UM appears to be normal as does the mRNA which is synthesized at a normal rate but is severely reduced in steady-state measurements of mutant cells. A rescue experiment was performed by increasing levels of UM in mutant cells by means of transfection with a UM expression vector. The resulting cells expressed abundant UM mRNA and protein but were still unable to form compacted aggregates and did not differentiate into embryoid bodies. Interestingly, the stability of endogenous UM mRNA was improved in the presence of exogenous UM; therefore, a positive feedback mechanism contributes to low mRNA levels in mutant cells. The accumulated data suggest that UM in 5.51 cells is unable to mount a compaction activity because a distal connecting link in the multicomponent process initiated by UM is missing or or aberrant. The missing component is likely to connect UM to actin and the cytoskeleton of the cell.     

Poly(ADP-ribose) in the skin and in melanomas

Cutaneous melanoma (CM) and uveal melanoma (UM) represent the most aggressive pigment cell tumor types. Our investigation examined the signaling molecule poly(ADP-ribose) (PAR) in CM and UM. We have demonstrated PAR in keratinocytes, sebocytes, hair follicles, endothelial cells and in subcutaneous adipocytes in the normal skin indicating that PAR may regulate physiological functions in these cell types. Furthermore, CM cells were PAR positive and tumor invasion level/thickness of CM correlated with the PAR content of the cell nuclei, with higher Clark and Breslow indices and AJCC scores associating with higher PAR content. This correlation was especially marked in the samples of female patients. In UM tumors (n=12) a slight overall and strong perivascular PAR staining was observed with considerable individual variations. In view of recent successful clinical trials with PARP inhibitors as adjuvant chemotherapeutic agents, our results suggest that melanomas may display differential sensitivity towards this novel therapeutic modality which should be considered for the selection of patients.     

Nanobodies against surface biomarkers enable the analysis of tumor genetic heterogeneity in uveal melanoma patient‐derived xenografts

Monoclonal antibodies specific for biomarkers expressed on the surface of uveal melanoma (UM) cells would simplify the immune capture and genomic characterization of heterogeneous tumor cells originated from patient‐derived xenografts (PDXs). Antibodies against four independent tumor antigens were isolated by panning a nanobody synthetic library. Such antibodies enabled flow cytometry‐based sorting of distinct cell subpopulations from UM PDXs and to analyze their genomic features. The complexity and specificity of the biochemical and genomic biomarker combinations mirrored the UM tumor polyclonality. The data showed that MUC18 is highly and universally displayed on the surface of UM cells with different genetic background and consequently represents a reliable pan‐biomarker for their identification and purification. In contrast, the other three biomarkers were detected in very variable combinations in UM PDX cells. The availability of the identified nanobodies will be instrumental in developing clone‐specific drug evaluation and rational clinical strategies based on accurate genomic profiling.     

The 4th Bologna Winter School: hot topics in structural genomics

The 4th Bologna Winter School on Biotechnologies was held on 9-15 February 2003 at the University of Bologna, Italy, with the specific aim of discussing recent developments in bioinformatics. The school provided an opportunity for students and scientists to debate current problems in computational biology and possible solutions. The course, co-supported (as last year) by the European Science Foundation program on Functional Genomics, focused mainly on hot topics in structural genomics, including recent CASP and CAPRI results, recent and promising genomewide predictions, protein-protein and protein-DNA interaction predictions and genome functional annotation. The topics were organized into four main sections (http://www.biocomp.unibo.it).     

Engineered riboswitches as novel tools in molecular biology

During the last years the great importance of RNA for regulating gene expression in all organisms has become obvious. Consequently, several recent approaches aim to utilize the outstanding chemical properties of RNA to develop artificial RNA regulators for conditional gene expression systems. A combination of rational design, in vitro selection and in vivo screening systems has been used to create a versatile set of RNA based molecular switches. These tools rely on diverse mechanisms and exhibit activity in several organisms. In this review, we summarize recent developments in the application of engineered riboswitches for gene regulation in vivo.     

The AMP-dependent kinase pathway is upregulated in BAP1 mutant uveal melanoma

Metastatic uveal melanoma (UM) responds poorly to targeted therapies and immune checkpoint inhibitors. Loss of BRCA1-associated protein 1 (BAP1) via inactivating mutations in the BAP1 gene is associated with UM progression. Thus, molecular alterations caused by BAP1 dysfunction may be novel therapeutic targets for metastatic UM. Here, we found that phosphorylation of AMP-dependent kinase (AMPK) was elevated in BAP1-altered (or mutant) compared to BAP1-unaltered (or wild-type [WT]) UM tumors. As a readout of AMPK pathway activation, phosphorylation of an AMPK downstream effector, acetyl-CoA-carboxylase (ACC), was also elevated. BAP1 re-expression in BAP1-null UM cell lines decreased phospho-AMPK (pAMPK) and phospho-ACC (pACC) levels. AMPK phosphorylation is mediated by calcium/calmodulin dependent protein kinase kinase 2 (CaMKK2) and potentially liver kinase B1 (LKB1) in BAP1 mutant UM cells. Knockdown of AMPKα1/2 reduced the viability of BAP1 mutant UM cells, indicating a survival function of AMPK in BAP1 mutant UM. Our data suggest that the AMPK pathway is an important mechanism mediating the survival of BAP1 mutant UM. Targeting the AMPK pathway may be a novel therapeutic strategy for metastatic UM.     

棘尾虫对折右纵断片的再生和纤毛模式形成的研究

应用切割嫁接方法获得的棘尾虫完全对折和部分对拆右纵断片都经历了一面调整极性、一面再生和形态发生的过程。推测这两种断片在纤毛模式形成中发生的诸多现象可能与所在断片再生时的极性调整变化状态有关。     

Biomass measurement online: the performance of in situ measurements and software sensors

Biomass measurement is one of the most critical measurements in biotechnological processes. The technologies developed for the measurement of biomass in situ have developed over the years. Because it has been over 10 years since the last review concentrating on practical issues concerning biomass measurements, it is time to evaluate recent developments in the field. This review concentrates on the applications of dielectric spectroscopy, optical density, infrared spectroscopy, and fluorescence for in situ measurement of biomass. The advantages offered by these methods and an economic way of estimating biomass concentration, the software sensors, are considered.     

Progress in understanding of ginsenoside biosynthesis

Ginseng is an economically important medicinal plant. The major bioactive ingredients of ginseng are ginsenosides, which are triterpene saponins. Because of difficulties in ginseng cultivation and the low productivity of ginseng cell and tissue culture, it has become important to improve ginsenoside levels by using metabolic engineering based on the biosynthetic pathway of ginsenosides. During the last decade, substantial advances have been made in biosynthesis of ginsenosides. This review is concerned with recent developments in our understanding of the biosynthesis of ginsenosides.     

TILLING in extremis

Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non-transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next-generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silico procedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.     

Drivers of compartmentalization in a Mediterranean pollination network

We study compartmentalization in a Mediterranean pollination network using three different analytical approaches: unipartite modularity (UM), bipartite modularity (BM) and the group model (GM). Our objectives are to compare compartments obtained with these three approaches and to explore the role of several species attributes related to pollination syndromes, species phenology, abundance and connectivity in structuring compartmentalization. BM could not identify compartments in our network. By contrast, UM revealed four modules composed of plants and pollinators, and GM four groups of plants and five of pollinators. Phenology had a major influence on compartmentalization, and compartments (both UM and GM) had distinct phenophases. Compartments were also strongly characterized by species degree (number of connections) and betweenness centrality. These two attributes were highly related to each other and to phenophase duration. Differences among compartments in abundance were only apparent with GM. We attribute this to the fact that abundance is strongly correlated with Degree, and the GM algorithm is particularly powerful at discriminating species based on degree. On the other hand, the role of pollination syndrome‐related features in compartmentalization mostly emerged with UM. Only UM compartments differed in corolla length and pollen production. Both UM and GM compartments differed in their pollinator spectra. We found inconsistent reciprocity between plant attributes and pollinator spectra, thus it is difficult to conclude compartments follow clear‐cut syndromes. Also, both UM and GM identified a compartment composed of pollinators with long activity periods that acted as connectors, linking all compartments providing cohesiveness to the network.     

Comparison of two cell-adhesion molecules, uvomorulin and cell-CAM 105

Two cell adhesion molecules, cell-CAM 105 and uvomorulin (UM), were compared by analysing their antigenic structures, their activity in cell aggregation assays and their expression in various tissues. Cell-CAM 105 is a membrane glycoprotein which mediates the intercellular adhesion of reaggregating rat hepatocytes, and UM was first described to be involved in the compaction of preimplantation mouse embryos and embryonal carcinoma cells. UM is not only expressed during embryonic development but also in various adult tissues including liver, epithelia of lung, gut, kidney and uterus. A similar distribution for UM was found in rat tissues on cell types where cell-CAM 105 is known to be present. Our studies show that (i) cell-CAM 105 and UM are distinct and different proteins; (ii) uvomorulin is involved in the compaction of rat preimplantation embryos but Fab anti-UM has no effect on reaggregating rat hepatocytes, where Fab anti-cell CAM is effective; (iii) distribution studies show that UM is expressed on a broader range of epithelial cells while cell-CAM 105 is more restricted to hepatocytes and simple epithelia. In cases where both cell adhesion molecules are expressed on the same cell types they can be localized to different parts of the cell surface.     

Exploiting evolutionary relationships for predicting protein structures

In the last few years there have been many developments in computational biology, particularly with regard to novel, imaginative exploitation of genomic data. Disappointingly, there has been a lack of progress in the methodology for prediction of protein structures. In the last several years, however, promising new methods have finally begun to emerge. These methods are increasing the power and scope of the methodology, but, most importantly, they are generating new areas of investigation that we believe will accelerate progress in the field. In this review we describe recent developments and highlight the implications of their success as well as areas where efforts should be focused.