Showing papers by "Ghent University published in 2005"

BiNGO : a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Abstract: Summary: The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape's versatile visualization environment to produce an intuitive and customizable visual representation of the results. Availability: http://www.psb.ugent.be/cbd/papers/BiNGO/ Contact: martin.kuiper@psb.ugent.be

Classification of cell death: recommendations of the Nomenclature Committee on Cell Death

Abstract: Different types of cell death are often defined by morphological criteria, without a clear reference to precise biochemical mechanisms. The Nomenclature Committee on Cell Death (NCCD) proposes unified criteria for the definition of cell death and of its different morphologies, while formulating several caveats against the misuse of words and concepts that slow down progress in the area of cell death research. Authors, reviewers and editors of scientific periodicals are invited to abandon expressions like 'percentage apoptosis' and to replace them with more accurate descriptions of the biochemical and cellular parameters that are actually measured. Moreover, at the present stage, it should be accepted that caspase-independent mechanisms can cooperate with (or substitute for) caspases in the execution of lethal signaling pathways and that 'autophagic cell death' is a type of cell death occurring together with (but not necessarily by) autophagic vacuolization. This study details the 2009 recommendations of the NCCD on the use of cell death-related terminology including 'entosis', 'mitotic catastrophe', 'necrosis', 'necroptosis' and 'pyroptosis'.

A syndrome of altered cardiovascular, craniofacial, neurocognitive and skeletal development caused by mutations in TGFBR1 or TGFBR2

Abstract: We report heterozygous mutations in the genes encoding either type I or type II transforming growth factor β receptor in ten families with a newly described human phenotype that includes widespread perturbations in cardiovascular, craniofacial, neurocognitive and skeletal development. Despite evidence that receptors derived from selected mutated alleles cannot support TGFβ signal propagation, cells derived from individuals heterozygous with respect to these mutations did not show altered kinetics of the acute phase response to administered ligand. Furthermore, tissues derived from affected individuals showed increased expression of both collagen and connective tissue growth factor, as well as nuclear enrichment of phosphorylated Smad2, indicative of increased TGFβ signaling. These data definitively implicate perturbation of TGFβ signaling in many common human phenotypes, including craniosynostosis, cleft palate, arterial aneurysms, congenital heart disease and mental retardation, and suggest that comprehensive mechanistic insight will require consideration of both primary and compensatory events.

Comparison of overweight and obesity prevalence in school-aged youth from 34 countries and their relationships with physical activity and dietary patterns

Abstract: The purposes of this systematic review were to present and compare recent estimates of the prevalence of overweight and obesity in school-aged youth from 34 countries and to examine associations between overweight and selected dietary and physical activity patterns. Data consisted of a cross-sectional survey of 137 593 youth (10-16 years) from the 34 (primarily European) participating countries of the 2001-2002 Health Behaviour in School-Aged Children Study. The prevalence of overweight and obesity was determined based on self-reported height and weight and the international child body mass index standards. Logistic regression was employed to examine associations between overweight status with selected dietary and physical activity patterns. The two countries with the highest prevalence of overweight (pre-obese + obese) and obese youth were Malta (25.4% and 7.9%) and the United States (25.1% and 6.8%) while the two countries with the lowest prevalence were Lithuania (5.1% and 0.4%) and Latvia (5.9% and 0.5%). Overweight and obesity prevalence was particularly high in countries located in North America, Great Britain, and south-western Europe. Within most countries physical activity levels were lower and television viewing times were higher in overweight compared to normal weight youth. In 91% of the countries examined, the frequency of sweets intake was lower in overweight than normal weight youth. Overweight status was not associated with the intake of fruits, vegetables, and soft drinks or time spent on the computer. In conclusion, the adolescent obesity epidemic is a global issue. Increasing physical activity participation and decreasing television viewing should be the focus of strategies aimed at preventing and treating overweight and obesity in youth.

Re-evaluating prokaryotic species

Abstract: There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.

From 2R to 3R: evidence for a fish‐specific genome duplication (FSGD)

Abstract: Summary An important mechanism for the evolution of phenotypic complexity, diversity and innovation, and the origin of novel gene functions is the duplication of genes and entire genomes. Recent phylogenomic studies suggest that, during the evolution of vertebrates, the entire genomewasduplicatedintworounds(2R)ofduplication. Later, � 350mya,inthestemlineageofray-finned(actinopterygian) fishes, but not in that of the land vertebrates, a third genome duplication occurred—the fish-specific genome duplication (FSGD or 3R), leading, at least initially, to up to eight copies of the ancestral deuterostome genome. Therefore, the sarcopterygian (lobe-finned fishes and tetrapods) genome possessed originally only half as many genes compared to the derived fishes, just like the most-basal and species-poor lineages of extant fishes that diverged from the fish stem lineage before the 3R duplication. Most duplicated genes were secondarily lost, yet some evolved new functions. The genomic complexity of the teleosts might be the reason for their evolutionary success and astounding biological diversity. BioEssays 27:937–945, 2005. 2005 Wiley Periodicals, Inc.

Microbial phenazine production enhances electron transfer in biofuel cells

Abstract: High-rate electron transfer toward an anode in microbial fuel cells(MFCs) has thus far not been described for bacteria-producing soluble redox mediators. To study the mechanism of electron transfer, we used a MFC isolate, Pseudomonas aeruginosa strain KRP1. Bacterial electron transfer toward the MFC anode was enabled through pyocyanin and phenazine-l-carboxamide. The presence of the anode stimulated pyocyanin production. Mutant strains, deficient in the synthesis of pyocyanin and phenazine-1-carboxamide, were unable to achieve substantial electron transfer and reached only 5% of the wild type's power output. Upon pyocyanin addition, the power output was restored to 50%. Pyocyanin was not only used by P. aeruginosa to improve electron transfer but as well enhanced electron transfer by other bacterial species. The finding that one bacterium can produce electron shuttles, which can be used also by other bacteria, to enhance electron-transfer rate and growth, has not been shown before. These findings have considerable implications with respect to the power output attainable in MFCs.

Modeling gene and genome duplications in eukaryotes.

Abstract: Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.

Nanophotonic waveguides in silicon-on-insulator fabricated with CMOS technology

Abstract: High-index-contrast, wavelength-scale structures are key to ultracompact integration of photonic integrated circuits. The fabrication of these nanophotonic structures in silicon-on-insulator using complementary metal-oxide-semiconductor processing techniques, including deep ultraviolet lithography, was studied. It is concluded that this technology is capable of commercially manufacturing nanophotonic integrated circuits. The possibilities of photonic wires and photonic-crystal waveguides for photonic integration are compared. It is shown that, with similar fabrication techniques, photonic wires perform at least an order of magnitude better than photonic-crystal waveguides with respect to propagation losses. Measurements indicate propagation losses as low as 0.24 dB/mm for photonic wires but 7.5 dB/mm for photonic-crystal waveguides.

DeltaEF1 is a transcriptional repressor of E-cadherin and regulates epithelial plasticity in breast cancer cells.

Abstract: Downregulation of E-cadherin is a crucial event for epithelial to mesenchymal transition (EMT) in embryonic development and cancer progression. Using the EpFosER mammary tumour model we show that during EMT, upregulation of the transcriptional regulator deltaEF1 coincided with transcriptional repression of E-cadherin. Ectopic expression of deltaEF1 in epithelial cells was sufficient to downregulate E-cadherin and to induce EMT. Analysis of E-cadherin promoter activity and chromatin immunoprecipitation identified deltaEF1 as direct transcriptional repressor of E-cadherin. In human cancer cells, transcript levels of deltaEF1 correlated directly with the extent of E-cadherin repression and loss of the epithelial phenotype. The protein was enriched in nuclei of human cancer cells and physically associated with the E-cadherin promoter. RNA interference-mediated downregulation of deltaEF1 in cancer cells was sufficient to derepress E-cadherin expression and restore cell to cell adhesion, suggesting that deltaEF1 is a key player in late stage carcinogenesis.

Tubular microbial fuel cells for efficient electricity generation.

Abstract: A tubular, single-chambered, continuous microbial fuel cell (MFC) that generates high power outputs using a granular graphite matrix as the anode and a ferricyanide solution as the cathode is described. The maximal power outputs obtained were 90 and 66 W m(-3) net anodic compartment (NAC) (48 and 38 W m(-3) total anodic compartment (TAC)) for feed streams based on acetate and glucose, respectively, and 59 and 48 W m(-3) NAC for digester effluent and domestic wastewater, respectively. For acetate and glucose, the total Coulombic conversion efficiencies were 75 +/- 5% and 59 +/- 4%, respectively, at loading rates of 1.1 kg chemical oxygen demand m(-3) NAC volume day(-1). When wastewater was used, of the organic matter effectively removed (i.e., 22% at a loading of 2 kg organic matter m(-3) NAC day(-1)), up to 96% was converted to electricity on a Coulombic basis. The lower overall efficiency of the wastewater-treating reactors is related to the presence of nonreadily biodegradable organics and the interference of alternative electron acceptors such as sulfate present in the wastewater. To further improve MFCs, focus has to be placed on the enhanced conversion of nonrapidly biodegradable material and the better directing of the anode flow toward the electrode instead of to alternative electron acceptors. Also the use of sustainable, open-air cathodes is a critical issue for practical implementation.

Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression

Abstract: Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development.

Chronic kidney disease as cause of cardiovascular morbidity and mortality.

Abstract: To make an evidence-based evaluation of the relationship between kidney failure and cardiovascular risk, we reviewed the literature obtained from a PubMed search using pre-defined keywords related to both conditions and covering 18 years (1986 until end 2003). Eighty-five publications, covering 552 258 subjects, are summarized. All but three studies support a link between kidney dysfunction and cardiovascular risk. More importantly, the association is observed very early during the evolution of renal failure: an accelerated cardiovascular risk appears at varying glomerular filtration rate (GFR) cut-off values, which were >/=60 ml/min in at least 20 studies. Many studies lacked a clear definition of cardiovascular disease and/or used a single determination of serum creatinine or GFR as an index of kidney function, which is not necessarily corresponding to well-defined chronic kidney disease. In six studies, however, chronic kidney dysfunction and cardiovascular disease were well defined and the results of these confirm the impact of kidney dysfunction. It is concluded that there is an undeniable link between kidney dysfunction and cardiovascular risk and that the presence of even subtle kidney dysfunction should be considered as one of the conditions necessitating intensive prevention of this cardiovascular risk.

How to assess physical activity? How to assess physical fitness?

Abstract: Regular aerobic physical activity (PA) increases exercise capacity and physical fitness (PF), which can lead to many health benefits. Accurate quantification of PA and PF becomes essential in terms of health outcome and effectiveness of intervention programmes. In this manuscript we present a review

PRIDE: The proteomics identifications database

Abstract: The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large-scale proteomics projects about to disseminate their data, this trend is not likely to flatten out any time soon. However, the publication mechanism of these identified proteins has lagged behind in technical terms. Often very long lists of identifications are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, making it practically impossible for computer programs to interpret them, let alone efficiently query them. Here we propose the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/pride) as a means to finally turn publicly available data into publicly accessible data. PRIDE offers a web-based query interface, a user-friendly data upload facility, and a documented application programming interface for direct computational access. The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation.

SIP1/ZEB2 induces EMT by repressing genes of different epithelial cell–cell junctions

Abstract: SIP1/ZEB2 is a member of the δEF-1 family of two-handed zinc finger nuclear factors. The expression of these transcription factors is associated with epithelial mesenchymal transitions (EMT) during development. SIP1 is also expressed in some breast cancer cell lines and was detected in intestinal gastric carcinomas, where its expression is inversely correlated with that of E-cadherin. Here, we show that expression of SIP1 in human epithelial cells results in a clear morphological change from an epithelial to a mesenchymal phenotype. Induction of this epithelial dedifferentiation was accompanied by repression of several cell junctional proteins, with concomitant repression of their mRNA levels. Besides E-cadherin, other genes coding for crucial proteins of tight junctions, desmosomes and gap junctions were found to be transcriptionally regulated by the transcriptional repressor SIP1. Moreover, study of the promoter regions of selected genes by luciferase reporter assays and chromatin immunoprecipitation shows that repression is directly mediated by SIP1. These data indicate that, during epithelial dedifferentiation, SIP1 represses in a coordinated manner the transcription of genes coding for junctional proteins contributing to the dedifferentiated state; this repression occurs by a general mechanism mediated by Smad Interacting Protein 1 (SIP1)-binding sites.

Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal

Abstract: Re-orientation of Arabidopsis seedlings induces a rapid, asymmetric release of the growth regulator auxin from gravity-sensing columella cells at the root apex. The resulting lateral auxin gradient is hypothesized to drive differential cell expansion in elongation-zone tissues. We mapped those root tissues that function to transport or respond to auxin during a gravitropic response. Targeted expression of the auxin influx facilitator AUX1 demonstrated that root gravitropism requires auxin to be transported via the lateral root cap to all elongating epidermal cells. A three-dimensional model of the root elongation zone predicted that AUX1 causes the majority of auxin to accumulate in the epidermis. Selectively disrupting the auxin responsiveness of expanding epidermal cells by expressing a mutant form of the AUX/IAA17 protein, axr3-1, abolished root gravitropism. We conclude that gravitropic curvature in Arabidopsis roots is primarily driven by the differential expansion of epidermal cells in response to an influx-carrier-dependent auxin gradient.

Human antimicrobial peptides: defensins, cathelicidins and histatins.

Abstract: Antimicrobial peptides, which have been isolated from many bacteria, fungi, plants, invertebrates and vertebrates, are an important component of the natural defenses of most living organisms. The isolated peptides are very heterogeneous in length, sequence and structure, but most of them are small, cationic and amphipathic. These peptides exhibit broad-spectrum activity against Gram-positive and Gram-negative bacteria, yeasts, fungi and enveloped viruses. A wide variety of human proteins and peptides also have antimicrobial activity and play important roles in innate immunity. In this review we discuss three important groups of human antimicrobial peptides. The defensins are cationic non-glycosylated peptides containing six cysteine residues that form three intramolecular disulfide bridges, resulting in a triple-stranded beta-sheet structure. In humans, two classes of defensins can be found: alpha-defensins and beta-defensins. The defensin-related HE2 isoforms will also be discussed. The second group is the family of histatins, which are small, cationic, histidine-rich peptides present in human saliva. Histatins adopt a random coil conformation in aqueous solvents and form alpha-helices in non-aqueous solvents. The third group comprises only one antimicrobial peptide, the cathelicidin LL-37. This peptide is derived proteolytically from the C-terminal end of the human CAP18 protein. Just like the histatins, it adopts a largely random coil conformation in a hydrophilic environment, and forms an alpha-helical structure in a hydrophobic environment.

Treatment of motoneuron degeneration by intracerebroventricular delivery of VEGF in a rat model of ALS

Abstract: Treatment of motoneuron degeneration by intracerebroventricular delivery of VEGF in a rat model of ALS

Real-Space Observation of Ultraslow Light in Photonic Crystal Waveguides

Abstract: We show the real-space observation of fast and slow pulses propagating inside a photonic crystal waveguide by time-resolved near-field scanning optical microscopy. Local phase and group velocities of modes are measured. For a specific optical frequency we observe a localized pattern associated with a flat band in the dispersion diagram. During at least 3 ps, movement of this field is hardly discernible: its group velocity would be at most c/1000. The huge trapping times without the use of a cavity reveal new perspectives for dispersion and time control within photonic crystals.

Facing others in pain: the effects of empathy.

Abstract: Department of Experimental-Clinical and Health Psychology, Ghent University, Ghent, Belgium Research Institute for Psychology & Health, Utrecht, The Netherlands Department of Psychology, University of British Columbia, Vancouver, BC, Canada Academic Unit of Psychiatry & Behavioural Sciences, University of Leeds, Leeds, UK Department of Psychology, University of Montreal, Quebec, Canada Sub-Department of Clinical Health Psychology, University College London, London, UK Department of Psychology, Wayne State University, Detroit, MI, USA

Genome-Wide Analysis of Hydrogen Peroxide-Regulated Gene Expression in Arabidopsis Reveals a High Light-Induced Transcriptional Cluster Involved in Anthocyanin Biosynthesis

Abstract: In plants, reactive oxygen species and, more particularly, hydrogen peroxide (H2O2) play a dual role as toxic by-products of normal cell metabolism and as regulatory molecules in stress perception and signal transduction. Peroxisomal catalases are an important sink for photorespiratory H2O2. Using ATH1 Affymetrix microarrays, expression profiles were compared between control and catalase-deficient Arabidopsis (Arabidopsis thaliana) plants. Reduced catalase levels already provoked differences in nuclear gene expression under ambient growth conditions, and these effects were amplified by high light exposure in a sun simulator for 3 and 8 h. This genome-wide expression analysis allowed us to reveal the expression characteristics of complete pathways and functional categories during H2O2 stress. In total, 349 transcripts were significantly up-regulated by high light in catalase-deficient plants and 88 were down-regulated. From this data set, H2O2 was inferred to play a key role in the transcriptional up-regulation of small heat shock proteins during high light stress. In addition, several transcription factors and candidate regulatory genes involved in H2O2 transcriptional gene networks were identified. Comparisons with other publicly available transcriptome data sets of abiotically stressed Arabidopsis revealed an important intersection with H2O2-deregulated genes, positioning elevated H2O2 levels as an important signal within abiotic stress-induced gene expression. Finally, analysis of transcriptional changes in a combination of a genetic (catalase deficiency) and an environmental (high light) perturbation identified a transcriptional cluster that was strongly and rapidly induced by high light in control plants, but impaired in catalase-deficient plants. This cluster comprises the complete known anthocyanin regulatory and biosynthetic pathway, together with genes encoding unknown proteins.

Local kinematics of K and M giants from CORAVEL/Hipparcos/Tycho-2 data: Revisiting the concept of superclusters

Abstract: The availability of the Hipparcos Catalogue has triggered many kinematic and dynamical studies of the solar neighbourhood. Nevertheless, those studies generally lacked the third component of the space velocities, i.e., the radial velocities. This work presents the kinematic analysis of 5952 K and 739 M giants in the solar neighbourhood which includes for the first time radial velocity data from a large survey performed with the CORAVEL spectrovelocimeter. It also uses proper motions from the Tycho-2 catalogue, which are expected to be more accurate than the Hipparcos ones. An important by-product of this study is the observed fraction of only 5.7% of spectroscopic binaries among M giants as compared to 13.7% for K giants. After excluding the binaries for which no center-of-mass velocity could be estimated, 5311 K and 719 M giants remain in the final sample. The UV -plane constructed from these data for the stars with precise parallaxes (%) reveals a rich small-scale structure, with several clumps corresponding to the Hercules stream, the Sirius moving group, and the Hyades and Pleiades superclusters. A maximum-likelihood method, based on a Bayesian approach, has been applied to the data, in order to make full use of all the available stars (not only those with precise parallaxes) and to derive the kinematic properties of these subgroups. Isochrones in the Hertzsprung-Russell diagram reveal a very wide range of ages for stars belonging to these groups. These groups are most probably related to the dynamical perturbation by transient spiral waves (as recently modelled by De Simone et al. [CITE]) rather than to cluster remnants. A possible explanation for the presence of young group/clusters in the same area of the UV -plane is that they have been put there by the spiral wave associated with their formation, while the kinematics of the older stars of our sample has also been disturbed by the same wave. The emerging picture is thus one of dynamical streams pervading the solar neighbourhood and travelling in the Galaxy with similar space velocities. The term dynamical stream is more appropriate than the traditional term supercluster since it involves stars of different ages, not born at the same place nor at the same time. The position of those streams in the UV -plane is responsible for the vertex deviation of for the whole sample. Our study suggests that the vertex deviation for younger populations could have the same dynamical origin. The underlying velocity ellipsoid, extracted by the maximum-likelihood method after removal of the streams, is not centered on the value commonly accepted for the radial antisolar motion: it is centered on km s-1 . However, the full data set (including the various streams) does yield the usual value for the radial solar motion, when properly accounting for the biases inherent to this kind of analysis (namely, km s-1 ). This discrepancy clearly raises the essential question of how to derive the solar motion in the presence of dynamical perturbations altering the kinematics of the solar neighbourhood: does there exist in the solar neighbourhood a subset of stars having no net radial motion which can be used as a reference against which to measure the solar motion?