Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo

MOTIVATION: Gene expression profiling is a powerful approach to identify genes that may be involved in a specific biological process on a global scale. For example, gene expression profiling of mutant animals that lack or contain an excess of certain cell types is a common way to identify genes that are important for the development and maintenance of given cell types. However, it is difficult for traditional computational methods, including unsupervised and supervised learning methods, to detect relevant genes from a large collection of expression profiles with high sensitivity and specificity. Unsupervised methods group similar gene expressions together while ignoring important prior biological knowledge. Supervised methods utilize training data from prior biological knowledge to classify gene expression. However, for many biological problems, little prior knowledge is available, which limits the prediction performance of most supervised methods. RESULTS: We present a Bayesian semi-supervised learning method, called BGEN, that improves upon supervised and unsupervised methods by both capturing relevant expression profiles and using prior biological knowledge from literature and experimental validation. Unlike currently available semi-supervised learning methods, this new method trains a kernel classifier based on labeled and unlabeled gene expression examples. The semi-supervised trained classifier can then be used to efficiently classify the remaining genes in the dataset. Moreover, we model the confidence of microarray probes and probabilistically combine multiple probe predictions into gene predictions. We apply BGEN to identify genes involved in the development of a specific cell lineage in the C. elegans embryo, and to further identify the tissues in which these genes are enriched. Compared to K-means clustering and SVM classification, BGEN achieves higher sensitivity and specificity. We confirm certain predictions by biological experiments. AVAILABILITY: The results are available at http://www.csail.mit.edu/~alanqi/projects/BGEN.html.     

Larval habits, host-plant associations, and speciation in nematine sawflies (Hymenoptera: Tenthredinidae)

Adaptive radiations consist of two intertwined processes, diversification of species and diversification of their ecological niches, but it is unclear whether there is a causal link between the processes. In phytophagous insects, ecological diversification mainly involves shifts in host-plant associations and in larval feeding habits (internal or external) on different plant parts, and several observations indicate that speciation is facilitated by host shifts. Data on host use in individual species suggest that internal feeders are less likely to colonize new hosts than external-feeding taxa and, consequently, increases in collective host ranges and species numbers should be slowed down in endophagous lineages. We tested these related hypotheses by using phylogenetic information to reconstruct the evolutionary history of larval resource use in the sawfly subfamily Nematinae, a group of 1000 plus species with a broad range of niches: the subfamily's combined host range includes over 20 plant families, and larvae may feed externally on leaves or needles, or internally, for example, in buds, fruits, leaves, or galls. The results show that: (1) Most internally feeding groups have evolved independently from external-feeding ancestors, but several distinct internal habits have appeared convergently multiple times; (2) Shifts among host taxa are clearly more common than changes in larval habits; (3) The majority of host switches have occurred among phylogenetically close plant groups, but many shifts are manifest among distantly related, ecologically proximate hosts; (4) Although external feeding characteristic of the common ancestor of Nematinae is associated with relatively high rates of host-shifting, internal feeders are very conservative in their host use; (5) In contrast, the effect of endophagy on speciation probabilities is more variable: net speciation rates are lowered in most internal-feeding groups, but a striking exception is found in species that induce galls on Salicaceae. The loose connection between collective host ranges and species diversity provides empirical support for theoretical models suggesting that speciation rates are a function of a complex interplay between "intrinsic" niche width and resource heterogeneity.     

Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine

The flavoenzyme proline dehydrogenase catalyzes the first step of proline catabolism, the oxidation of proline to pyrroline-5-carboxylate. Here we report the first crystal structure of an irreversibly inactivated proline dehydrogenase. The 1.9 A resolution structure of Thermus thermophilus proline dehydrogenase inactivated by the mechanism-based inhibitor N-propargylglycine shows that N5 of the flavin cofactor is covalently connected to the -amino group of Lys99 via a three-carbon linkage, consistent with the mass spectral analysis of the inactivated enzyme. The isoalloxazine ring has a butterfly angle of 25 degrees , which suggests that the flavin cofactor is reduced. Two mechanisms can account for these observations. In both, N-propargylglycine is oxidized to N-propargyliminoglycine. In one mechanism, this alpha,beta-unsaturated iminium compound is attacked by the N5 atom of the now reduced flavin to produce a 1,4-addition product. Schiff base formation between Lys99 and the imine of the 1,4-addition product releases glycine and links the enzyme to the modified flavin. In the second mechanism, hydrolysis of N-propargyliminoglycine yields propynal and glycine. A 1,4-addition reaction with propynal coupled with Schiff base formation between Lys99 and the carbonyl group tethers the enzyme to the flavin via a three-carbon chain. The presumed nonenzymatic hydrolysis of N-propargyliminoglycine and the subsequent rebinding of propynal to the enzyme make the latter mechanism less likely.     

Seasonal Rhythms of Body Temperature in the Free‐Ranging Raccoon Dog (Nyctereutes procyonoides) with Special Emphasis on Winter Sleep

The raccoon dog (Nyctereutes procyonoides) is the only canid with passive overwintering in areas with cold winters, but the depth and rhythmicity of wintertime hypothermia in the wild raccoon dog are unknown. To study the seasonal rhythms of body temperature (T_b), seven free‐ranging animals were captured and implanted with intra‐abdominal T_b loggers and radio‐tracked during years 2004–2006. The average size of the home ranges was 306±26 ha, and the average 24 h T_b was 38.0±<0.01°C during the snow‐free period (May–November). The highest and lowest T_b were usually recorded around midnight (21∶00–02∶00 h) and between 05∶00–11∶00 h, respectively, and the range of the 24 h oscillations was 1.2±0.01°C. The animals lost approximately 43±6% of body mass in winter (December–April), when the average size of the home ranges was 372±108 ha. During the 2–9‐wk periods of passivity in January–March, the average 24 h T_b decreased by 1.4–2.1°C compared to the snow‐free period. The raccoon dogs were hypothermic for 5 h in the morning (06∶00–11∶00 h), whereas the highest T_b values were recorded between 16∶00–23∶00 h. The range of the 24 h oscillations increased by approximately 0.6°C, and the rhythmicity was more pronounced than in the snow‐free period. The ambient temperature and depth of snow cover were important determinants of the seasonal T_b rhythms. The overwintering strategy of the raccoon dog resembled the patterns of winter sleep in bears and badgers, but the wintertime passivity of the species was more intermittent and the decrease in the T_b less pronounced.     

Relationships between polyamines, ethylene, osmoprotectants and antioxidant enzymes activities in wheat seedlings after short-term PEG- and NaCl-induced stresses

Contents of ethylene, osmoprotectants, levels and forms of polyamines (PAs) and activities of antioxidant enzymes in the leaves and roots were investigated for five wheat cultivar seedlings (differing in drought tolerance) exposed to osmotic stress (?1.5 MPa). Stress was induced by 2-day-long treatment of plants with polyethylene glycol 6000 (PEG) or NaCl added to hydroponic cultures. Nawra, Parabola and Manu cv. (drought tolerant) showed a marked increase in osmoprotectors (proline and soluble carbohydrates, mainly glucose, saccharose and maltose), free PAs (putrescine Put, spermidine Spd and spermine Spm) and Spd-conjugated levels, in both leaves and roots, after PEG-treatments. Radunia and Raweta (drought sensitive) exhibited smaller changes in the content of these substances. The analysis of enzymes involved in proline metabolism revealed the glutamate as a precursor of proline synthesis in PEG-induced stress conditions. The increase in the activity of antioxidative enzymes, especially catalase and peroxidases, was characteristic for tolerant wheat plants, but for sensitive ones, a decrease in superoxide dismutase and an increase in mainly glutathione reductase activities were observed. After NaCl-treatment smaller changes of all biochemical parameters were registered in comparison with PEG-induced stress. Exceptions were the higher values of ethylene content and a significant increase in saccharose, raffinose and maltose levels (only in stress sensitive plants). The proline synthesis pathway was stimulated from both glutamate and ornithine precursors. These results suggest that the accumulation of inorganic ions in NaCl-stressed plants may be involved in protective mechanisms as an additional osmoregultor. Thus, a weaker stressogenic effect as determined as water deficit by leaf relative water content and relative dry weight increase rate and differences in metabolite synthesis in comparison with PEG stress was observed. Proline seems to be the most important osmo-protector in osmotic stress initiated by both PEG and NaCl. The synthesis of sugars and PAs may be stimulated in a stronger stress conditions (PEG).     

ARLTS1 and Prostate Cancer Risk - Analysis of Expression and Regulation

Prostate cancer (PCa) is a heterogeneous trait for which several susceptibility loci have been implicated by genome-wide linkage and association studies. The genomic region 13q14 is frequently deleted in tumour tissues of both sporadic and familial PCa patients and is consequently recognised as a possible locus of tumour suppressor gene(s). Deletions of this region have been found in many other cancers. Recently, we showed that homozygous carriers for the T442C variant of the ARLTS1 gene (ADP-ribosylation factor-like tumour suppressor protein 1 or ARL11, located at 13q14) are associated with an increased risk for both unselected and familial PCa. Furthermore, the variant T442C was observed in greater frequency among malignant tissue samples, PCa cell lines and xenografts, supporting its role in PCa tumourigenesis. In this study, 84 PCa cases and 15 controls were analysed for ARLTS1 expression status in blood-derived RNA. A statistically significant (p = 0.0037) decrease of ARLTS1 expression in PCa cases was detected. Regulation of ARLTS1 expression was analysed with eQTL (expression quantitative trait loci) methods. Altogether fourteen significant cis-eQTLs affecting the ARLTS1 expression level were found. In addition, epistatic interactions of ARLTS1 genomic variants with genes involved in immune system processes were predicted with the MDR program. In conclusion, this study further supports the role of ARLTS1 as a tumour suppressor gene and reveals that the expression is regulated through variants localised in regulatory regions.     

Dysregulation of Complement System and CD4+ T Cell Activation Pathways Implicated in Allergic Response

Allergy is a complex disease that is likely to involve dysregulated CD4+ T cell activation. Here we propose a novel methodology to gain insight into how coordinated behaviour emerges between disease-dysregulated pathways in response to pathophysiological stimuli. Using peripheral blood mononuclear cells of allergic rhinitis patients and controls cultured with and without pollen allergens, we integrate CD4+ T cell gene expression from microarray data and genetic markers of allergic sensitisation from GWAS data at the pathway level using enrichment analysis; implicating the complement system in both cellular and systemic response to pollen allergens. We delineate a novel disease network linking T cell activation to the complement system that is significantly enriched for genes exhibiting correlated gene expression and protein-protein interactions, suggesting a tight biological coordination that is dysregulated in the disease state in response to pollen allergen but not to diluent. This novel disease network has high predictive power for the gene and protein expression of the Th2 cytokine profile (IL-4, IL-5, IL-10, IL-13) and of the Th2 master regulator (GATA3), suggesting its involvement in the early stages of CD4+ T cell differentiation. Dissection of the complement system gene expression identifies 7 genes specifically associated with atopic response to pollen, including C1QR1, CFD, CFP, ITGB2, ITGAX and confirms the role of C3AR1 and C5AR1. Two of these genes (ITGB2 and C3AR1) are also implicated in the network linking complement system to T cell activation, which comprises 6 differentially expressed genes. C3AR1 is also significantly associated with allergic sensitisation in GWAS data.     

Evolution of Camouflage Drives Rapid Ecological Change in an Insect Community

1. Download : Download high-res image (465KB)
2. Download : Download full-size image

     

The impact of the receptor binding profiles of the vascular endothelial growth factors on their angiogenic features

Background

Vascular endothelial growth factors (VEGFs) are potential therapeutic agents for treatment of ischemic diseases. Their angiogenic effects are mainly mediated through VEGF receptor 2 (VEGFR2).

Methods

Receptor binding, signaling, and biological efficacy of several VEGFR2 ligands were compared to determine their characteristics regarding angiogenic activity and vascular permeability.

Results

Tested VEGFR2 ligands induced receptor tyrosine phosphorylation with different efficacy depending on their binding affinities. However, the tyrosine phosphorylation pattern and the activation of the major downstream signaling pathways were comparable. The maximal angiogenic effect stimulated by different VEGFR2 ligands was dependent on their ability to bind to co-receptor Neuropilin (Nrp), which was shown to form complexes with VEGFR2. The ability of these VEGFR2 ligands to induce vascular permeability was dependent on their concentration and VEGFR2 affinity, but not on Nrp binding.

Conclusions

VEGFR2 activation alone is sufficient for inducing endothelial cell proliferation, formation of tube-like structures and vascular permeability. The level of VEGFR2 activation is dependent on the binding properties of the ligand used. However, closely similar activation pattern of the receptor kinase domain is seen with all VEGFR2 ligands. Nrp binding strengthens the angiogenic potency without increasing vascular permeability.

General significance

This study sheds light on how different structurally closely related VEGFR2 ligands bind to and signal via VEGFR2/Nrp complex to induce angiogenesis and vascular permeability. The knowledge of this study could be used for designing VEGFR2/Nrp ligands with improved therapeutic properties.     

Reciprocal diversification in a complex plant-herbivore-parasitoid food web

Background  

Plants, plant-feeding insects, and insect parasitoids form some of the most complex and species-rich food webs. According to the classic escape-and-radiate (EAR) hypothesis, these hyperdiverse communities result from coevolutionary arms races consisting of successive cycles of enemy escape, radiation, and colonization by new enemy lineages. It has also been suggested that "enemy-free space" provided by novel host plants could promote host shifts by herbivores, and that parasitoids could similarly drive diversification of gall form in insects that induce galls on plants. Because these central coevolutionary hypotheses have never been tested in a phylogenetic framework, we combined phylogenetic information on willow-galling sawflies with data on their host plants, gall types, and enemy communities.