Benchmarking B cell epitope prediction: underperformance of existing methods

Sequence profiling is used routinely to predict the location of B-cell epitopes. In the postgenomic era, the need for reliable epitope prediction is clear. We assessed 484 amino acid propensity scales in combination with ranges of plotting parameters to examine exhaustively the correlation of peaks and epitope location within 50 proteins mapped for polyclonal responses. After examining more than 10(6) combinations, we found that even the best set of scales and parameters performed only marginally better than random. Our results confirm the null hypothesis: Single-scale amino acid propensity profiles cannot be used to predict epitope location reliably. The implication for studies using such methods is obvious.     

alpha-Synuclein, oxidative stress and apoptosis from the perspective of a yeast model of Parkinson's disease

The neuronal protein α-synuclein (α-syn) has been suggested to be one of the factors linked to Parkinson's disease (PD). Several organisms, including the rat, mouse, worm, and fruit fly, are being used to study α-syn pathobiology. A new model organism was recently added to this armamentarium: the budding yeast Saccharomyces cerevisiae . The yeast system recapitulates many of the findings made with higher eukaryotes. For example, yeast cells expressing α-syn accumulate lipid droplets, have vacuolar/lysosomal defects, and exhibit markers of apoptosis, including the externalization of phosphatidylserine, the release of cytochrome c , and the accumulation of reactive oxygen species. This MiniReview focuses on the mechanisms by which α-syn induces oxidative stress and the mechanisms by which yeast cells respond to this stress. Three classes of therapeutics are discussed.     

THE PERFORMANCE OF SPRAY‐IRRIGATED ULVA LACTUCA (ULVOPHYCEAE,CHLOROPHYTA) AS A CROP AND AS A BIOFILTER OF FISHPOND EFFLUENTS1

The seaweed Ulva lactuca L. was spray cultured by mariculture effluents in a mattress‐like layer, held in air on slanted boards by plastic netting. Air‐agitated seaweed suspension tanks were the reference. Growth rate, yield, and ammonia‐N removal rate were 11.8% · d^?1, 171 g fresh weight (fwt) · m^?2 · d^?1, and 5 g N · m^?2 · d^?1, respectively, by the spray‐cultured U. lactuca, and 16.9% · d^?1, 283 g fwt · m^?2 · d^?1, and 7 g N · m^?2 · d^?1, respectively, by the tank U. lactuca. Biomass protein content was similar in both treatments. Dissolved oxygen in the fishpond effluent water was raised by >3 mg · L^?1 and pH by up to half a unit, upon passage through both culture systems. The data suggest that spray‐irrigation culture of U. lactuca in this simple green‐mattress‐like system supplies the seaweed all it needs to grow and biofilter at rates close to those in standard air‐agitated tank culture.     

Ostracods and the Holocene palaeolimnology of Lake Qarun, with special reference to past human–environment interactions in the Faiyum (Egypt)

We present an ostracod record covering the past two millennia from an 8.25-m core taken from Lake Qarun, in the Faiyum Depression of Egypt. The occurrence of ostracod species in the lake is controlled primarily by variations in solute composition, which are in turn related to shifts in catchment land use. At times when the Faiyum Depression supported thriving agriculture, lake water contained Na⁺–Cl^? brine, and Cyprideis torosa dominated the ostracod assemblage. When the Faiyum Depression experienced periods of environmental and economic decline, lake water contained Na⁺–HCO₃ ^? brine, and Limnocythere inopinata dominated. The relative abundance of other ostracod species provides additional information about past conditions in Lake Qarun including salinity and lake level changes. Overall, the ostracod assemblages provide evidence for human influences in the Faiyum, which extend back before instrumental or detailed observational records began.     

Recovery Deficiency Following Tree Mortality in Mangroves of Two Caribbean Islands: Field Survey and Statistical Classification

Mangrove species are well adapted to the harsh ecological conditions of their environment throughout the tropics. However, in the islands of Guadeloupe and Martinique (Lesser Antilles), deficient forest recovery was evidenced in 43 mangrove sites (>1000 m²) affected by apparently natural tree mortality. Such sites were recorded from four chronological sets of aerial photographs between 1950 and 1995, and field-investigated in terms of environment and vegetation characteristics. Given the speculative relationship between the slow-regenerating vegetation and its present environment within non-steady state, disturbed sites, statistical analyses arbitrarily matching physicochemical and biological data were primarily avoided. On one hand, principal component analysis (PCA), combined with an agglomerative hierarchical classification, was performed on environmental, rank-ordered data; on the other hand, multidimensional scaling (MDS) was implemented on vegetation data. Discriminant analyses (DA) further characterized the environment/vegetation interrelationships for each site type. Ultimately, three main types of mortality sites have been distinguished among the study areas. One type clustered the sites showing the lowest salinity values and the highest surge vulnerability whose dominant mangrove species is Rhizophora. Another type presented highly saline sites having clayey soils with pure, stunted, Avicennia stands. The last type consisted of peculiar forest gaps on deep, compact, peat soils. During the rainy season, these sites turned into shallow ponds scattered with living, young Rhizophora and large, standing, dead Avicennia. The authors suggest that this classification may serve as a comprehensive framework to test subsequent hypotheses (hurricanes, droughts…) on the origins of natural massive tree mortality and the causes of recovery deficiency in mangroves of the Caribbean.     

Spatial and temporal profiles for anti-inflammatory gene expression in leukocytes during a resolving model of peritonitis

The recent appreciation of the role played by endogenous counterregulatory mechanisms in controlling the outcome of the host inflammatory response requires specific analysis of their spatial and temporal profiles. In this study, we have focused on the glucocorticoid-regulated anti-inflammatory mediator annexin 1. Induction of peritonitis in wild-type mice rapidly (4 h) produced the expected signs of inflammation, including marked activation of resident cells (e.g., mast cells), migration of blood-borne leukocytes, mirrored by blood neutrophilia. These changes subsided after 48-96 h. In annexin 1(null) mice, the peritonitis response was exaggerated ( approximately 40% at 4 h), with increased granulocyte migration and cytokine production. In blood leukocytes, annexin 1 gene expression was activated at 4, but not 24, h postzymosan, whereas protein levels were increased at both time points. Locally, endothelial and mast cell annexin 1 gene expression was not detectable in basal conditions, whereas it was switched on during the inflammatory response. The significance of annexin 1 system plasticity in the anti-inflammatory properties of dexamethasone was assessed. Clear induction of annexin 1 gene in response to dexamethasone treatment was evident in the circulating and migrated leukocytes, and in connective tissue mast cells; this was associated with the steroid failure to inhibit leukocyte trafficking, cytokine synthesis, and mast cell degranulation in the annexin 1(null) mouse. In conclusion, understanding how inflammation is brought under control will help clarify the complex interplay between pro- and anti-inflammatory pathways operating during the host response to injury and infection.     

Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models

Background  

The binding between peptide epitopes and major histocompatibility complex proteins (MHCs) is an important event in the cellular immune response. Accurate prediction of the binding between short peptides and the MHC molecules has long been a principal challenge for immunoinformatics. Recently, the modeling of MHC-peptide binding has come to emphasize quantitative predictions: instead of categorizing peptides as "binders" or "non-binders" or as "strong binders" and "weak binders", recent methods seek to make predictions about precise binding affinities.     

Anti-inflammatory drugs, eicosanoids and the annexin A1/FPR2 anti-inflammatory system

The action of anti-inflammatory and anti-allergic drugs on the eicosanoid system is briefly reviewed. In addition to the aspirin-like drugs, which directly inhibit the cyclo-oxygenase enzymes, other drugs such as the glucocorticoids and the cromones also inhibit the formation of eicosanoids. In the latter cases this is bought about through the release of a protein factor that acts through formyl peptide receptors on the target cell surface. Of growing interest, is the observation that this receptor is also a target for other eicosanoids, such as lipoxins and resolvins that modulate host defence systems.     

基因芯片技术在拟南芥研究中的应用

基因芯片是研究生物大分子功能的新技术,目前此技术已经广泛地应用到植物研究中。拟南芥是植物分子生物学领域的模式植物,通过对其基因结构及功能的详尽研究,可以更好地理解和认识遗传上更为复杂的高等植物的生长和发育过程。本综述了基因芯片在模式植物拟南芥研究中的应用。