Plant-induced cell death in the oomycete pathogen Phytophthora parasitica

The activation of programmed cell death in the host during plant-pathogen interactions is an important component of the plant disease resistance mechanism. In this study we show that activation of programmed cell death in microorganisms also regulates plant-pathogen interactions. We found that a form of vacuolar cell death is induced in the oomycete Phytophthora parasitica--the agent that causes black shank disease in Nicotiana tabacum--by extracellular stimuli from resistant tobacco. The single-celled zoospores underwent cell death characterized by dynamic membrane rearrangements, cell shrinkage, formation of numerous large vacuoles in the cytoplasm and degradation of cytoplasmic components before plasma membrane disruption. Phytophthora cell death required protein synthesis but not caspase activation, and was associated with the production of intracellular reactive oxygen species. This characterization of plant-mediated cell death signalling in pathogens will enhance our understanding of the biological processes regulating plant-pathogen interactions, and improve our ability to control crop diseases.     

Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

Background  

The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain.     

Polarized membrane expression of brush-border hydrolases in primary cultures of kidney proximal tubular cells depends on cell differentiation and is induced by dexamethasone

To analyze the influence of cell differentiation and the effects of hormones on the subcellular distribution of apical antigens in polarized epithelial cells, we have compared the localization of three brush border (BB) hydrolases [neutral endopeptidase (ENDO), aminopeptidase N (APN), and dipeptidylpeptidase IV (DPPIV)] in primary cultures of renal proximal tubule cells grown in various culture media. The degree of cell differentiation modulated by medium composition was estimated by measuring proximal functions, including glucose transport, specific enzymatic activities, and PTH responsiveness. In the dedifferentiated state observed in cells grown in 1% fetal calf serum (FCS)-supplemented medium, the three hydrolases are abnormally concentrated in a cytoplasmic vesicle compartment with weak expression on both membrane domains. By contrast, in serum-free hormonally defined medium (DM: insulin, 5 microgram/ml; dexamethasone, 5 x 10(-8) M), which markedly enhances morphological and functional cell differentiation, the distribution of hydrolases parallels that observed in the normal tubule. When added to the DM devoid of hormones, insulin has little polarizing effect, whereas dexamethasone dramatically increases the apical expression of the hydrolases, which then almost disappear from the basolateral membrane and cytoplasmic vesicular compartments. This glucocorticoid hormone augments the amount of immunoreactive antigen detectable on the apical domain in paraformaldehyde-fixed cells but does not change the total enzymatic activity. This suggests the presence in tubular cells of a dexamethasone-dependent polarizing machinery that requires de novo RNA and protein synthesis, and probably acts mainly by targeting a storage cytoplasmic pool of enzyme to the apical domain.     

Estimating synonymous and nonsynonymous substitution rates

Partitioning the total substitution rate into synnonymous and nonsynonymous components is a key aspect of many analyses in molecular evolution. Numerous methods exist for estimating these rates. However, until recently none of the estimation procedures were based on a sound statistical footing. In this paper, the evolutionary model of Muse and Gaut (1994) is used as the basis for two sets of parameters quantifying silent and replacement substitution rates. The parameters are shown to be equal when the four nucleotides are equally frequent and unequal otherwise. Maximum-likelihood estimation of these parameters is described, and the performance of these estimates is compared to that of existing estimation procedures. It is shown that the estimates of Nei and Gojobori (1986) are not unbiased for either set of parameters, although they provide very good estimates for one set as long as sequence divergence is not too high. However, some disturbing properties are found for the Nei and Gojobori estimates. In particular, it is shown that the expected value of the Nei and Gojobori estimate of silent substitution rate is a function of both the silent and replacement substitution rates. The maximum-likelihood estimates have no such problems.      

Loss of prion protein control of glucose metabolism promotes neurodegeneration in model of prion diseases

Corruption of cellular prion protein (PrP^C) function(s) at the plasma membrane of neurons is at the root of prion diseases, such as Creutzfeldt-Jakob disease and its variant in humans, and Bovine Spongiform Encephalopathies, better known as mad cow disease, in cattle. The roles exerted by PrP^C, however, remain poorly elucidated. With the perspective to grasp the molecular pathways of neurodegeneration occurring in prion diseases, and to identify therapeutic targets, achieving a better understanding of PrP^C roles is a priority. Based on global approaches that compare the proteome and metabolome of the PrP^C expressing 1C11 neuronal stem cell line to those of PrP^null-1C11 cells stably repressed for PrP^C expression, we here unravel that PrP^C contributes to the regulation of the energetic metabolism by orienting cells towards mitochondrial oxidative degradation of glucose. Through its coupling to cAMP/protein kinase A signaling, PrP^C tones down the expression of the pyruvate dehydrogenase kinase 4 (PDK4). Such an event favors the transfer of pyruvate into mitochondria and its conversion into acetyl-CoA by the pyruvate dehydrogenase complex and, thereby, limits fatty acids β-oxidation and subsequent onset of oxidative stress conditions. The corruption of PrP^C metabolic role by pathogenic prions PrP^Sc causes in the mouse hippocampus an imbalance between glucose oxidative degradation and fatty acids β-oxidation in a PDK4-dependent manner. The inhibition of PDK4 extends the survival of prion-infected mice, supporting that PrP^Sc-induced deregulation of PDK4 activity and subsequent metabolic derangements contribute to prion diseases. Our study posits PDK4 as a potential therapeutic target to fight against prion diseases.     

Recent lethal yellowing outbreak: why is the Malayan Yellow Dwarf Coconut no longer resistant in Jamaica?

In Jamaica, the Maypan, a hybrid of Malayan Yellow Dwarf (MYD) and Panama Tall coconut, previously considered highly resistant, is currently being devastated by an epidemic outbreak of lethal yellowing disease. There are several possible causes for this change. In this study, we checked that affected planting material in Jamaica is genetically the same as the material shown to be resistant. We compared the deoxyribonucleic acid (DNA) of MYD sampled in four locations in Jamaica with a reference DNA of the same cultivar collected in five different countries. The results of our analyses showed more variation at 34 simple sequence repeat loci in Jamaica than in the rest of the world providing clear evidence for the presence of about 16% of alleles that do not match the usual typical MYD genotype. These alleles appear to have already been present in the introduced germplasm. This rules out a possible cause of the new outbreak: The observed heterogeneity may have caused some loss of resistance but is insufficient to explain a massive outbreak of the disease.     

Effects of space allowance on the welfare of dry sows kept in dynamic groups and fed with an electronic sow feeder

The minimal legal space allowance for grouped pregnant sows in the EU is 2.25 m²/sow. The effect of higher space per animal on agonistic behaviour and social stress of animals living in dynamic groups is not known.Two groups of 34 pregnant Belgian Landrace sows were housed in two pens of respectively 102 m² (3 m²/sow) and 76.5 m² (2.25 m²/sow). Each sow lived there for 15 weeks. Sows were fed through an electronic sow feeder. According to the dynamic system, one third of each group (i.e. 11 or 12 nearly parturient sows) was replaced every 5 weeks by the same number of recently inseminated sows. Welfare indicators were collected during six of these 5 week-periods: performance, agonistic behaviour, skin lesion score and salivary cortisol. No differences were observed for production parameters, or for fighting activity. However, the mean number of one-way aggressions, when observed during 2 h-periods at 3 and 8 days after grouping, was significantly lower in the large pen than in the small one (respectively 16 ± 2 versus 26 ± 3, p < 0.01, and 10 ± 2 versus 20 ± 5, p < 0.05). The mean number of injuries was also lower with the 3 m² space allowance, when collected on the introduced sows one, 2 and 3 weeks after grouping. Some contradictory differences in salivary cortisol were noted 2 and 26 h after mixing, but without reaching statistical significance. An available area 33% higher than the EU legal minimum reduced agonistic behaviour and consecutive wounds and thus induced better welfare conditions for sows living in dynamic groups and fed with an electronic sow feeder. The impact on productivity and social physiological stress need further research.     

Predation by feral cats threatens great albatrosses

Biological Invasions - Feral cats (Felis catus) are a potential threat for several seabird species including medium sized albatrosses, but studies documenting predation behavior, demographic...     

Large scale mtDNA sequencing reveals sequence and functional conservation as major determinants of homoplasmic mtDNA variant distribution

The mitochondrial DNA (mtDNA) is highly variable, containing large numbers of pathogenic mutations and neutral polymorphisms. The spectrum of homoplasmic mtDNA variation was characterized in 730 subjects and compared with known pathogenic sites. The frequency and distribution of variants in protein coding genes were inversely correlated with conservation at the amino acid level. Analysis of tRNA secondary structures indicated a preference of variants for the loops and some acceptor stem positions. This comprehensive overview of mtDNA variants distinguishes between regions and positions which are likely not critical, mainly conserved regions with pathogenic mutations and essential regions containing no mutations at all.     

Comparison of otolith and scale readings for age and growth estimation of common dentex Dentex dentex

Three methods of age estimation were compared for Dentex dentex. Based on sectioned otoliths, scales appeared to be relevant only up to 5 years and whole otoliths up to 12 years. The maximum estimated age was 36 years, which constitutes to date the oldest age reported.