An ordered EST catalogue and gene expression profiles of cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis>) at key growth stages

A cDNA library was constructed from the root tissues of cassava variety Huanan 124 at the root bulking stage. A total of 9,600 cDNA clones from the library were sequenced with single-pass from the 5′-terminus to establish a catalogue of expressed sequence tags (ESTs). Assembly of the resulting EST sequences resulted in 2,878 putative unigenes. Blastn analysis showed that 62.6% of the unigenes matched with known cassava ESTs and the rest had no ‘hits’ against the cassava database in the integrative PlantGDB database. Blastx analysis showed that 1,715 (59.59%) of the unigenes matched with one or more GenBank protein entries and 1,163 (40.41%) had no ‘hits’. A cDNA microarray with 2,878 unigenes was developed and used to analyze gene expression profiling of Huanan 124 at key growth stages including seedling, formation of root system, root bulking, and starch maturity. Array data analysis revealed that (1) the higher ratio of up-regulated ribosome-related genes was accompanied by a high ratio of up-regulated ubiquitin, proteasome-related and protease genes in cassava roots; (2) starch formation and degradation simultaneously occur at the early stages of root development but starch degradation is declined partially due to decrease in UDP-glucose dehydrogenase activity with root maturity; (3) starch may also be synthesized in situ in roots; (4) starch synthesis, translocation, and accumulation are also associated probably with signaling pathways that parallel Wnt, LAM, TCS and ErbB signaling pathways in animals; (5) constitutive expression of stress-responsive genes may be due to the adaptation of cassava to harsh environments during long-term evolution.     

Neurons and Neuronal Stem Cells Survive in Glucose-Free Lactate and in High Glucose Cell Culture Medium During Normoxia and Anoxia

Several questions concerning the survival of isolated neurons and neuronal stem and progenitor cells (NPCs) have not been answered in the past: (1) If lactate is discussed as a major physiological substrate of neurons, do neurons and NPCs survive in a glucose-free lactate environment? (2) If elevated levels of glucose are detrimental to neuronal survival during ischemia, do high concentrations of glucose (up to 40 mmol/L) damage neurons and NPCs? (3) Which is the detrimental factor in oxygen glucose deprivation (OGD), lack of oxygen, lack of glucose, or the combination of both? Therefore, in the present study, we exposed rat cortical neurons and NPCs to different concentrations of d-glucose ranging from 0 to 40 mmol/L, or 10 and 20 mmol/L l-lactate under normoxic and anoxic conditions, as well as in OGD. After 24 h, we measured cellular viability by biochemical assays and automated cytochemical morphometry, pH values, bicarbonate, lactate and glucose concentrations in the cell culture media, and caspases activities. We found that (1) neurons and NPCs survived in a glucose-free lactate environment at least up to 24 h, (2) high glucose concentrations >5 mmol/L had no effect on cell viability, and (3) cell viability was reduced in normoxic glucose deprivation to 50% compared to 10 mmol/L glucose, whereas cell viability in OGD did not differ from that in anoxia with lactate which reduced cell viability to 30%. Total caspases activities were increased in the anoxic glucose groups only. Our data indicate that (1) neurons and NPCs can survive with lactate as exclusive metabolic substrate, (2) the viability of isolated neurons and NPCs is not impaired by high glucose concentrations during normoxia or anoxia, and (3) in OGD, low glucose concentrations, but not low oxygen levels are detrimental for neurons and NPCs.     

Spatial dynamics of Norwegian tetraonid populations

Different species in a given site or population of a given species in different sites may fluctuate in synchrony if they are affected similarly by factors such as spatially autocorrelated climate, predation, or by dispersal between populations of one species. We used county wise time series of hunting bag records of four Norwegian tetraonid species covering 24 years to examine patterns of interspecific and intraspecific synchrony. We estimated synchrony at three spatial scales; national, regional (consisting of counties with similar climate), and county level. Ecologically related species with overlapping distributions exhibited strong synchrony across Norway, but there was much variation between the different regions and counties. Regions with a long coastline to both the North Sea and the Norwegian Ocean exhibited an overall stronger synchrony than those consisting of more continental areas. Intraspecific synchrony was generally low across all counties, but stronger synchrony between counties within regions defined by climatic conditions. Synchrony was negatively related to distance between populations in three of four species. Only the synchrony in willow ptarmigan showed a clear negative relationship with distance, while the other species had both strong positive and negative correlations at short distances. Strong interspecific synchrony between some species pairs within regions and weak intraspecific synchrony across counties within regions suggest a stronger synchronizing effect from environmental factors such as weather or predation and less effect from dispersal. Our results suggest that the complete tetraonid community is structured by environmental factors affecting the different species similarly and causes widespread interspecific synchrony. Local factors affecting the population dynamics nevertheless frequently forces neighbouring populations out of phase.     

Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets

Background  

Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein is natively unfolded requires laborious experimental investigations, then reliable sequence-only methods for predicting whether a sequence corresponds to a folded or to an unfolded protein are of interest in fundamental and applicative studies. Many proteins have amino acidic compositions compatible both with the folded and unfolded status, and belong to a twilight zone between order and disorder. This makes difficult a dichotomic classification of protein sequences into folded and natively unfolded ones. In this work we propose an operational method to identify proteins belonging to the twilight zone by combining into a consensus score good performing single predictors of folding.     

WAMI: a web server for the analysis of minisatellite maps

Background  

Minisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time.     

Ivermectin-dependent release of IL-1beta in response to ATP by peritoneal macrophages from P2X<Subscript>7</Subscript>-KO mice

The response to ATP of peritoneal macrophages from wild-type (WT) and P2X₇-invalidated (KO) mice was tested. Low concentrations (1–100 μM) of ATP transiently increased the intracellular concentration of calcium ([Ca²⁺]_i) in cells from both mice. The inhibition of the polyphosphoinositide-specific phospholipase C with U73122 inhibited this response especially in WT mice suggesting that the responses coupled to P2Y receptors were potentiated by the expression of P2X₇ receptors. One millimolar ATP provoked a sustained increase in the [Ca²⁺]_i only in WT mice. The response to 10 μM ATP was potentiated and prolonged by ivermectin in both mice. One millimolar ATP increased the influx of extracellular calcium, decreased the intracellular concentration of potassium ([K⁺]_i) and stimulated the secretion of interleukin-1β (IL-1β) only in cells from WT mice. Ten micromolar ATP in combination with 3 μM ivermectin reproduced these responses both in WT and KO mice. The secretion of IL-1β was also increased by nigericin in WT mice and the secretory effect of a combination of ivermectin with ATP in KO mice was suppressed in a medium containing a high concentration of potassium. In WT mice, 150 μM BzATP stimulated the uptake of YOPRO-1. Incubation of macrophages from WT and KO mice with 10 μM ATP resulted in a small increase of YOPRO-1 uptake, which was potentiated by addition of 3 μM ivermectin. The uptake of this dye was unaffected by pannexin-1 blockers. In conclusion, prolonged stimulation of P2X₄ receptors by a combination of low concentrations of ATP plus ivermectin produced a sustained activation of the non-selective cation channel coupled to this receptor. The ensuing variations of the [K⁺]_i triggered the secretion of IL-1β. Pore formation was also triggered by activation of P2X₄ receptors. Higher concentrations of ATP elicited similar responses after binding to P2X₇ receptors. The expression of the P2X₇ receptors was also coupled to a better response to P2Y receptors.     

A comparative analysis of the complete mitochondrial genome of the Eurasian otter <Emphasis Type="Italic">Lutra lutra</Emphasis> (Carnivora; Mustelidae)

Otter populations are declining throughout the world and most otter species are considered endangered. Molecular methods are suitable tools for population genetic research on endangered species. In the present study, we analyzed the complete mitochondrial genome (mitogenome) sequence of the Eurasian otter Lutra lutra. The mitochondrial DNA sequence of the Eurasian otter is 16,505 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (CR). The CR sequence of otters from Europe and Asia showed nearly identical numbers and nucleotide sequences of minisatellites. Phylogenetic analysis of Mustelidae mitogenomes, including individual genes, revealed that Lutrinae and Mustelinae form a clade, and that L. lutra and Enhydra lutris are sister taxa within the Lutrinae. Phylogenetic analyses revealed that of the 13 mitochondrial protein-coding genes, ND5 is the most reliable marker for analysis of phylogenetic relationships within the Mustelidae.     

The role of the soil seed and seedling bank in the regeneration of diverse plant communities in the subtropical Ailao Mountains,Southwest China

We compared species composition and diversity of the soil seed and seedling banks in three secondary vegetation types (shrubland, Populus bonatii forest, Lithocarpus regrowth forest) and a primary old-growth forest in the subtropical Ailao Mountains of southwestern China to clarify the importance of seed and seedling banks for forest dynamics. The average species richness was the highest in soil samples from the shrubland (26.80 ± 1.98), and the lowest from the primary forest (9.93 ± 0.50). The density of germinable tree seeds increased from the secondary vegetation to the primary forest, and the density of shrub, forb, and graminoid seeds decreased significantly. The most abundant seedlings recorded in soil samples were light-demanding species in the shrubland and Populus bonatii forest. For ground flora, the number of shrub seedlings strongly decreased with the increase in stand age, and shade-tolerant tree seedlings tended to increase. The species similarity between the seed bank and the aboveground vegetation in all sites was low (Sørensen’s index = 0.11–0.33), however, the shrubland had higher similarity compared with the other three plant communities. In the primary forest, light-demanding woody species dominated in soil seed banks, while shade-tolerant species dominated in the overstory and the forest floor. In the primary forest, seedlings of dominant tree species were rare in the understory, and no seeds of the dominant species were found in the soil. Results indicated that the early stages of vegetation recovery should take into account the possibility of recovering soil seed bank processes. However, colonization and establishment of tree seedlings will be difficult once a primary forest is destroyed.     

The Content of Elements in Rainwater and its Relation to the Frequency of Hospitalization for Diabetes and Obesity in Opole Voivodship,Poland, During 2000–2002

Environmental factors significantly influence the incidence and course of metabolic syndrome diseases such as diabetes and obesity. The content of elements in rainwater is an indirect indicator of their presence in dust suspended in the air. In this paper we present the relationships between the content of selected elements in rainwater and hospitalization frequencies due to diabetes (E10–E13) and obesity (E66). It was assumed that the hospitalization frequency could be taken as a measure of deterioration of the metabolic process in the course of diabetes and its complications. The observations concerned the population of Opole Voivodeship, Poland (one million inhabitants), distributed in small communities of 44,000 to 151,000 inhabitants during the years 2000–2002. In cases of diabetes E10–E13 for all subjects relevant correlation indicators were found for chromium (r = 0.71), cadmium (r = 0.65), and lead (r = 0.66). Borderline relevance was seen for copper (r = 0.57) and zinc (r = 056). For diabetic men the statistically relevant correlations were chromium (r = 0.79), lead (r = 0.77), cadmium (r = 0.74), copper (r = 0.70), chloride (r = 0.69), zinc (r = 0.68), and iron (r = 0.64). For women the only relevant correlations were chromium (r = 0.62) and cadmium (r = 0.55). No significant correlations were found in obese individuals of both sexes.