Expression patterns and association analysis of the porcine DHX58 gene

RIG-1 signalling is responsible for the detection of cytoplasmic viral RNA molecules. DEXH (Asp-Glu-X-His) box polypeptide 58 (encoded by DHX58) is a negative regulator of the RIG-1 signalling pathway. In human, the DHX58 gene can be upregulated and can inhibit the RIG-1 signalling pathway during viral infection. In this study, porcine DHX58 gene expression patterns were studied. According to our results, the porcine DHX58 gene was upregulated not only by the stimulation of Poly I:C but also by the stimulation of 1ipopolysaccharides (LPS). One polymorphism (g.4919G>C), detected in the ninth intron, was significantly associated with some blood parameters including the red cell distribution width of 1-day-old pigs and white blood cell counts, lymphocyte absolute counts, and platelet distribution width of 17-day-old pigs (P < 0.05). Moreover, the individuals with the genotype GG have a significantly higher mean white blood cell count than individuals with genotype CC or GC (P < 0.05). Our study indicates that DHX58 is an important gene that is associated with the immune response in swine.     

Floristic variation,chorological types and diversity: do they correspond at broad and local scales?

Abstract. The relationships between biogeographical patterns and local‐scale patterns based on microscale features, such as topoclimate, are well known in plant biogeography. Here we present a method of determining this correspondence using constrained ordination and correlations. We examined compositional gradients at two different scales, biogeographical chorotypes, and diversity. Compositional data (124 taxa × 113 plots) were sampled at four regularly spaced sites in south‐eastern Spain. Longitude (LONGI) was used as a spatial variable representing an east–west climate gradient, together with a radiation index (RADIN), elevation, and a disturbance indicator. All factors correlated with the compositional gradients, but the local‐topoclimate factor (RADIN) and the broad‐scale factor (LONGI) were most important. These two, spatially independent factors were both correlated with the two first ordination axes, and therefore should relate to the same general trend in species‐turnover. There was a significant Spearman's rank correlation between the species order along these two gradients. This is interpreted as an ecological self‐similar pattern, i.e. coenoclines repeating at different scales. A consistent order of species along local‐ and broad‐scale coenoclines may indicate that similar operational factors act at several scales, here related to moisture and temperature. The distribution of Mediterraneo–Macaronesian, Mediterraneo–Saharo–Arabian and Ibero–Maghribian species confirmed the correspondence between the broad‐ and local‐scale gradients. The former group decreases in number with increasing aridity along both gradients, whereas the two latter groups increase. A discordant pattern was found with south‐eastern Iberian endemics, but this may be explained by several of them being edaphic (saxicolous) specialists. There is a significant decrease in species richness with high radiation, but the expected increase along the longitudinal gradient from west (dry) to east (moist) was not statistically significant. This may be due to the correspondence between high richness and disturbance, both occurring in the middle of the broad‐scale gradient.     

Chromatographic separation of extruded iron-sulfur cores from the apoproteins of Clostridium pasteurianum and spinach ferredoxins in aqueous Triton X-100/urea

Iron-sulfur core extrusions from spinach [( 2Fe-2S]) and Clostridium pasteurianum (2[4Fe-4S]) ferredoxins in aqueous Triton X-100/urea containing excess benzenethiol yield quantitatively [FenSn(SPh)4]2- with n = 2 and n = 4, respectively. The iron-sulfur cluster can be separated from the corresponding apoprotein by rapid passage of the extrusion mixture over a small anaerobic column of Whatman DE-52 anion-exchange cellulose. Essentially quantitative recovery of [FenSn (SPh)4]2- is achieved in the eluate. The apoprotein remaining on the column can be eluted with 0.5 M NaCl. Most of the residual Triton X-100 and benzenethiol can be removed by passage of the apoprotein eluate over a small column of Bio-Beads SM-2, a hydrophobic polystyrene adsorbent. Apoprotein recovery is comparable to that obtained by other chromatographic methods. At least with spinach ferredoxin, the apoprotein prepared in this fashion can be reconstituted. The procedures developed in this work are potentially most applicable to selective removal of [2Fe-2S] and [4Fe-4S] centers from a multicenter enzyme without irreversible denaturation.     

Preparing nuclei from cells in monolayer cultures suitable for counting and for following synchronized cells through the cell cycle

A procedure is described for preparing nuclei from cells in monolayer culture so that they may be counted using an electronic particle counter. It takes only 10 to 15 min, and consists of swelling the cells in hypotonic buffer and then lysing them with the quaternary ammonium salt, ethylhexadecyldimethylammonium bromide. The cells are completely lysed, yielding a suspension of clean single nuclei which is stable, free of debris, and easily counted. The method was developed for a cell line of epithelial origin (MCF-7), which is often difficult to trypsinize to single cells. It works equally well at all cell densities up to and beyond confluence, and has been used with a variety of cells in culture, including 3T3 cells, bovine macrophages, rat mammary epithelial cells, mouse mammary tumor cell lines, and human fibroblasts. The size of the nuclei produced by this procedure is related to their DNA content, and the method is thus suitable for following cultures of synchronized cells through the cell cycle, and for performing differential counts of cells with substantial differences in DNA content.     

Analysis by electron microscopy of the variable segment in the maxi-circle of kinetoplast DNA from Trypanosoma brucei

The 20.5-kbp maxi-circle from the kinetoplast DNA of Trypanosoma brucei contains a 5-kbp segment which is not cut by most restriction endonucleases and which varies in size in closely-related trypanosome strains (Borst, P., Fase-Fowler, F., Hoeijmakers, J.H.J. and Frasch, A.C.C. (1980) Biochim. Biophys. Acta 610, 197–210). We have now analysed partial denaturation maps of the linearized maxi-circles by electron microscopy and find that the variable segment is not more AT-rich than the remainder of the maxi-circle. Early denaturation begins at two separate regions of the maxi-circle outside the variable region and one of these corresponds with the position of the gene for the large (12 S) ribosomal RNA. Denaturation-renaturation of maxi-circles leads to the formation of partially mismatched duplexes that look like underwound loops in electron micrographs. These loops are only found in the variable region and they vary in size and appearance. Under our renaturation conditions single-stranded maxi-circle DNA is devoid of secondary structure and this suggests that the underwound loops arise by misalignment of straight tandem repeats in the DNA. We have also analysed heteroduplexes between maxi-circles from two closely related T. brucei strains that differ by 1 kbp in the size of their variable segment. Most molecules had no underwound loops and contained mismatched regions in the variable segment only. The appearance of these regions is diverse, varying from fully duplex with two single-stranded loops to molecules with a heterogeneous array of smaller loops. The total size of single-stranded DNA in the heteroduplexes may be as high as 1.2 μm, i.e., a factor 4 higher than the size difference between the heteroduplex partners. We conclude that the variable region consists of imperfect tandem repeats of a sequence that evolves rapidly. This region might contain the origin of maxi-circle replication.     

The small-scale pattern of Cynodon dactylon in Mediterranean pastures

The abundance of Cynodon dactylon was recorded in 50 plots presenting different geomorphological conditions and along a transect of 16 500 2×2 cm contiguous quadrats within a small basin 330 m in length, in the granite pediment of the Sierra de Guadarrama (Central Spain). Soil analyses were undertaken on samples from the 50 plots and the soil information matrix obtained was analysed using Principal Components Analysis and Discriminant Analysis. Results showed that in the Mediterranean pastures Cynodon dactylon was restricted to deep, well developed soils with relatively high values of cations, conductivity and organic matter, and could be used as an indicator of such soil conditions in these grasslands. The spatial pattern of the species was analysed using New Local Variances which revealed the existence of a small-scale pattern, ranging from 8 to 18 cm, present at all levels of the analysis. The size of small-scale patterns was positively correlated with species abundance and was interpreted as a relation between plant vigour and favourable soil conditions.I would like to thank Professor González Bernáldez for his interest and encouragement.     

Entomofauna resource distribution associated with pig cadavers in Bogotá DC

A cadaver represents a temporal energy‐loaded resource, which provides arthropods with food, protection and a place in which to find a mate. Insects are usually the first organisms to discover and colonize a cadaver; as decomposition progresses, insects colonize cadavers in a predictable sequence. This work aimed to establish cadaverous entomofauna relationships with regard to stages of decomposition and environmental conditions using multiple correspondence analysis and thereby to identify the way in which insects distribute a perishable and changing resource. Entomofauna were thus collected in a semi‐rural area near Bogotá from the cadavers of three pigs (Sus scrofa L.) which had been shot. Environmental variables were recorded for each sampling. Multiple correspondence analyses were carried out for adult forms belonging to Diptera and Coleoptera families and stages of decomposition, and for Diptera and Coleoptera adult forms and environmental conditions. Stages of decomposition were a primary determining factor for structuring four guilds of entomofauna. However, environmental conditions influenced insect activity and were therefore a relevant factor in the structure of the entomofauna community. The results showed that the insects' distribution of available resources was related to changes in the stage of decomposition.     

Effect of long-term NPK application on secondary and micro nutrient contents ofCoffea canephora Pierre

Summary The Ca, Mg, S, Mn and Cu contents in leaves ofCoffea canephora trees selected in 64 plots under a 4×4×2 NPK trial were determined after seven years of fertilizer application. It was observed that NPK applications increased Mn uptake, P application increased the uptake of Cu, Ca and S while application of N and K did not enhance the uptake of Cu, Mg, Ca and S. It was shown that as a result of NPK applications, Ca and Mg had become deficient in coffee leaves, which corroborates earlier findings based on soil analysis.     

Variation in Volatile Leaf Oils of Eleven Eucalyptus Species Harvested from Korbous Arboreta (Tunisia)

Hydrodistillation of the dried leaves of eleven species of the genus Eucalyptus L 'Hér ., i.e., E. astringens Maiden , E. camaldulensis Dehnh ., E. diversifolia Bonpl ., E. falcata Turcz ., E. ficifolia F. Muell ., E. gomphocephala DC., E. lehmannii (Schauer ) Benth ., E. maculata Hook ., E. platypus Hook ., E. polyanthemos Schauer, and E. rudis Endl ., harvested from Korbous arboreta (region of Nabeul, northeast of Tunisia) in April 2006, afforded essential oils in yields varying from 0.1±0.1 to 3.8±0.1%, dependent on the species. E. astringens and E. ficifolia showed the highest and the lowest mean percentage of essential oil amongst all the species examined, respectively. Analysis by GC (RI) and GC/MS allowed the identification of 138 components, representing 74.0 to 99.1% of the total oil. The contents of the different samples varied according to the species. The main components were 1,8‐cineole, followed by trans‐pinocarveol ( 1 ), spathulenol ( 2 ), α‐pinene, p‐cymene, (E,E)‐farnesol, cryptone, globulol ( 3 ), β‐phellandrene, α‐terpineol, viridiflorol, and α‐eudesmol. The principal‐component and the hierarchical‐cluster analyses separated the eleven Eucalyptus leaf essential oils into seven groups, each constituting a chemotype.