Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices

The importance of the promoter sequences in the function regulation of several important mycobacterial pathogens creates the necessity to design simple and fast theoretical models that can predict them. This work proposes two DNA promoter QSAR models based on pseudo-folding lattice network (LN) and star-graphs (SG) topological indices. In addition, a comparative study with the previous RNA electrostatic parameters of thermodynamically-driven secondary structure folding representations has been carried out. The best model of this work was obtained with only two LN stochastic electrostatic potentials and it is characterized by accuracy, selectivity and specificity of 90.87%, 82.96% and 92.95%, respectively. In addition, we pointed out the SG result dependence on the DNA sequence codification and we proposed a QSAR model based on codons and only three SG spectral moments.     

Plant-soil interactions in a fertigated ‘Manzanilla de Sevilla’ olive orchard

Main processes governing the plant-soil interactions in adult olive (Olea europaea L.) trees under fertigation were studied to better understand the response of the trees to this agricultural practice widely used in new olive orchards. Our final objective was to obtain soundly based scientific evidences for a rational choice of the fertilizer dose. Measurements were made in a ‘Manzanilla de Sevilla’ olive orchard in which 200 g N, 400 g N and 600 g N per tree and irrigation period (T200, T400 and T600, respectively) of a 4N-1P-3K fertilizer were applied by fertigation for 5 years (1999–2003); a control treatment (unfertilized) was also established. Four years after the start of the experiment mean values of soil P and K concentrations were greater in the fertigation treatments than in the control. For K, concentrations increased with fertilizer dose. The profile of NO₃-N, P and K concentrations within the irrigation wetted zone was studied in 2003; in the top soil layer, the concentrations of the three elements increased with fertilizer dose, generally showing linear responses to the different doses; in deeper soil layers, concentrations also increased with fertigation, but to a lesser extent; the concentrations of NO₃-N, P and K recorded at 0.8–0.9 m depth in the soil of T600, together with observations of root distribution, were enough to suggest leaching losses and possible groundwater contamination. As a consequence of the higher soil nutrient availability, leaf N, P and K increased generally with dose. Leaf N deficiencies and low, but not deficient, leaf K levels were found in control trees in 2002 and 2003, as well as in T200 trees in 2003. Differences between treatments in shoot length, trunk circumference and canopy volume were not significant, for any studied year. Nevertheless, between February 1999 and November 2003 there was a significant increase in canopy volume with fertilizer dose. In 2003, fruit yield increased with fertilizer dose, as a consequence of an increase both in fruit number and weight. Cumulative yield for the experimental period also increased with fertilizer dose. These results are further evidence to confirm previous research made with the same experimental set-up: T400 for oil quality and T600 for table olive quality seem to be the most appropriate treatments, although there is a risk for leaching losses and the possibility of groundwater contamination with T600.     

Structure-activity relationship of wedelolactone analogues: structural requirements for inhibition of Na+, K+ -ATPase and binding to the central benzodiazepine receptor

Coumestans 2a-i, bearing different patterns of substitution in A- and D-rings, were synthesized and evaluated as inhibitors of kidney Na+, K+ -ATPase and ligands for the central benzodiazepine (BZP) receptor. The presence of a hydroxyl group in position 2 favours the effect on Na+, K+ -ATPase but decreases the affinity for the BZP receptor, allowing the design of more selective molecules than the natural wedelolactone. On the other hand, the presence of a catechol in ring D is important for the effect on both molecular targets.     

Host-mediated volatile polymorphism in a parasitic plant influences its attractiveness to pollinators

Host-plants can mediate the interactions between herbivores and their mutualists and also between parasitic plants and their mutualists. The present study reveals how a hemiparasitic plant parasitizing three host species gives rise to three distinct hemiparasite-host neighborhoods which differ in terms of volatile composition and pollinator attractiveness. The study was performed in a population of the mistletoe Tristerix verticillatus infecting three different species of hosts occurring in sympatry within a small area, thus exposing all individuals studied to similar abiotic conditions and pollinator diversity; we assessed the effect of hosts on the hemiparasites’ visual and olfactory cues for pollinator attraction. During the study period, the hemiparasite individuals were flowering but the hosts were past their flowering stage. We collected volatile organic compounds from the hemiparasite and its hosts, measured floral display characteristics and monitored bird and insect visitors to inflorescences of T. verticillatus. We showed that: (1) floral patches did not differ in terms of floral display potentially involved in the attraction of pollinators, (2) hosts and hemiparasites on each host were discriminated as distinct chemical populations in terms of their volatile chemical profiles, (3) insect visitation rates differed between hemiparasites parasitizing different hosts, and (4) volatile compounds from the host and the hemiparasite influenced the visitation of hemiparasite flowers by insects. The study showed that a species regarded as “ornithophilic” by its floral morphology was actually mostly visited by insects that interacted with its sexual organs during their visits and carried its pollen, and that host-specific plant-volatile profiles within the T. verticillatus population were associated with differential attractiveness to pollinating insects.     

Pathogenicity of hyphomycet fungi to aphids Aphis gossypii Glover and Myzus persicae (Sulzer) (Hemiptera: Aphididae)

The aphids Aphis gossypii and Myzus persicae are cosmopolitan, poliphagous and damage cultivated plants. The effects of the entomopathogenic fungi Beauveria bassiana (isolate IBCB 66), Metarhizium anisopliae (isolate IBCB 121), Paecilomyces fumosoroseus (isolate IBCB 141) and Lecanicillium (= Verticillium) lecanii (isolate JAB 02) on third instar nymphs of A. gossypii and M. persicae were evaluated in the laboratory at 25 degrees C, 70 +/- 10% RH and 12h photophase. The aphids were transferred to petri dishes with a foliar disk (cotton or pepper) with a layer of 1 cm tick of agar-water. The fungi were applied in a suspension containing 1.0 x 106 to 1.0 x 108 conidia/ml. In the control treatment 1 ml of sterilized water was added to the foliar disks. The mortality of aphids was evaluated daily. B. bassiana and M. anisopliae caused 100% mortality at the seventh day after inoculation, for both species. L. lecanii was the fungus that provided mortality later in the aphids and M. persicae was more susceptible to both fungi than A. gossypii.     

A new karyotype of an endangered primate species (Callicebus personatus) from the Brazilian Atlantic forests

The genus Callicebus has 28 species arranged in five groups: donacophilus, torquatus, moloch, cupreus and personatus. The personatus group occurs in the Brazilian Atlantic forests where it is isolated from the other Callicebus groups. The present paper is the first report on the karyotype of Callicebuspersonatus. We compared the karyotypes of C. personatus and C. nigrifrons utilizing the following classic banding techniques: G-, C-, NOR banding, G/C- and G/NOR sequential banding. The karyotype of C. personatus has 2n=44, while C. nigrifrons presented 2n=42. Both the species diverge in the diploid number in consequence of a rearrangement type centric fusion/fission. Our results support personatus as a valid group and the specific status for C. personatus and C. nigrifrons.     

Experimental vertical transmission of Piscirickettsia salmonis and in vitro study of attachment and mode of entrance into the fish ovum

Piscirickettsia salmonis is a pathogenic bacterial agent causing septicaemic disease in salmon. Since its isolation in Chile in 1989, P. salmonis has continually produced high mortality rates in salmon farms. Little information exists regarding the mechanisms of vertical transmission of this pathogen. Experimental vertical transmission was established in the present study by inoculation of male and female rainbow trout broodstock with P. salmonis. The bacterium was subsequently detected using indirect immunofluorescence in milt and coelomic fluid of the majority of inoculated broodstock (14/15). Bacteria were detected in the fry when 1 or both parents were inoculated, although none of the infected fry presented signs of the disease. P. salmonis was also detected in progeny obtained through fertilisation ova from non-inoculated females incubated in a medium containing a bacterial suspension, demonstrating transmission during the process of fertilisation. Ova infected in vitro were examined at sample periods from 30 s to 60 min using scanning electron microscopy. This demonstrated that the bacterium attaches to the ova by means of membrane extensions, structures which we have called 'piscirickettsial attachment complex' (PAC) and which would allow later penetration into the ovum.     

Immunohistochemical analysis of Bin1/Amphiphysin II in human tissues: diverse sites of nuclear expression and losses in prostate cancer

The Bin1/Amphiphysin II gene encodes at least seven alternately spliced adapter proteins that have been implicated in membrane dynamics and nuclear processes. Nuclear localized Bin1 polypeptides have tumor suppressor and proapoptotic activities, suggesting that Bin1 may suppress cancer in tissues where nuclear expression may occur. One question is the extent to which human tissues express nuclear Bin1 isoforms. A secondary issue has been the need for a specific antibody that can detect all the splice isoforms expressed by the human, mouse, and rat Bin1 genes. Using a novel mouse monoclonal antibody with these characteristics, we performed an immunohistochemical analysis of Bin1 expression in a panel of normal human tissues. We also compared the expression profile of Bin1 in normal or malignant tissues derived from human prostate, where Bin1 is a candidate tumor suppressor gene. In brain, a distinct nuclear staining pattern overlapped with a cytosolic staining pattern present in certain layers of the cerebral cortex and cerebellum. Bone marrow cells displayed mainly nuclear localization whereas peripheral lymphoid cells exhibited mainly cytosolic localization. In several epithelial tissues, nuclear or nucleocytosolic staining patterns were displayed by basal cells in skin, breast, or prostate, whereas cytosolic or plasma membrane-associated staining patterns were noted in gastrointestinal cells. Interestingly, a striking gradient of expression was observed in gastrointestinal epithelia, particularly in the large intestine, with the strongest staining displayed by cells destined to undergo apoptosis at the villus tip. In prostate, Bin1 staining was frequently absent in cases of primary prostate adenocarcinoma. This study used a novel reagent to document the extent of expression of nuclear Bin1 isoforms, which exhibit cancer suppression and proapoptotic activity in human cells.     

On the mechanism of activation of the plasma membrane Ca2+-ATPase by ATP and acidic phospholipids

The activation of purified and phospholipid-depleted plasma membrane Ca2+-ATPase by phospholipids and ATP was studied. Enzyme activity increased with [ATP] along biphasic curves representing the sum of two Michaelis-Menten equations. Acidic phospholipids (phosphatidylinositol (PI) and phosphatidylserine (PS)) increased Vmax without affecting apparent affinities of the ATP sites. In the presence of 20 microm ATP, phosphorylation of the enzyme preincubated with Ca2+ (CaE1) was very fast (kapp congruent with 400 s-1). vo of phosphorylation of CaE1 increased with [ATP] along a Michaelis-Menten curve (Km of 15 microm) and was phospholipid-independent. Without Ca2+ preincubation (E1 + E2), vo of phosphorylation was also phospholipid-independent, but was slower and increased with [ATP] along biphasic curves. The high affinity component reflected rapid phosphorylation of CaE1, the low affinity component the E2 --> E1 shift, which accelerated to a rate higher than that of the ATPase activity when ATP was bound to the regulatory site. Dephosphorylation of EP did not occur without ATP. Dephosphorylation increased along a biphasic curve with increasing [ATP], showing that ATP accelerated dephosphorylation independently of phospholipid. PI, but not phosphatidylethanolamine (PE), accelerated dephosphorylation even in the absence of ATP. kapp for dephosphorylation was 57 s-1 at 0 microM ATP; that rate was further increased by ATP. Steady-state [EP] x kapp for dephosphorylation varied with [ATP], and matched the Ca2+-ATPase activity measured under the same conditions. Apparently, the catalytic cycle is rate-limited by dephosphorylation. Acidic phospholipids stimulate Ca2+-ATPase activity by accelerating dephosphorylation, while ATP accelerates both dephosphorylation and the conformational change from E2 to E1, further stimulating the ATPase activity.