Identification and characterization of a well-defined series of coronatine biosynthetic mutants of Pseudomonas syringae pv. tomato DC3000

To identify Pseudomonas syringae pv. tomato genes involved in pathogenesis, we carried out a screen for Tn5 mutants of P. syringae pv. tomato DC3000 with reduced virulence on Arabidopsis thaliana. Several mutants defining both known and novel virulence loci were identified. Six mutants contained insertions in biosynthetic genes for the phytotoxin coronatine (COR). The P. syringae pv. tomato DC3000 COR genes are chromosomally encoded and are arranged in two separate clusters, which encode enzymes responsible for the synthesis of coronafacic acid (CFA) or coronamic acid (CMA), the two defined intermediates in COR biosynthesis. High-performance liquid chromatography fractionation and exogenous feeding studies confirmed that Tn5 insertions in the cfa and cma genes disrupt CFA and CMA biosynthesis, respectively. All six COR biosynthetic mutants were significantly impaired in their ability to multiply to high levels and to elicit disease symptoms on A. thaliana plants. To assess the relative contributions of CFA, CMA, and COR in virulence, we constructed and characterized cfa6 cmaA double mutant strains. These exhibited virulence phenotypes on A. thalliana identical to those observed for the cmaA or cfa6 single mutants, suggesting that reduced virulence of these mutants on A. thaliana is caused by the absence of the intact COR toxin. This is the first study to use biochemically and genetically defined COR mutants to address the role of COR in pathogenesis.     

Mazahua ethnobotany and subsistence in the monarch butterfly biosphere reserve, Mexico

This is the first report on Mazahua knowledge and classification of plants and mushrooms and the roles of these resources in the local economy in the Monarch Butterfly Biosphere Reserve, Mexico. A total of 213 useful plant species and 31 species of edible mushrooms were recorded. Fruits ofPrunus serotina, Rubus liebmanii, andCrataegus mexicana were the main wild fruit gathered by people (7.47, 4.40, and 1.82 tons of fruits per year, respectively), whereas their availability in the territory of the village was approximately 302.6, 6.0, and 34.188 tons.Brassica campestris, Rorippa nasturtium-aquaticum, Chenopodium berlandieri, and Amaranthus hybridus were the principal non-cultivated greens consumed by people (4.3, 0.5, 0.7, and 0.9 tons per year, while 23.6, 3.78, traces, and 46.0 tons, respectively, were available). Extraction of medicinal plants is low but gathering ofTernstroemia spp. flowers endangers local populations of these plants. All households of the village used fuelwood (1,767.2 tons per year), mainly of pine and oak species. Strategies for sustainable use of these resources are discussed     

Nest Defence Behaviour and Testosterone Levels in Female Pied Flycatchers

Nesting holes are a scarce resource for obligated cavity‐nesting birds and an important selective force for the evolution of aggressive female behaviours, which may be mediated by testosterone (T) levels. It is known that during periods of intense intrasexual competition such as initial breeding stages, females are highly aggressive towards intruding females. Here, we studied the implications of T levels for female–female competition by comparing levels of aggressiveness towards simulated female intruders (decoys) in two populations of the pied flycatcher (Ficedula hypoleuca) with a marked difference in breeding density. To this end, we exposed free‐living females to simulated territorial intrusions during 30 min when nest construction was almost complete. T levels of females were measured at the beginning of incubation under the assumption that they are positively associated with T levels during nest building. We also related aggressiveness to T levels in both populations. Furthermore, we aimed at detecting whether variation of T levels may explain female incubation attendance. Females showed higher T levels in the populations where pied flycatchers were exposed to a higher likelihood of conspecific interactions (high breeding density) than in the population with low breeding density. Female territorial presence, vigilance at the nest box and proximity to decoys were negatively related to circulating T levels in the high‐density population, but not in the low‐density population. Differences in T levels between populations did not result in differences in female incubation attendance, but T levels were negatively related to the incubation attendance in females from the population showing high T levels. In our populations, T levels in females prior to laying reflect the need to defend nesting cavities which is higher at high breeding density and in subdominant females. High T levels are costly in terms of incubation attendance.     

Gilthead seabream (Sparus aurata L.) innate immune response after dietary administration of heat-inactivated potential probiotics

The effects of the dietary administration of two heat-inactivated whole bacteria from the Vibrionaceae family, singly or combined, on innate immune response of the seabream were studied. The two bacteria (Pdp11 and 51M6), which were obtained from the skin of gilthead seabream, showed in vitro characteristics that suggested they could be considered as potential fish probiotics. The fish were fed four different diets: control (non-supplemented), or diets supplemented with heat-inactivated bacteria at 10(8) cfu g(-1) Pdp11, 10(8) cfu g(-1) 51M6 or with 0.5 x 10(8) cfu g(-1) Pdp11 plus 0.5 x 10(8) cfu g(-1) 51M6 for 4 weeks. Six fish were sampled at weeks 1, 2, 3 and 4, when the main humoral (natural haemolytic complement activity and serum peroxidase content) and cellular innate immune responses (leucocyte peroxidase content, phagocytosis, respiratory burst and cytotoxicity) were evaluated. The serum peroxidase content and the natural haemolytic complement activity increased with time, reaching the highest values in the third and fourth weeks of feeding, respectively. The phagocytic ability of specimens fed the mixture of the two inactivated bacteria was significantly higher than in the controls after 2 and 3 weeks of treatment. The same activity increased significantly in seabream fed the Pdp11 diet for 2 weeks or the 51M6 diet for 3 weeks. Respiratory burst activity was unaffected by all the experimental diets at all times assayed. Cytotoxic activity had significantly increased after 3 weeks in fish fed the 51M6 diet. These results are discussed in terms of the usefulness of incorporating inactivated probiotic bacteria into fish diets.     

Diadenosine tetraphosphate contributes to carbachol-induced tear secretion

The purpose of this study is to investigate if the cholinergic stimulation by carbachol on tear secretion is a direct process or if it is also mediated by purinergic mechanisms. Experiments were performed in New Zealand male rabbits. The amount of tear secretion was measured with Schirmer’s test and then analyzed by a HPLC protocol in order to study the nucleotide levels. Animal eyes were instilled with carbachol (a cholinergic agonist), pirenzepine, gallamine and 4-DAMP (muscarinic antagonists), PPADS, suramin and reactive blue 2 (purinergic antagonists), and a P2Y₂ receptor small interfering RNA (siRNA). Tear secretion increased with the instillation of carbachol, approximately 84 % over control values 20 min after the instillation and so did Ap₄A and ATP release. When we applied carbachol in the presence of muscarinic antagonists, tear volume only increased to 4 % with atropine, 12 % in the case of pirenzepine, 3 % with gallamine, and 8 % with 4-DAMP. In the presence of carbachol and purinergic antagonists, tear secretion was increased to 12 % (all values compared to basal tear secretion). By analyzing tear secretion induced with carbachol in presence of a P2Y₂ receptor siRNA, we found that tear secretion was diminished to 60 %. The inhibition of tear secretion in the presence of carbachol and purinergic antagonists or P2Y₂ siRNA occurred with no apparent change in the tear amount of Ap₄A. These experiments demonstrated the participation of Ap₄A in lacrimal secretion process.     

Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox‐based modifications

Reactive oxidative species (ROS) and S‐glutathionylation modulate the activity of plant cytosolic triosephosphate isomerases (cTPI). Arabidopsis thaliana cTPI (AtcTPI) is subject of redox regulation at two reactive cysteines that function as thiol switches. Here we investigate the role of these residues, AtcTPI‐Cys13 and At‐Cys218, by substituting them with aspartic acid that mimics the irreversible oxidation of cysteine to sulfinic acid and with amino acids that mimic thiol conjugation. Crystallographic studies show that mimicking AtcTPI‐Cys13 oxidation promotes the formation of inactive monomers by reposition residue Phe75 of the neighboring subunit, into a conformation that destabilizes the dimer interface. Mutations in residue AtcTPI‐Cys218 to Asp, Lys, or Tyr generate TPI variants with a decreased enzymatic activity by creating structural modifications in two loops (loop 7 and loop 6) whose integrity is necessary to assemble the active site. In contrast with mutations in residue AtcTPI‐Cys13, mutations in AtcTPI‐Cys218 do not alter the dimeric nature of AtcTPI. Therefore, modifications of residues AtcTPI‐Cys13 and AtcTPI‐Cys218 modulate AtcTPI activity by inducing the formation of inactive monomers and by altering the active site of the dimeric enzyme, respectively. The identity of residue AtcTPI‐Cys218 is conserved in the majority of plant cytosolic TPIs, this conservation and its solvent‐exposed localization make it the most probable target for TPI regulation upon oxidative damage by reactive oxygen species. Our data reveal the structural mechanisms by which S‐glutathionylation protects AtcTPI from irreversible chemical modifications and re‐routes carbon metabolism to the pentose phosphate pathway to decrease oxidative stress.     

Bioremediation of Crude Oil–Contaminated Soil By Immobilized Bacteria on an Agroindustrial Waste—Sunflower Seed Husks

This study reports the immobilization and performance of a hydrocarbon-degrading Rhodococcus sp. strain (designated as QBTo) on sunflower seed husks (SH) for the bioremediation of soils polluted with crude oil. The SH performance as inoculants carrier was compared with peat, which is a vegetal material traditionally used in carrier-based inoculants production. The stability of the immobilized culture under storage conditions was assessed by viability at different times when stored at 25°C and 10°C. The catabolic activity of immobilized and free QTBo cells introduced into sandy loam soil, freshly contaminated with crude oil, was studied in microcosms. A higher number of viable QTBo cells were recovered from the inoculants formulated with SH (QTBo-SH) after prolonged storage at 10°C and 25°C. The microcosms amended with QTBo-SH inoculants showed a removal of about 66% of total petroleum hydrocarbons (TPH), whereas in those inoculated with QTBo-peat inoculants, the decrease was of about 47%. In the control microcosms (noninoculated) and liquid culture–amended soils, the TPH removal was about 28%. SH is a waste of edible oil industry, nontoxic, and biodegradable and has demonstrated to confer to the immobilized cultures greater potential to survive not only during storage but also in the soil environment, improving bioremediation process.     

AnthropoAge,a novel approach to integrate body composition into the estimation of biological age

Aging is believed to occur across multiple domains, one of which is body composition; however, attempts to integrate it into biological age (BA) have been limited. Here, we consider the sex-dependent role of anthropometry for the prediction of 10-year all-cause mortality using data from 18,794 NHANES participants to generate and validate a new BA metric. Our data-driven approach pointed to sex-specific contributors for BA estimation: WHtR, arm and thigh circumferences for men; weight, WHtR, thigh circumference, subscapular and triceps skinfolds for women. We used these measurements to generate AnthropoAge, which predicted all-cause mortality (AUROC 0.876, 95%CI 0.864–0.887) and cause-specific mortality independently of ethnicity, sex, and comorbidities; AnthropoAge was a better predictor than PhenoAge for cerebrovascular, Alzheimer, and COPD mortality. A metric of age acceleration was also derived and used to assess sexual dimorphisms linked to accelerated aging, where women had an increase in overall body mass plus an important subcutaneous to visceral fat redistribution, and men displayed a marked decrease in fat and muscle mass. Finally, we showed that consideration of multiple BA metrics may identify unique aging trajectories with increased mortality (HR for multidomain acceleration 2.43, 95%CI 2.25–2.62) and comorbidity profiles. A simplified version of AnthropoAge (S-AnthropoAge) was generated using only BMI and WHtR, all results were preserved using this metric. In conclusion, AnthropoAge is a useful proxy of BA that captures cause-specific mortality and sex dimorphisms in body composition, and it could be used for future multidomain assessments of aging to better characterize the heterogeneity of this phenomenon.     

Protein homology detection and fold inference through multiple alignment entropy profiles

Homology detection and protein structure prediction are central themes in bioinformatics. Establishment of relationship between protein sequences or prediction of their structure by sequence comparison methods finds limitations when there is low sequence similarity. Recent works demonstrate that the use of profiles improves homology detection and protein structure prediction. Profiles can be inferred from protein multiple alignments using different approaches. The "Conservatism-of-Conservatism" is an effective profile analysis method to identify structural features between proteins having the same fold but no detectable sequence similarity. The information obtained from protein multiple alignments varies according to the amino acid classification employed to calculate the profile. In this work, we calculated entropy profiles from PSI-BLAST-derived multiple alignments and used different amino acid classifications summarizing almost 500 different attributes. These entropy profiles were converted into pseudocodes which were compared using the FASTA program with an ad-hoc matrix. We tested the performance of our method to identify relationships between proteins with similar fold using a nonredundant subset of sequences having less than 40% of identity. We then compared our results using Coverage Versus Error per query curves, to those obtained by methods like PSI-BLAST, COMPASS and HHSEARCH. Our method, named HIP (Homology Identification with Profiles) presented higher accuracy detecting relationships between proteins with the same fold. The use of different amino acid classifications reflecting a large number of amino acid attributes, improved the recognition of distantly related folds. We propose the use of pseudocodes representing profile information as a fast and powerful tool for homology detection, fold assignment and analysis of evolutionary information enclosed in protein profiles.