A mechanistic model may explain the dissimilar biological efficiency of the fungal elicitors cerato-platanin and cerato-populin

Among their various functions, the members of the cerato-platanin family can stimulate plants' defense responses and induce resistance against microbial pathogens. Recent results suggest that conserved loops, also involved in chitin binding, might be a structural motif central for their eliciting activity. Here, we focus on cerato-platanin and its orthologous cerato-populin, searching for a rationale of their diverse efficiency to elicit plants' defense and to interact with oligosaccharides. A 3D model of cerato-populin has been generated by homology modeling using the NMR-derived cerato-platanin structure as template, and it has been validated by fitting with residual dipolar couplings. Loops β1-β2 and β2-β3 have been indicated as important for some CPPs members to express their biological function. When compared to cerato-platanin, in cerato-populin they present two mutations and an insertion that significantly modify their electrostatic surface. NMR relaxation experiments point to a reduced conformational plasticity of cerato-populin loops with respect to the ones of cerato-platanin. The different electrostatic surface of the loops combined with a distinct network of intra-molecular interactions are expected to be factors that, by leading to a diverse spatial organization and dissimilar collective motions, can regulate the eliciting efficacy of the two proteins and their affinity for oligosaccharides.     

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo–West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes– Bayesian PTP (PTP–bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.     

Humic Acids Interfere with Nutrient Sensing in Plants Owing to the Differential Expression of TOR

Journal of Plant Growth Regulation - The environmental consequences of industrial agriculture have increasingly called attention to new biotechnologies. The use of biostimulants based on humic...     

Proteomic Analysis of Developing Somatic Embryos of Coffea arabica

Differential protein profiles of three stages of somatic embryogenesis, including globular, torpedo, and cotyledonary somatic embryos, of Coffea arabica cv. Catuaí Vermelho were analyzed in an attempt to better understand somatic embryogenesis in coffee plants. Somatic embryos at these different stages of development were collected from in vitro-grown cultures, and then macerated in liquid nitrogen. Proteins were extracted with phenol and further quantified using the Bradford method. The bidimensional electrophoresis analysis revealed a wide range of proteins ranging between 10 and 160?kDa and of pH values ranging from 3 to 10. Several differentially expressed proteins were identified by mass spectrometry, and some were found to be specific to these different stages of somatic embryogenesis in coffee. The enolase and 11S storage globulin proteins, for example, could be used as molecular markers for somatic embryo development stages and for embryogenic and non-embryogenic genotype differentiation, respectively.     

Pools of water in anhydrobiotic organisms: A thermally stimulated depolarization current study

The ability to survive the removal of water in anhydrous biosystems is especially remarkable as a departure from the manifold structural and functional dependences on the presence of H₂O molecules. Identifiable pools of water present in dry soybean axes were investigated by means of the thermally stimulated depolarization current method. Samples were examined in the temperature range 100-340 K and over water contents (h, in gram H₂O per gram sample dry weight) ranging from h = 0.05 to 0.30 g/g. Three water-dependent relaxation mechanisms were detected; one attributed to dipolar reorientation of H₂O molecules hydrogen-bonded to other water molecules, one to reorientation of CH₂OH groups, and one to a glass transition in sugar-water domains. These glassy domains can protect intracellular components against destruction in the dehydrated state. Interestingly, protecting glassy domains were not found in dehydration intolerant seeds, supporting the hypothesis that the ability to withstand dehydration is associated with intracellular glass formation. A model for the state of cell water at interfaces is proposed.     

The geography of demography: long-term demographic studies and species distribution models reveal a species border limited by adaptation

Potential causes of species' geographic distribution limits fall into two broad classes: (1) limited adaptation across spatially variable environments and (2) limited opportunities to colonize unoccupied areas. Combining demographic studies, analyses of demographic responses to environmental variation, and species distribution models, we investigated the causes of range limits in a model system, the eastern border of the California annual plant Clarkia xantiana ssp. xantiana. Vital rates of 20 populations varied with growing season temperature and precipitation: fruit number and overwinter survival of 1-year-old seeds declined steeply, while current-year seed germination increased modestly along west-to-east gradients in decreasing temperature, decreasing mean precipitation, and increasing variation in precipitation. Long-term stochastic finite rate of increase, λ(s), exhibited a fourfold range and varied among geologic surface materials as well as with temperature and precipitation. Growth rate declined significantly toward the eastern border, falling below 1 in three of the five easternmost populations. Distribution models employing demographically important environmental variables predicted low habitat favorability beyond the eastern border. Models that filtered or weighted population presences by λ(s) predicted steeper eastward declines in favorability and assigned greater roles in setting the distribution to among-year variation in precipitation and to geologic surface material. These analyses reveal a species border likely set by limited adaptation to declining environmental quality.     

The GLUT9 gene is associated with serum uric acid levels in Sardinia and Chianti cohorts

High serum uric acid levels elevate pro-inflammatory–state gout crystal arthropathy and place individuals at high risk for cardiovascular morbidity and mortality. Genome-wide scans in the genetically isolated Sardinian population identified variants associated with serum uric acid levels as a quantitative trait. They mapped within GLUT9, a Chromosome 4 glucose transporter gene predominantly expressed in liver and kidney. SNP rs6855911 showed the strongest association (p = 1.84 × 10⁻¹⁶), along with eight others (p = 7.75 × 10⁻¹⁶ to 6.05 × 10⁻¹¹). Individuals homozygous for the rare allele of rs6855911 (minor allele frequency = 0.26) had 0.6 mg/dl less uric acid than those homozygous for the common allele; the results were replicated in an unrelated cohort from Tuscany. Our results suggest that polymorphisms in GLUT9 could affect glucose metabolism and uric acid synthesis and/or renal reabsorption, influencing serum uric acid levels over a wide range of values.     

Molecular strategies for protein stabilization: the case of a trehalose/maltose-binding protein from Thermus thermophilus

The trehalose/maltose-binding protein (MalE1) is one component of trehalose and maltose uptake system in the thermophilic organism Thermus thermophilus. MalE1 is a monomeric 48 kDa protein predominantly organized in alpha-helix conformation with a minor content of beta-structure. In this work, we used Fourier-infrared spectroscopy and in silico methodologies for investigating the structural stability properties of MalE1. The protein was studied in the absence and in the presence of maltose as well as in the absence and in the presence of SDS at different p(2)H values (neutral p(2)H and at p(2)H 9.8). In the absence of SDS, the results pointed out a high thermostability of the MalE1 alpha-helices, maintained also at basic p(2)H values. However, the obtained data also showed that at high temperatures the MalE1 beta-sheets underwent to structural rearrangements that were totally reversible when the temperature was lowered. At room temperature, the addition of SDS to the protein solution slightly modified the MalE1 secondary structure content by decreasing the protein thermostability. The infrared data, corroborated by molecular dynamics simulation experiments performed on the structure of MalE1, indicated that the protein hydrophobic interactions have an important role in the MalE1 high thermostability. Finally, the results obtained on MalE1 are also discussed in comparison with the data on similar thermostable proteins already studied in our laboratories.     

The Berger–Parker index as an effective tool for monitoring the biodiversity of disturbed soils: a case study on Mediterranean oribatid (Acari: Oribatida) assemblages

Recent data on oribatid mites (Acari: Oribatida) indicates that Mediterranean soil communities tend to show uneven patterns of species abundance distribution (SAD) that are well fitted by a simple model such as the geometric series. In the case of linear distributions, the fraction of total sampled individuals that is contributed by the most abundant species, known as the Berger–Parker index, synthetically describes the SAD of disturbed communities. This study assessed the bioindicator potential of the Berger–Parker index by comparing its variations among Mediterranean oribatid assemblages under different types of soil disturbance. The index significantly changes between undisturbed and disturbed soils reaching the highest values in areas with strong physical disturbance due to agricultural management. The Berger–Parker index is therefore a practical and effective tool for monitoring biodiversity impairment linked to human disturbance in soil ecosystems.