Culturable bacteria associated with Antarctic lichens: affiliation and psychrotolerance

Antarctic habitats harbour yet unexplored niches for microbial communities. Among these, lichen symbioses are very long-living and stable microenvironments for bacterial colonization. In this work, we present a first assessment of the culturable fraction of bacteria associated with Antarctic lichens. A phylogenetic analysis based on 16S rRNA gene sequence of 30 bacterial strains isolated from five epilithic lichens belonging to four species (Lecanora fuscobrunnea, Umbilicaria decussata, Usnea antarctica, Xanthoria elegans) shows that these represent the main bacterial lineages Actinobacteria, Firmicutes, Proteobacteria and Deinococcus-Thermus. Within the Actinomycetales, two strains group in the genera Arthrobacter and Knoellia, respectively. Most of the other Actinobacteria form well-supported groups, but could be assigned with certainty only at the family level, and one is in isolated position in the Mycobacteriaceae. The strains in Firmicutes and Proteobacteria belong to the genera Paenibacillus, Bacillus and Pseudomonas, which were already reported from lichen thalli. Some genera such as Burkholderia and Azotobacter, reported in the literature as also associated with lichens, have not been detected in this study. One strain represents the first record of Deinococcus in epilithic lichens; it is related to the species Deinococcus alpinitundrae from Alpine environments and may represent a new species. Further separated and well-supported clades indicate the presence of possibly new entities. Some of the examined strains are related to known psychrophilic bacteria isolated from ice and other extreme environments, others with bacteria distributed worldwide even in temperate climates. Most of the strains tested were able to grow at low temperatures, but tolerated a wider range of temperature. Ecological and evolutionary implications of these lichen-associated bacteria are discussed.     

Ambiguous external genitalia due to defect of 5-α-reductase in seven Iraqi patients: Prevalence of a novel mutation

We report on seven Iraqi patients with 46,XY karyotype and ambiguous genitalia characterized by perineo-scrotal hypospadias, bifid scrotum, clitoris like phallus, palpable testes in inguinal canal and pseudovagina. Patients were raised five as females and two as males. They are all unrelated with the exception of two couples of brothers. The diagnosis of 5-α-reductase-2 deficiency syndrome was first hypothesized on clinical grounds and then confirmed by molecular analysis. Direct sequencing analysis of the SRD5A2 gene revealed in five patients a novel homozygous frame-shift mutation (c.453delC) and in two related patients a previous reported missense mutation. The presence of the same mutation in unrelated patients of the same population suggests a possible founder effect. This report brings the 5-α-reductase-2 deficiency syndrome to the attention of clinical geneticists and child surgeons and discusses the appropriate clinical and surgical strategies for treating these patients.     

Evidence for a C4 NADP-ME photosynthetic pathway in Vetiveria zizanioides Stapf

ABSTRACT

Leaf anatomy (light and transmission electron microscopy), immunogold localization of Rubisco, photosynthetic enzyme activities, CO₂ assimilation and stomatal conductance were studied in Vetiveria zizanioides Stapf., a graminaceous plant native to tropical and subtropical areas, and cultivated in temperate climates (Northwestern Italy). Leaves possess a NADP-ME Kranz anatomy with bundle sheath cells containing chloroplasts located in a centrifugal position. Dimorphic chloroplasts were also observed; they are agranal and starchy in the bundle sheath and granal starchless in the mesophyll cells. Rubisco immunolocalization studies indicate that this enzyme occurs solely in the bundle sheath chloroplasts. Pyruvate-orthophosphate dikinase, NADP-dependent malate dehydrogenase (NADP-MDH), NADP-dependent malic enzyme (NADP-ME), PEP-carboxykinase and NAD-dependent malic enzyme (NAD-ME) activities were determined. Enzyme activity and some kinetic properties of NADP-ME and NADP-MDH as well as CO₂ compensation point and stomatal conductance values were calculated indicating a NADP-ME C₄ photosynthetic pathway. Biochemical and structural results indicate that V. zizanioides belongs to the C₄ NADP-ME variant. This plant appears to be well adapted to the varying environmental conditions typical of temperate climates, by retaining high enzyme activities and a low CO₂ compensation point.     

Tropospheric ozone reduces carbon assimilation in trees: estimates from analysis of continuous flux measurements

High ground‐level ozone concentrations are typical of Mediterranean climates. Plant exposure to this oxidant is known to reduce carbon assimilation. Ozone damage has been traditionally measured through manipulative experiments that do not consider long‐term exposure and propagate large uncertainty by up‐scaling leaf‐level observations to ecosystem‐level interpretations. We analyzed long‐term continuous measurements (>9 site‐years at 30 min resolution) of environmental and eco‐physiological parameters at three Mediterranean ecosystems: (i) forest site dominated by Pinus ponderosa in the Sierra Mountains in California, USA; (ii) forest site composed of a mixture of Quercus spp. and P. pinea in the Tyrrhenian sea coast near Rome, Italy; and (iii) orchard site of Citrus sinensis cultivated in the California Central Valley, USA. We hypothesized that higher levels of ozone concentration in the atmosphere result in a decrease in carbon assimilation by trees under field conditions. This hypothesis was tested using time series analysis such as wavelet coherence and spectral Granger causality, and complemented with multivariate linear and nonlinear statistical analyses. We found that reduction in carbon assimilation was more related to stomatal ozone deposition than to ozone concentration. The negative effects of ozone occurred within a day of exposure/uptake. Decoupling between carbon assimilation and stomatal aperture increased with the amount of ozone pollution. Up to 12–19% of the carbon assimilation reduction in P. ponderosa and in the Citrus plantation was explained by higher stomatal ozone deposition. In contrast, the Italian site did not show reductions in gross primary productivity either by ozone concentration or stomatal ozone deposition, mainly due to the lower ozone concentrations in the periurban site over the shorter period of investigation. These results highlight the importance of plant adaptation/sensitivity under field conditions, and the importance of continuous long‐term measurements to explain ozone damage to real‐world forests and calculate metrics for ozone‐risk assessment.     

Human C-type lectin domain family 4, member C (CLEC4C/BDCA-2/CD303) is a receptor for asialo-galactosyl-oligosaccharides

Plasmacytoid dendritic cells are specialized in the production of type I interferon (type I IFN), which promotes antiviral and antitumor responses, as well as autoimmune disorders. Activation of type I IFN secretion depends on the pattern recognition receptors TLR7 and TLR9, which sense microbial RNA and DNA, respectively. Type I IFN production is modulated by several receptors, including the type II C-type lectin domain family 4, member C (CLEC4C). The natural ligand of CLEC4C is unknown. To identify it, here we probed a glycan array with a soluble form of the CLEC4C ectodomain. We found that CLEC4C recognizes complex type sugars with terminal galactose. Importantly, soluble CLEC4C bound peripheral blood leukocytes and tumor cells that express glycans with galactose residues at the non-reducing ends. The positive and negative modulation of galactose residues on cell membranes was paralleled by the regulation of type I IFN secretion by plasmacytoid dendritic cells in co-culture experiments in vitro. These results suggest that the modulation in the expression of non-sialylated oligosaccharides by invading pathogens or transformed cells may affect type I IFN response and immune surveillance.     

Urinary Signatures of Renal Cell Carcinoma Investigated by Peptidomic Approaches

Renal Cell Carcinoma (RCC) is typically asymptomatic and surgery usually increases patient''s lifespan only for early stage tumours. Moreover, solid renal masses cannot be confidently differentiated from RCC. Therefore, markers to distinguish malignant kidney tumours and for their detection are needed. Two different peptide signatures were obtained by a MALDI-TOF profiling approach based on urine pre-purification by C8 magnetic beads. One cluster of 12 signals could differentiate malignant tumours (n = 137) from benign renal masses and controls (n = 153) with sensitivity of 76% and specificity of 87% in the validation set. A second cluster of 12 signals distinguished clear cell RCC (n = 118) from controls (n = 137) with sensitivity and specificity values of 84% and 91%, respectively. Most of the peptide signals used in the two models were observed at higher abundance in patient urines and could be identified as fragments of proteins involved in tumour pathogenesis and progression. Among them: the Meprin 1α with a pro-angiogenic activity, the Probable G-protein coupled receptor 162, belonging to the GPCRs family and known to be associated with several key functions in cancer, the Osteopontin that strongly correlates to tumour stages and invasiveness, the Phosphorylase b kinase regulatory subunit alpha and the SeCreted and TransMembrane protein 1.     

The effect of molecular inhibition on evolutionary learning: studies in the hypernetwork architecture

The hypernetwork architecture is a biologically inspired learning model based on abstract molecules and molecular interactions that exhibits functional and organizational correlation with biological systems. Hypernetwork organisms were trained, by molecular evolution, to solve N-input parity tasks. We found that learning improves when molecules exhibit inhibitory sites, allowing molecular inhibition and opening the possibility of forming negative feedback regulatory pathways. Optimal learning is achieved when at least 20% of the molecules in each cell have inhibitory sites. Intra-cellular as well as inter-cellular molecular inhibitions play an important role in the information processing of hypernetwork organisms, by maintaining a balance of the molecular cascade reactions. Similar mechanisms inside neurons are considered important for memory.     

Nuclear proteome analysis reveals a role of Vav1 in modulating RNA processing during maturation of tumoral promyelocytes

Vav1 is a key molecule in the ATRA-induced acquisition of a mature phenotype by tumoral myeloid precursors. Since ATRA acts throughout events that require extensive changes of nuclear architecture and activity and considering that Vav1 accumulates inside the nuclear compartment of differentiating APL-derived cells, the possible role of this protein in modulating the nuclear proteome was investigated. Membrane-depleted nuclei purified from NB4 cells induced to differentiate with ATRA in the presence of forcedly down-modulated Vav1 were subjected to 2D-DIGE followed by mass spectra analysis. The obtained data demonstrated that, in NB4 cells treated with ATRA, Vav1 is involved in determining the nuclear amount of proteins involved in molecular complexes with DNA and may participate to RNA processing by carrying in the nucleus molecules involved in modulating mRNA production and stability, like hnRNPs and SR proteins. Our results provide the first evidence that, at least in maturation of tumoral myeloid precursors, Vav1 is part of interconnected networks of functionally related proteins ended to regulate different aspects of gene expression. Since defects in mRNA processing are common in tumor development, our data suggest that Vav1 is a potential target molecule for developing new anti-cancer strategies.