Mining cancer biology through bioinformatic analysis of proteomic data

ABSTRACT

Introduction: Discovery proteomics for cancer research generates complex datasets of diagnostic, prognostic, and therapeutic significance in human cancer. With the advent of high-resolution mass spectrometers, able to identify thousands of proteins in complex biological samples, only the application of bioinformatics can lead to the interpretation of data which can be relevant for cancer research.

Areas covered: Here, we give an overview of the current bioinformatic tools used in cancer proteomics. Moreover, we describe their applications in cancer proteomics studies of cell lines, serum, and tissues, highlighting recent results and critically evaluating their outcomes.

Expert opinion: The use of bioinformatic tools is a fundamental step in order to manage the large amount of proteins (from hundreds to thousands) that can be identified and quantified in a cancer biological samples by proteomics. To handle this challenge and obtain useful data for translational medicine, it is important the combined use of different bioinformatic tools. Moreover, a particular attention to the global experimental design, and the integration of multidisciplinary skills are essential for best setting of tool parameters and best interpretation of bioinformatics output.     

Gender-biased nectar targets different behavioural traits of flower visitors

Plant Ecology - Floral nectar is a chemically complex aqueous solution within which several secondary metabolites have been identified that affect attractiveness for pollinators. Understanding...     

Root fungal endophytes: identity,phylogeny and roles in plant tolerance to metal stress

Metal trace elements accumulate in soils mainly because of anthropic activities, leading living organisms to develop strategies to handle metal toxicity. Plants often associate with root endophytic fungi, including nonmycorrhizal fungi, and some of these organisms are associated with metal tolerance. The lack of synthetic analyses of plant-endophyte-metal tripartite systems and the scant consideration for taxonomy led to this review aiming (1) to inventory non-mycorrhizal root fungal endophytes described with respect to their taxonomic diversity and (2) to determine the mutualistic roles of these plant-fungus associations under metal stress. More than 1500 species in 100 orders (mainly Hypocreales and Pleosporales) were reported from a wide variety of environments and hosts. Most reported endophytes had a positive effect on their host under metal stress, but with various effects on metal uptake or translocation and no clear taxonomic consistency. Future research considering the functional patterns and dynamics of these associations is thus encouraged.     

Two bromeliad species with contrasting functional traits partition the understory space in a South American xerophytic forest: correlative evidence of environmental control and limited dispersal

We examined the spatial distribution of two bromeliad species with contrasting functional traits in the understory of a xerophytic South American Chaco forest. Aechmea distichantha is a facultative terrestrial species with well-developed phytotelma and short rhizomes, whereas Bromelia serra is a strictly terrestrial species with soil-exploring roots and long rhizomes. Both bromeliads develop colonies on relatively elevated patches in Schinopsis balansae forests. We evaluated the roles of environmental controls, limited dispersal, and interspecific competition as drivers of the different distribution of these bromeliads. We mapped the overstory, understory and topography of 16 forest plots with bromeliads (400 m² each, subdivided in 100 4-m² subplots). We sampled soil characteristics on sectors dominated by each bromeliad species. We used structural equation modeling to assess direct and indirect associations of each bromeliad species cover with environmental conditions, abundance of conspecifics in the vicinity, and local abundance of the other species. A. distichantha cover increased on elevated subplots with high tree/shrub basal area, whereas B. serra cover showed the opposite pattern. In addition, A. distichantha cover was negatively associated with B. serra cover, but not vice versa, and cover of both species increased with the abundance of nearby conspecifics, suggesting that limited vegetative dispersal partly accounted for their distribution. Sectors dominated by A. distichantha had lower soil bulk density and higher organic matter content than those dominated by B. serra. According to our model, influences of competition and limited vegetative dispersal reinforce the association between distribution of these bromeliads and environmental heterogeneity of the forest understory.     

Monocot leaves are eaten less than dicot leaves in tropical lowland rain forests: correlations with toughness and leaf presentation

Background and Aims

In tropical lowland rain forest (TLRF) the leaves of most monocots differ from those of most dicots in two ways that may reduce attack by herbivores. Firstly, they are tougher. Secondly, the immature leaves are tightly folded or rolled until 50–100 % of their final length. It was hypothesized that (a) losses of leaf area to herbivorous invertebrates are generally greatest during leaf expansion and smaller for monocots than for dicots, and (b) where losses after expansion are appreciable any difference between monocots and dicots then is smaller than that found during expansion.

Methods

At six sites on four continents, estimates were made of lamina area loss from the four most recently mature leaves of focal monocots and of the nearest dicot shoot. Measurements of leaf mass per unit area, and the concentrations of water and nitrogen were made for many of the species. In Panama, the losses from monocots (palms) and dicots were also measured after placing fully expanded palm leaflets and whole dicot leaves on trails of leaf-cutter ants.

Key Results

At five of six sites monocots experienced significantly smaller leaf area loss than dicots. The results were not explicable in terms of leaf mass per unit area, or concentrations of water or nitrogen. At only one site was the increase in loss from first to fourth mature leaf significant (also large and the same in monocots and dicots), but the losses sustained during expansion were much smaller in the monocots. In the leaf-cutter ant experiment, losses were much smaller for palms than for dicots.

Conclusions

The relationship between toughness and herbivory is complex; despite the negative findings of some recent authors for dicots we hypothesize that either greater toughness or late folding can protect monocot leaves against herbivorous insects in tropical lowland rain forest, and that the relative importance varies widely with species. The difficulties of establishing unequivocally the roles of leaf toughness and leaf folding or rolling in a given case are discussed.Key words: anti-herbivore defences, dicots, herbivory, leaf folding, leaf rolling, leaf toughness, monocots, palms, tropical rain forest     

SPIR01 and SPIR02: a two-year 1-day point prevalence multicenter study of infections in intensive care units in Piedmont, Italy

This study reports the results of a one-day point prevalence study of infections performed in 2001 (SPIR01) and 2002 (SPIR02) in a Regional network of ICUs in Piedmont, Italy. The study aims were to illustrate the overall proportion of infected patients and the rate of ICU-acquired infections. Mortality rate was evaluated three weeks after the study days. Resistance pattern of Staphylococcus aureus, coagulase negative Staphylococci and Pseudomonas aeruginosa were recorded. The primary end-point of the study was to document the prevalence and associated risk factors of the ICU-acquired infections, and the impact of infections on mortality. The prevalence of ICU-acquired infection was 30% in SPIR01, and 38.3% in SPIR02. The rate of methicillin-resistance was high among isolates of Staphylococcus aureus and coagulase-negative Staphylococci. The prevalence of ICU-acquired infections was lower than that reported in the EPIC study. In our experience, this Regional survey stimulated further research and collaboration to improve the prophylaxis, diagnosis and treatment of ICU-acquired infections.     

Effect of indigenous mycobiota on ochratoxin A production by Aspergillus carbonarius isolated from soil

This study determined the biotic interaction between 30 non-toxigenic indigenous strains of Aspergillus niger aggregate, Aspergillus flavus, Trichoderma spp., Mucor spp., Cladosporium spp., Ulocladium spp., Curvularia spp., Absidia spp., Geotrichum spp. and Acremonium spp., isolated from soil destined for maize crops, with respect to their ability to prevent ochratoxin A (OTA) production by A. carbonarius on “in vitro” assay, on liquid and solid medium. OTA production was completely inhibited when A. carbonarius was inoculated in a interactive mixed culture with all A. niger aggregate strains assayed, a 80 % of Trichoderma spp. strains, a 40 % of Cladosporium spp. strains, Acremonium spp and Geotrichum spp; only one strain of A. flavus tested was able to completely inhibit the mycotoxin accumulation. OTA production increased when A. carbonarius ACS 8 was growing on liquid interactive mixed culture with Mucor spp strains. These results demonstrated that OTA production by Aspergillua carbonarius strain was significantly influenced by the presence of different non-toxigenic fungal strains when growing together on paired cultures.     

The rice coleoptile: an example of anaerobic nitrate assimilation

Nitrate present in rice caryopses can be reduced to ammonium and the ammonium subsequently assimilated by the coleoptile during anaerobic germination. All the enzymes of nitrate reduction and ammonia assimilation are present in the coleoptile. The supply of ¹⁵NO₃ confirms that the nitrate nitrogen is anaerobically incorporated into amino acids. Under anoxia, nitrate and nitrite reductase activities are increased in the coleoptile by exogenous nitrate. The importance of nitrate utilization during the anaerobic germination of rice caryopses is discussed.     

5''-ADENINE MONONUCLEOTIDES TN SYNAPTOSOMAL PREPARATIONS FROM GUINEA PIG NEOCORTEX: THEIR CHANGE ON INCUBATION, SUPERFUSION AND STIMULATION

–(l) The contents of potassium and of ATP, ADP and AMP of homogenates of guinea pig neocortex in 0.32 M-SUCROSE, and of synaptosomal preparations derived therefrom, were determined and effects of incubation, superfusion and stimulation of the preparation were examined. The synaptosome preparations in M-SUCTOSe carried a smaller content of 5′-nucleotide per unit protein than did the homogenate from which they were derived. However, the proportion of synaptosomal nucleotides present as ATP was markedly greater than in the homogenate as a whole, the adenylate energy-charge being 83% greater in the synaptosomes than in the homogenate. Dilution of the synaptosomal preparation from the 1 M-sucrose to isotonic sucrose, decreased the contcnt of ATP per unit protein, but did not change the sum ATP + ADP + AMP. (2) Examined as deposited beds during 5 to 20 min incubation in oxygenated glucose-bicarbonate salines, synaptosomal K content and adenylate energy charge increased. These changes were sustained during a subsequent 40 min of incubation and also during superfusion. During such continued superfusion, electrical stimulation caused diminution of the ATP and the adenylate energy charge of the beds, as also did superfusion with fluids of increased K-content. (3) Lactate formation by the superfused beds was relatively stable during 30 min incubation. By electrical stimulation, the rate of lactate formation was increased by up to 30%. Increase in the potassium content of superfusion fluids could however increase lactate production 2.4-fold. The basis for these actions is discussed.