Computational annotation of genes differentially expressed along olive fruit development

Background  

Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software.     

Possible involvement of histidine residues in the loss of enzymatic activity of rat liver malic enzyme during aging

During aging there is a decrease in activity of the malic enzyme in rat liver. The "old" malic enzyme is about 36% less active than the "young" enzyme. Some properties and modifications of amino acid residues are studied here (--SH, arginine, methionine, histidine, lysine) to try and check on the existence of any relationship between them and the loss of enzymatic activity during aging. Diethyl pyrocarbonate measurements indicate that the old enzyme has 1 histidine residue less than the young enzyme. Moreover, the treatment of the young enzyme with ascorbate for 15 min produces the loss of 36% of the enzymatic activity and the loss of 1.2 histidine residues. These results suggest that during aging the modification of the histidine residue could be involved in the loss of its enzymatic activity.     

Involvement of diminution of glutathione, produced by deficiency of methionine in the diet, in the elevation of malic enzyme level in rat liver

Rats fed on a low protein diet show an increase in the specific activity of malic enzyme and a concomitant decrease of glutathione concentration. We have studied the effect on malic enzyme activity of supplementing of low protein diet with essential amino acids. Only when methionine was excluded from the diet did the specific activity of malic enzyme increase to the same extent as found in rats fed with low protein diet. Immunoprecipitation of malic enzyme indicated that specific activity changes are the result of changes in the amounts of enzyme. Under all dietary conditions studied, the increase in malic enzyme activity is associated with a decrease in the concentration of GSH. To evaluate the possible causative role of GSH in malic enzyme induction, the specific activity of malic enzyme was measured in rats treated with BSO, an inhibitor of GSH biosynthesis. The results show that in BSO-treated rats the decrease of GSH levels is also accompanied by an increase in the activity of malic enzyme.     

Influence of elevated CO2 and nitrogen supply on the carbon assimilation performance and cell composition of the unicellular alga Dunaliella viridis

The carbon assimilation efficiency and the internal composition of the chlorophyte Dunaliella viridis have been studied under conditions of current (0.035%) and enriched (1%) levels of CO₂, with and without N limitation (supplied as nitrate). Results show that both photosynthesis and growth rates are enhanced by high CO₂, but the strategy of acclimation also involves the light harvesting machinery and the nutritional metabolism in an N supply dependent manner. D. viridis carried out a qualitative rather than a quantitative acclimation of the light harvesting system leading to increased PSII quantum yields. Total internal C decreased as a consequence of either active growth or organic carbon release to the external medium. The latter process allowed photosynthetic electron transport to proceed at higher rates than under normal CO₂ conditions, and maintained the internal C:N balance in a narrow range (under N sufficiency). N limitation generally prevented the effects of high CO₂, with some exceptions such as the photosynthetic O₂ evolution rate.     

Bimodal Epidemic Size Distributions for Near-Critical SIR with Vaccination

We introduce a recursive algorithm which enables the computation of the distribution of epidemic size in a stochastic SIR model for very large population sizes. In the important parameter region where the model is just slightly supercritical, the distribution of epidemic size is decidedly bimodal. We find close agreement between the distribution for large populations and the limiting case where the distribution is that of the time a Brownian motion hits a quadratic curve. The model includes the possibility of vaccination during the epidemic. The effects of the parameters, including vaccination level, on the form of the epidemic size distribution are explored.     

MBP (version 1.0): a software package to optimize maize breeding procedures based on doubled haploid lines

We developed MBP (version 1.0), a software package for optimizing maize (Zea mays L.) breeding procedures based on doubled haploid lines. This software accounts for both recurrent selection and the development of hybrid parent lines. Based on quantitative genetic model calculations, MBP (version 1.0) maximizes the expected genetic gain per year as a function of various genetic parameters and operational variables under the restriction of a given annual breeding budget. Exact formulae for the prediction of the effective population size are implemented, which allows to optimize breeding procedures under limited relative annual loss of genetic variance.     

Adaptive responses and cellular behaviour of biphenyl-degrading bacteria toward polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) are one of the most widely distributed classes of chlorinated chemicals in the environment. For cleanup of large areas of PCB-contaminated environments, bioremediation seems to be a promising approach. However, the multitude of PCB congeners, their low bioavailability and high toxicity are important factors that affect the cleanup progression. Elucidating how the PCB-degrading microorganisms involved in the process adapt to and deal with the stressing conditions caused by this class of compounds may help to improve the bioremediation process. Also specific physiological characteristics of biphenyl-utilizing bacteria involved in the degradation of PCBs may enhance their availability to these compounds and therefore contribute to a better microbial mineralization. This review will focus in the stress responses caused in aerobic biphenyl-utilizing bacteria by PCBs and its metabolic intermediates and will also analyze bacterial properties such as motility and chemotaxis, adherence to solid surfaces, biosurfactant production and biofilm development, all properties found to enhance bacteria-pollutant interaction.     

The PINE study: rationale and design of a randomised comparison of epidural injection of local anaesthetics and steroids versus care-as-usual to prevent postherpetic neuralgia in the elderly [ISRCTN32866390]

BACKGROUND: Postherpetic neuralgia (PHN) is by far the most common complication of herpes zoster (HZ) and one of the most intractable pain disorders. Since PHN is seen most often in the elderly, the number of patients with this disorder is expected to increase in our ageing society. PHN may last for months to years and has a high impact on the quality of life. The results of PHN treatment are rather disappointing. Epidural injection of local anaesthetics and steroids in the acute phase of HZ is a promising therapy for the prevention of PHN. Since randomised trials on the effectiveness of this intervention are lacking, the PINE (Prevention by epidural Injection of postherpetic Neuralgia in the Elderly) study was set up. The PINE study compares the effectiveness and cost-effectiveness of a single epidural injection of local anaesthetics and steroids during the acute phase of HZ with that of care-as-usual (i.e. antivirals and analgesics) in preventing PHN in elderly patients. METHODS / DESIGN: The PINE study is an open, multicenter clinical trial in which 550 elderly (age >/= 50 yr.) patients who consult their general practitioner in the acute phase of HZ (rash < 7 days) are randomised to one of the treatment groups. The primary clinical endpoint is the presence of HZ-related pain one month after the onset of the rash. Secondary endpoints include duration and severity of pain, re-interventions aiming to treat the existing pain, side effects, quality of life, and cost-effectiveness. CONCLUSION: The PINE study is aimed to quantify the (cost-) effectiveness of a single epidural injection during the acute phase of HZ on the prevention of PHN.     

Tumor‐stroma interactions differentially alter drug sensitivity based on the origin of stromal cells

Due to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear, however, what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor microenvironment. Using a large‐scale coculture assay optimized to measure drug‐induced cell death, we identify tumor–stroma interactions that modulate drug sensitivity. Our data show that the chemo‐insensitivity typically associated with aggressive subtypes of breast cancer is not observed if these cells are grown in 2D or 3D monoculture, but is manifested when these cells are cocultured with stromal cells, such as fibroblasts. Furthermore, we find that fibroblasts influence drug responses in two distinct and divergent manners, associated with the tissue from which the fibroblasts were harvested. These divergent phenotypes occur regardless of the drug tested and result from modulation of apoptotic priming within tumor cells. Our study highlights unexpected diversity in tumor–stroma interactions, and we reveal new principles that dictate how fibroblasts alter tumor drug responses.