Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.

Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.

Peroxisome proliferator-activated receptors and lipid metabolism.

PPARs are nuclear hormone receptors which, like the retinoid, thyroid hormone, vitamin D, and steroid hormone receptors, are ligand-activated transcription factors mediating the hormonal control of gene expression. Two lines of evidence indicate that PPARs have an important function in fatty acid metabolism. First, PPARs are activated by hypolipidemic drugs and physiological concentrations of fatty acids, and second, PPARs control the peroxisomal beta-oxidation pathway of fatty acids through transcriptional induction of the gene encoding the acyl-CoA oxidase (ACO), which is the rate-limiting enzyme of the pathway. Furthermore, the PPAR signaling pathway appears to converge with the 9-cis retinoic acid receptor (RXR) signaling pathway in the regulation of the ACO gene because heterodimerization between PPAR and RXR is essential for in vitro binding to the PPRE and because the strongest stimulation of this gene is observed when both receptors are exposed simultaneously to their activators. Thus, it appears that PPARs are involved in the 9-cis retinoic acid signaling pathway and that they play a pivotal role in the hormonal control of lipid metabolism.

Appraising and selecting strategies to combat and mitigate desertification based on stakeholder knowledge and globalbest practices in Cape Verde Archipelago

Cape Verde is considered part of Sahelian Africa, where drought and desertification are common occurrences. The main activity of the rural population is rain-fed agriculture, which over time has been increasingly challenged by high temporal and spatial rainfall variability, lack of inputs, limited land area, fragmentation of land, steep slopes, pests, lack of mechanization and loss of top soil by water erosion. Human activities, largely through poor farming practices and deforestation (Gomez, 1989) have accelerated natural erosion processes, shifting the balance between soil erosion and soil formation (Norton, 1987). According to previous studies, vegetation cover is one of the most important factors in controlling soil loss (Cyr et al., 1995; Hupy, 2004; Zhang et al., 2004; Zhou et al., 2006). For this reason, reforestation is a touchstone of the Cape Verdean policy to combat desertification. After Independence in 1975, the Cape Verde government had pressing and closely entangled environmental and socio-economic issues to address, as long-term desertification had resulted in a lack of soil cover, severe soil erosion and a scarcity of water resources and fuel wood. Across the archipelago, desertification was resulting from a variety of processes including poor farming practices, soil erosion by water and wind, soil and water salinity in coastal areas due to over pumping and seawater intrusion, drought and unplanned urbanization (DGA-MAAP, 2004). All these issues directly affected socio-economic vulnerability in rural areas, where about 70% of people depended directly or indirectly on agriculture in 1975. By becoming part of the Inter- State Committee for the Fight against Drought in the Sahel in 1975, the government of Cape Verde gained structured support to address these issues more efficiently. Presentday policies and strategies were defined on the basis of rational use of resources and human efforts and were incorporated into three subsequent national plans: the National Action Plan for Development (NDP) (1982–1986), the NDP (1986–1990) and the NDP (1991–1995) (Carvalho

Soil and Water Conservation Strategies in Cape Verde (Cabo Verde in Portuguese) and Their Impacts on Livelihoods - An Overview from the Ribeira Seca Watershed

Severe land degradation has strongly affected both people’s livelihood and the environment in Cape Verde (Cabo Verde in Portuguese), a natural resource poor country. Despite the enormous investment in soil and water conservation measures (SWC or SLM), which are visible throughout the landscape, and the recognition of their benefits, their biophysical and socioeconomic impacts have been poorly assessed and scientifically documented. This paper contributes to filling this gap, by bringing together insights from literature and policy review, field survey and participatory assessment in the Ribeira Seca Watershed through a concerted approach devised by the DESIRE project (the “Desire approach”). Specifically, we analyze government strategies towards building resilience against the harsh conditions, analyze the state of land degradation and its drivers, survey and map the existing SWC measures, and assess their effectiveness against land degradation, on crop yield and people’s livelihood. We infer that the relative success of Cape Verde in tackling desertification and rural poverty owes to an integrated governance strategy that comprises raising awareness, institutional framework development, financial resource allocation, capacity building, and active participation of rural communities. We recommend that specific, scientific-based monitoring and assessment studies be carried out on the biophysical and socioeconomic impact of SLM and that the “Desire approach” be scaled-up to other watersheds in the country.

Emergence of Cooperation on Static and Dynamic Networks

Game theory is a branch of applied mathematics used to analyze situation where two or more agents are interacting. Originally it was developed as a model for conflicts and collaborations between rational and intelligent individuals. Now it finds applications in social sciences, eco- nomics, biology (particularly evolutionary biology and ecology), engineering, political science, international relations, computer science, and philosophy. Networks are an abstract representation of interactions, dependencies or relationships. Net- works are extensively used in all the fields mentioned above and in many more. Many useful informations about a system can be discovered by analyzing the current state of a network representation of such system. In this work we will apply some of the methods of game theory to populations of agents that are interconnected. A population is in fact represented by a network of players where one can only interact with another if there is a connection between them. In the first part of this work we will show that the structure of the underlying network has a strong influence on the strategies that the players will decide to adopt to maximize their utility. We will then introduce a supplementary degree of freedom by allowing the structure of the population to be modified along the simulations. This modification allows the players to modify the structure of their environment to optimize the utility that they can obtain.

Historical contingency affects signaling strategies and competitive abilities in evolving populations of simulated robots.

One of the key innovations during the evolution of life on earth has been the emergence of efficient communication systems, yet little is known about the causes and consequences of the great diversity within and between species. By conducting experimental evolution in 20 independently evolving populations of cooperatively foraging simulated robots, we found that historical contingency in the occurrence order of novel phenotypic traits resulted in the emergence of two distinct communication strategies. The more complex foraging strategy was less efficient than the simpler strategy. However, when the 20 populations were placed in competition with each other, the populations with the more complex strategy outperformed the populations with the less complex strategy. These results demonstrate a tradeoff between communication efficiency and robustness and suggest that stochastic events have important effects on signal evolution and the outcome of competition between distinct populations.

Complementarity between technology make and buy in innovation strategies: Evidence from Belgiam manufacturing firms

This paper characterizes the innovation strategy of manufacturing firms andexamines the relation between the innovation strategy and importantindustry-, firm- and innovation-specific characteristics using Belgiandata from the Eurostat Community Innovation Survey. In addition to importantsize effects explaining innovation, we find that high perceived risks andcosts and low appropriability of innovations do not discourage innovation,but rather determine how the innovation sourcing strategy is chosen. Withrespect to the determinants of the decision of the innovative firm toproduce technology itself (Make) or to source technology externally (Buy),we find that small firms are more likely restrict their innovation strategyto an exclusive make or buy strategy, while large firms are more likely tocombine both internal and external knowledge acquisition in their innovationstrategy. An interesting result that highlights the complementary nature ofthe Make and Buy decisions, is that, controlled for firm size, companies forwhich internal information is an important source for innovation are morelikely to combine internal and external sources of technology. We find thisto be evidence of the fact that in-house R&D generates the necessaryabsorptive capacity to profit from external knowledge acquisition. Also theeffectiveness of different mechanisms to appropriate the benefits ofinnovations and the internal organizational resistance against change areimportant determinants of the firm's technology sourcing strategy.

Lipid and energy contents in the bodies of queens of Atta sexdens rubropilosa Forel (Hymenoptera, Formicidae): pre-and post-nuptial flight

The nuptial flight allows males and females to meet and copulate and both need energy to perform this activity. Before leaving the nest, males and females are well nourished and ready to mate. However, little is known about the lipid and energy contents in females before the nuptial flight (virgins) and after it (mated females). In this work we measured lipid concentrations in relation to body weight in these individuals. Our results showed that 16.82% of the bodies of young virgin females one month before mating flight are composed of lipids, contrasting with the 32.62% lipid content in mated females who had not excavated their nest yet, and 32.88% in those who had. The energy content measured for virgin females was 2942.63 J, contrasting with 6110.01 J for queens before excavating the nest and 5677.51 J after excavation. Based on our results, we conclude that the body mass, and therefore the lipid and energy contents in the bodies of Atta sexdens rubropilosa queens double during the last month before the nuptial flight. This energy resource is fundamental to the activities required during the nuptial flight, digging the nest and the founding of the colony.

Individual and dyadic coping strategies in the aftermath of a traumatic experience

This study was designed to explore individual and dyadic coping strategies in the aftermath of a traumatic event. Eighteen persons having experienced a physical assault or a road accident within six to twelve months before the study, and eighteen matched control persons were recruited together with their partners. Each participant and his/her partner filled in several questionnaires on individual and dyadic coping strategies, level of stress and PTSD-symptomatology. Results indicate that participants having experienced a trauma, compared to controls, report a general lack of dyadic coping and, when facing daily hassles, specific decreases in individual coping strategies. These differences are discussed in the context of marital coping processes.

Adverse events to antiretrovirals in the Swiss HIV Cohort Study: effect on mortality and treatment modification.

BACKGROUND: Antiretroviral therapy (ART) decreases morbidity and mortality in HIV-infected patients but is associated with considerable adverse events (AEs). METHODS: We examined the effect of AEs to ART on mortality, treatment modifications and drop-out in the Swiss HIV Cohort Study. A cross-sectional evaluation of prevalence of 13 clinical and 11 laboratory parameters was performed in 1999 in 1,078 patients on ART. AEs were defined as abnormalities probably or certainly related to ART. A score including the number and severity of AEs was defined. The subsequent progression to death, drop-out and treatment modification due to intolerance were evaluated according to the baseline AE score and characteristics of individual AEs. RESULTS: Of the 1,078 patients, laboratory AEs were reported in 23% and clinical AEs in 45%. During a median follow up of 5.9 years, laboratory AEs were associated with higher mortality with an adjusted hazard ratio (HR) of 1.3 (95% confidence interval [CI] 1.2-1.5; P < 0.001) per score point. For clinical AEs no significant association with increased mortality was found. In contrast, an increasing score for clinical AEs (HR 1.11,95% CI 1.04-1.18; P = 0.002), but not for laboratory AEs (HR 1.07, 95% CI 0.97-1.17; P = 0.17), was associated with antiretroviral treatment modification. AEs were not associated with a higher drop-out rate. CONCLUSIONS: The burden of laboratory AEs to antiretroviral drugs is associated with a higher mortality. Physicians seem to change treatments to relieve clinical symptoms, while accepting laboratory AEs. Minimizing laboratory drug toxicity seems warranted and its influence on survival should be further evaluated.

Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii.

ABSTRACT: BACKGROUND: Sphingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. Thus far, however, little is known about the adaptive strategies used by Sphingomonas bacteria to respond to changes in water potential. To improve our understanding, strain RW1 was perturbed with either the cell-permeating solute sodium chloride or the non-permeating solute polyethylene glycol with a molecular weight of 8000 (PEG8000). These solutes are assumed to simulate the solute and matric components of the total water potential, respectively. The responses to these perturbations were then assessed and compared using a combination of growth assays, transcriptome profiling, and membrane fatty acid analyses. RESULTS: Under conditions producing a similar decrease in water potential but without effect on growth rate, there was only a limited shared response to perturbation with sodium chloride or PEG8000. This shared response included the increased expression of genes involved with trehalose and exopolysaccharide biosynthesis and the reduced expression of genes involved with flagella biosynthesis. Mostly, the responses to perturbation with sodium chloride or PEG8000 were very different. Only sodium chloride triggered the increased expression of two ECF-type RNA polymerase sigma factors and the differential expression of many genes involved with outer membrane and amino acid metabolism. In contrast, only PEG8000 triggered the increased expression of a heat shock-type RNA polymerase sigma factor along with many genes involved with protein turnover and repair. Membrane fatty acid analyses further corroborated these differences. The degree of saturation of membrane fatty acids increased after perturbation with sodium chloride but had the opposite effect and decreased after perturbation with PEG8000. CONCLUSIONS: A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.

History of diabetes and risk of head and neck cancer: a pooled analysis from the international head and neck cancer epidemiology consortium.

BACKGROUND: A history of diabetes is associated with an increased risk of several types of cancers. Whether diabetes is a risk factor for head and neck cancer (HNC) has received little attention. METHODS: We pooled data from 12 case-control studies including 6,448 cases and 13,747 controls, and estimated odds ratios (OR) and 95% confidence intervals (CI) for the associations between diabetes and HNC, adjusted for age, education level, sex, race/ethnicity, study center, cigarette smoking, alcohol use and body mass index (BMI). RESULTS: We observed a weak association between diabetes and the incidence of HNC overall (OR, 1.09; 95% CI, 0.95-1.24). However, we observed a modest association among never smokers (OR, 1.59; 95% CI, 1.22-2.07), and no association among ever smokers (OR, 0.96; 95% CI, 0.83-1.11); likelihood ratio test for interaction p=0.001. CONCLUSIONS: A history of diabetes was weakly associated with HNC overall, but we observed evidence of effect modification by smoking status, with a positive association among those who never smoked cigarettes. Impact: This study suggests that glucose metabolism abnormalities may be a HNC risk factor in subgroups of the population. Prospective studies incorporating biomarkers are needed to improve our understanding of the relationship between diabetes and HNC risk, possibly providing new strategies in the prevention of HNC.

Foraging strategies of the ant Ectatomma vizottoi (Hymenoptera, Formicidae)

Foraging strategies of the ant Ectatomma vizottoi (Hymenoptera, Formicidae). Foraging activity may be limited by temperature, humidity, radiation, wind, and other abiotic factors, all of which can affect energy costs during foraging. Ectatomma vizottoi's biology has only recently been studied, and no detailed information is available on its foraging patterns or diet in the field. For this reason, and because foraging activity is an important part of the ecological success of social insects, the present study aimed to investigate E. vizottoi's foraging strategies and dietary habits. First, we determined how abiotic factors constrained E. vizottoi's foraging patterns in the field by monitoring the foraging activity of 16 colonies on eight different days across two seasons. Second, we characterized E. vizottoi's diet by monitoring another set of 26 colonies during peak foraging activity. Our results show that E. vizottoi has foraging strategies that are similar to those of congeneric species. In spite of having a low efficiency index, colonies adopted strategies that allowed them to successfully obtain food resources while avoiding adverse conditions. These strategies included preying on other ant species, a foraging tactic that could arise if a wide variety of food items are not available in the environment or if E. vizottoi simply prefers, regardless of resource availability, to prey on other invertebrates and especially on other ant species.