The nutritional status and eating habits of shift workers: a chronobiological approach

The eating habits of workers may vary according to the season of the year and corresponding work schedule. A study aiming at verifying the changes in their diet in summer and winter, as well as the nutritional status of those who work fixed shifts, was conducted. The distribution during the 24h in the quantity of calories and macronutrients ingested and the circadian rhythm of calories consumed were also analyzed. The study was conducted on 28 workers subject to three fixed work (morning, afternoon, and night) shifts at a transport company in the city of S?o Paulo, Brazil. The mean age of the workers was 32.8 (SD+/-5.3) yrs. Their food intake was ascertained by the use of a 3-day dietary record, and their nutritional status was evaluated by their body mass index (BMI), both in winter and summer. Two-way ANOVA (shift and season) showed food consumption--measured in calories/24 h--was significantly higher in winter than summer (F(1.25)=11.7; p<0.001). No statistically significant differences were found among shifts (F(2.25)=0.85; p<0.44), and the interaction effect between shift and season was also not significant (F(2.25) = 0.15; p < 0.86). No seasonal difference in BMI was detected (Kruskal-Wallis test). Cosinor analyses showed circadian rhythmicity in calories consumed by morning (p < 0.01) as well as afternoon shift workers (p < 0.001), both in the winter and summer. Circadian rhythmicity in calories consumed by night workers was found only in summer (p < 0.01). The changes observed in the workers' eating habits from one season to another and during the 24h period show the need for further studies to help develop educational programs to improve the nutrition of shift employees taking into consideration shift schedule and season of the year when work is performed.     

Lighting requirements of nocturnal primates in captivity: A chronobiological approach

From the results of chronobiological studies in 11 Aotus lemurinus (trivirgatus) griseimembra, 3 Galago garnettii, 5 Galago senegalensis, and 6 Microcebus murinus, inferences can be made on the most suitable lighting conditions for nocturnal primates kept in captivity. In each species studied light controls the daily periodic course of activity in a dual way. First, the light-dark (LD) cycle acts as the main Zeitgeber, entraining the endogenous circadian timing system (CTS) to the environmental periodicity. Second, the prevailing light intensity has a direct species-specific inhibiting or enhancing effect, masking the level of activity predetermined by the CTS. Marked inhibition of activity is caused especially by low light intensities during dark-time (D-time), which can also lead to drastically reduced food intake (e.g., in Aotus). Therefore, high-amplitude LD cycles should be applied which guarantee a stable external and internal synchronization of the various circadian rhythms of the organism, with a D-illumination intensity high enough to prevent light-induced impairments of the behavior of the animals. Up to now LD cycles of 12:12 h (100–1,000:0.5–0.01 lx; ≥5,000°K) have proved to be most suitable. Only in Microcebus should the D-illumination be reduced to about 10^?4 lx. Moreover, it must be considered that species with a photoperiodically controlled reproduction cycle require specific alterations of the L-time:D-time ratio.     

Integrating a functional proteomic approach into the target discovery process

Functional proteomics is a promising technique for the rational identification of novel therapeutic targets by elucidation of the function of newly identified proteins in disease-relevant cellular pathways. Of the recently described high-throughput approaches for analyzing protein-protein interactions, the yeast two-hybrid (Y2H) system has turned out to be one of the most suitable for genome-wide analysis. However, this system presents a challenging technical problem: the high prevalence of false positives and false negatives in datasets due to intrinsic limitations of the technology and the use of a high-throughput, genetic assay. We discuss here the different experimental strategies applied to Y2H assays, their general limitations and advantages. We also address the issue of the contribution of protein interaction mapping to functional biology, especially when combined with complementary genomic and proteomic analyses. Finally, we illustrate how the combination of protein interaction maps with relevant functional assays can provide biological support to large-scale protein interaction datasets and contribute to the identification and validation of potential therapeutic targets.     

Placing the North American invasion of Asian carp in a spatially explicit context

The bighead (Hypothalmichthys nobilis) and silver carp (H. molitrix) have invaded much of the Mississippi River. It is unclear how reproduction in northern impounded pools of the Upper Mississippi River System (UMRS) compares to unimpounded (open) southern reaches. During spring through summer 2005 and 2006 and once in spring 2007, we quantified larval and juvenile production in the pooled and open UMRS. We then simulated population dynamics in pools as a function of apparent reproductive success. Larvae occurred during about 2 weeks each spring. Peak density and apparent spawn duration were greater in the open reach. Larval production peaked when discharge was high plus rising and water temperatures reached 18°C. Most juveniles (>97%) occurred in the open reach. Low flow during drought years in the pools may limit reproductive success. The simulation demonstrated that, by treating dams as barriers to invasion from the lower open river (i.e., a source), climatic conditions may interact with flow in pools to limit populations by creating an isolated sink.     

Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex

The well-documented Floridian Gulf/Atlantic marine genetic disjunction provides an influential example of presumed vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. However, it is unclear if this disjunction represents a local anomaly for regionally distributed morphospecies, or if it is merely one of many such cryptic phylogenetic splits that underlay their assumed genetic cohesiveness. We aimed to place the previously characterized scorched mussel Gulf/Atlantic genetic disjunction into a regional phylogenetic perspective by incorporating genotypes of nominal conspecifics sampled throughout the Caribbean Basin as well as those of eastern Pacific potential geminate species. Our results show it to be one of multiple latent regional genetic disjunctions, involving five cryptic Caribbean species, that appear to be the product of a long history of regional cladogenesis. Disjunctions involving three stem lineages clearly predate formation of the Isthmus of Panama and of the Caribbean Sea, although four of the five cryptic species have within-basin sister relationships. Surprisingly, the Atlantic clade was also found to be widespread in the southern Caribbean, and ancestral demography calculations through time for Atlantic coast-specific genotypes are consistent with a northward range extension after the last glacial maximum. Our new data seriously undermine the hypothesis of a Floridian vicariant genesis and imply that the scorched mussel Gulf/Atlantic disjunction represents a case of geographic and temporal pseudocongruence. All five Caribbean Basin cryptic species exhibited an intriguing pattern of predominantly allopatric distribution characterized by distinct geographic areas of ecological dominance, often adjoining those of sister taxa. This pattern of distribution is consistent with allopatric speciation origins, coupled with restricted postspeciation range extensions. Several lines of indirect evidence favor the hypothesis that the predominantly allopatric distributions are maintained over evolutionary time scales, primarily by postrecruitment ecological filters rather than by oceanographic barriers to larval-mediated gene flow.     

Time, gender, and seasonality in vervet activity: A chronobiological approach

A chronobiological approach has been used to highlight the issue of how climatic factors and breeding seasonality may affect male and female diurnal activity budget. We investigated gender differences for vervet monkeys in the diurnal distribution of feeding, locomotion, inactivity, and social grooming within and between birth, pre-mating, and mating seasons. The main climatic traits were that days were shorter, drier, and cooler in the mating season. Non-parametric statistics showed that female activities changed with time of day to a greater extent than did male activities. When the constraints imposed by climatic factors and mate competition increased, from the birth to the mating season, male maintenance activities were more independent of the time of day whereas females continued to vary. Gender differences in timing were therefore greater in the mating season, except for social grooming; males and females were more coordinated in diurnal timing of their grooming in the mating season. It is argued that these changes may result in reduced levels of male-female contest competition, and may be related to higher levels of male-female socialization in the mating season. Finally, it is inferred that an out-of-phase synchronization between inactivity and feeding for males in the birth season, and for females in the mating season, may result from each sex investing more time feeding at the expense of resting in those periods.     

Placing Biebersteiniaceae, a herbaceous clade of Sapindales, in a temporal and geographic context

Biebersteiniaceae comprise a single genus with four species of perennial herbs occurring from central Asia to Greece. A previous molecular phylogenetic study placed one of the species in an isolated position in Sapindales, while morphological studies had placed Biebersteinia in or near Geraniaceae, albeit doubtfully. We tested the monophyly and placement of the family with data from the chloroplast genes rbcL and atpB obtained for all four species, other major clades of Sapindales and outgroups for a total of up to 114 taxa. Parsimony, Bayesian, and likelihood analyses place Biebersteinia in Sapindales, possibly as sister to the other eight families. Strict and relaxed molecular clocks constrained with fossils of Biebersteinia and up to eight other Sapindales suggest that the Biebersteinia crown group diversified in the Oligocene and Miocene, while the stem lineage dates back to the Late Paleocene. Ages for other sapindalean families are earlier than those obtained in more sparsely sampled analyses, although estimates for Burseraceae agree surprisingly well. Ancestral area analyses suggest that Biebersteinia expanded from the eastern part of its range (i.e. Tibet and Inner Mongolia) to the west, although analyses are hampered by the unclear sister group relationships.     

Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants

The tumor suppressor protein p53 can lose its function upon single-point missense mutations in the core DNA-binding domain (“cancer mutants”). Activity can be restored by second-site suppressor mutations (“rescue mutants”). This paper relates the functional activity of p53 cancer and rescue mutants to their overall molecular dynamics (MD), without focusing on local structural details. A novel global measure of protein flexibility for the p53 core DNA-binding domain, the number of clusters at a certain RMSD cutoff, was computed by clustering over 0.7 µs of explicitly solvated all-atom MD simulations. For wild-type p53 and a sample of p53 cancer or rescue mutants, the number of clusters was a good predictor of in vivo p53 functional activity in cell-based assays. This number-of-clusters (NOC) metric was strongly correlated (r² = 0.77) with reported values of experimentally measured ΔΔG protein thermodynamic stability. Interpreting the number of clusters as a measure of protein flexibility: (i) p53 cancer mutants were more flexible than wild-type protein, (ii) second-site rescue mutations decreased the flexibility of cancer mutants, and (iii) negative controls of non-rescue second-site mutants did not. This new method reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants.     

A metaproteomic approach gives functional insights into anaerobic digestion

Aims: The objective of this work was to provide functional evidence of key metabolic pathways important for anaerobic digestion processes through the identification of highly expressed proteins in a mixed anaerobic microbial consortium. Methods and Results: The microbial communities from an anaerobic industrial‐like wastewater treatment bioreactor were characterized using phylogenetic analyses and metaproteomics. Clone libraries indicated that the bacterial community in the bioreactor was diverse while the archaeal population was mainly composed of Methanocorpusculum‐like (76%) micro‐organisms. Three hundred and eighty‐eight reproducible protein spots were obtained on 2‐D gels, of which 70 were excised and 33 were identified. The putative functions of the proteins detected in the anaerobic bioreactor were related to cellular processes, including methanogenesis from CO₂ and acetate, glycolysis and the pentose phosphate pathway. Metaproteomics also indicated, by protein assignment, the presence of specific micro‐organisms in the bioreactor. However, only a limited overlap was observed between the phylogenetic and metaproteomic analyses. Conclusions: This study provides some direct evidence of the microbial activities taking place during anaerobic digestion. Significance and Impact of Study: This study demonstrates metaproteomics as a useful tool to uncover key biochemical pathways underpinning specific anaerobic bioprocesses.     

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

Background

Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.

Results

Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.

Conclusions

JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.     

Breaking functional connectivity into components: a novel approach using an individual-based model, and first outcomes

Landscape connectivity is a key factor determining the viability of populations in fragmented landscapes. Predicting 'functional connectivity', namely whether a patch or a landscape functions as connected from the perspective of a focal species, poses various challenges. First, empirical data on the movement behaviour of species is often scarce. Second, animal-landscape interactions are bound to yield complex patterns. Lastly, functional connectivity involves various components that are rarely assessed separately. We introduce the spatially explicit, individual-based model FunCon as means to distinguish between components of functional connectivity and to assess how each of them affects the sensitivity of species and communities to landscape structures. We then present the results of exploratory simulations over six landscapes of different fragmentation levels and across a range of hypothetical bird species that differ in their response to habitat edges. i) Our results demonstrate that estimations of functional connectivity depend not only on the response of species to edges (avoidance versus penetration into the matrix), the movement mode investigated (home range movements versus dispersal), and the way in which the matrix is being crossed (random walk versus gap crossing), but also on the choice of connectivity measure (in this case, the model output examined). ii) We further show a strong effect of the mortality scenario applied, indicating that movement decisions that do not fully match the mortality risks are likely to reduce connectivity and enhance sensitivity to fragmentation. iii) Despite these complexities, some consistent patterns emerged. For instance, the ranking order of landscapes in terms of functional connectivity was mostly consistent across the entire range of hypothetical species, indicating that simple landscape indices can potentially serve as valuable surrogates for functional connectivity. Yet such simplifications must be carefully evaluated in terms of the components of functional connectivity they actually predict.     

Stochastic functional data analysis: a diffusion model-based approach

This article presents a new modeling strategy in functional data analysis. We consider the problem of estimating an unknown smooth function given functional data with noise. The unknown function is treated as the realization of a stochastic process, which is incorporated into a diffusion model. The method of smoothing spline estimation is connected to a special case of this approach. The resulting models offer great flexibility to capture the dynamic features of functional data, and allow straightforward and meaningful interpretation. The likelihood of the models is derived with Euler approximation and data augmentation. A unified Bayesian inference method is carried out via a Markov chain Monte Carlo algorithm including a simulation smoother. The proposed models and methods are illustrated on some prostate-specific antigen data, where we also show how the models can be used for forecasting.     

Placing biodiversity and ecosystem functioning in context: environmental perturbations and the effects of species richness in a stream field experiment

Greater biodiversity is often associated with increased ecosystem process rates, and is expected to enhance the stability of ecosystem functioning under abiotic stress. However, these relationships might themselves be altered by environmental factors, complicating prediction of the effects of species loss in ecosystems subjected to abiotic stress. In boreal streams, we investigated effects of biodiversity and two abiotic perturbations on three related indices of ecosystem functioning: leaf decomposition, detritivore leaf processing efficiency (LPE) and detritivore growth. Replicate field enclosures containing leaves and detritivore assemblages were exposed to liming and nutrient enrichment, raising pH and nutrient levels. Both treatments constitute perturbations for our naturally acidic and nutrient-poor streams. We also varied detritivore species richness and density. The effects of the abiotic and diversity manipulations were similar in magnitude, but whereas leaf decomposition increased by 18% and 8% following liming and nutrient enrichment, respectively, increased detritivore richness reduced leaf decomposition (6%), detritivore LPE (19%) and detritivore growth (12%). The detritivore richness effect on growth was associated with negative trait-independent complementarity, indicating interspecific interference competition. These interactions were apparently alleviated in both enriched and limed enclosures, as trait-independent complementarity became less negative. LPE increased with detritivore density in the monocultures, indicating benefits of intra-specific aggregation that outweighed the costs of intra-specific competition, and dilution of these benefits probably contributed to lowered leaf decomposition in the species mixtures. Finally, the effects of liming were reduced in most species mixtures relative to the monocultures. These results demonstrate how environmental changes might regulate the consequences of species loss for functioning in anthropogenically perturbed ecosystems, and highlight potential influences of biodiversity on functional stability. Additionally, the negative effects of richness and positive effects of density in our field study were opposite to previous laboratory observations, further illustrating the importance of environmental context for biodiversity–ecosystem functioning relationships.     

PATIKAmad: putting microarray data into pathway context

High-throughput experiments, most significantly DNA microarrays, provide us with system-scale profiles. Connecting these data with existing biological networks poses a formidable challenge to uncover facts about a cell's proteome. Studies and tools with this purpose are limited to networks with simple structure, such as protein-protein interaction graphs, or do not go much beyond than simply displaying values on the network. We have built a microarray data analysis tool, named PATIKAmad, which can be used to associate microarray data with the pathway models in mechanistic detail, and provides facilities for visualization, clustering, querying, and navigation of biological graphs related with loaded microarray experiments. PATIKAmad is freely available to noncommercial users as a new module of PATIKAweb at http://web.patika.org.