Project description:Chickens (Cobb500FF) divergent in residual feed intake were analyzed for muscular (M. pectoralis), duodenal, jejunal and ileal transcriptomic profiles.
Project description:Bacteria like E. coli grow at vastly different rates on different substrates, however, the precise reason for this variability is poorly understood. Different growth rates have been attributed to 'nutrient quality', a key parameter in bacterial growth laws. However, it remains unclear to what extent nutrient quality is rooted in fundamental biochemical constraints like the energy content of nutrients, the protein cost required for their uptake and catabolism, or the capacity of the plasma membrane for nutrient transporters. Here, we show that while nutrient quality is indeed reflected in protein investment in substrate-specific transporters and enzymes, this is not a fundamental limitation on growth rate. We show that it is possible to turn mannose, one of the 'poorest' substrates of E. coli, into one of the 'best' substrates by reengineering chromosomal promoters of the mannose transporter and metabolic enzymes required for mannose degradation. However, we show that this faster growth rate comes at the cost of diverse cellular capabilities, reflected in longer lag phases, worse starvation survival and lower motility. We show that addition of cAMP to the medium can rescue these phenotypes but imposes a corresponding growth cost. Based on these data, we propose that nutrient quality is largely a self-determined, plastic property that can be modulated by the fraction of proteomic resources devoted to a specific substrate in the much larger proteome sector of catabolically activated genes. Rather than a fundamental biochemical limitation, nutrient quality reflects resource allocation decisions that are shaped by evolution in specific ecological niches and can be quickly adapted if necessary.
Project description:Bacteria like E. coli grow at vastly different rates on different substrates, however, the precise reason for this variability is poorly understood. Different growth rates have been attributed to 'nutrient quality', a key parameter in bacterial growth laws. However, it remains unclear to what extent nutrient quality is rooted in fundamental biochemical constraints like the energy content of nutrients, the protein cost required for their uptake and catabolism, or the capacity of the plasma membrane for nutrient transporters. Here, we show that while nutrient quality is indeed reflected in protein investment in substrate-specific transporters and enzymes, this is not a fundamental limitation on growth rate, at least for certain 'poor' substrates. We show that it is possible to turn mannose, one of the 'poorest' substrates of E. coli, into one of the 'best' substrates by reengineering chromosomal promoters of the mannose transporter and metabolic enzymes required for mannose degradation. This result falls in line with previous observations of more subtle growth rate improvement for many other carbon sources. However, we show that this faster growth rate comes at the cost of diverse cellular capabilities, reflected in longer lag phases, worse starvation survival and lower motility. We show that addition of cAMP to the medium can rescue these phenotypes but imposes a corresponding growth cost. Based on these data, we propose that nutrient quality is largely a self-determined, plastic property that can be modulated by the fraction of proteomic resources devoted to a specific substrate in the much larger proteome sector of catabolically activated genes. Rather than a fundamental biochemical limitation, nutrient quality reflects resource allocation decisions that are shaped by evolution in specific ecological niches and can be quickly adapted if necessary.
Project description:This paper considers the generic problem of a central authority selecting an appropriate subset of operators in order to perform a process (i.e. mission or task) in an optimized manner. The subset is selected from a given and usually large set of 'n' candidate operators, with each operator having a certain resource availability and capability. This general mission performance optimization problem is considered in terms of Unmanned Aerial Vehicles (UAVs) acting as firefighting operators in a fire extinguishing mission and from a deterministic and a stochastic algorithmic point of view. Thus the applicability and performance of certain computationally efficient stochastic multistage optimization schemes is examined and compared to that produced by corresponding deterministic schemes. The simulation results show acceptable accuracy as well as useful computational efficiency of the proposed schemes when applied to the time critical resource allocation optimization problem. Distinguishing features of this work include development of a comprehensive UAV firefighting mission framework, development of deterministic as well as stochastic resource allocation optimization techniques for the mission and development of time-efficient search schemes. The work presented here is also useful for other UAV applications such as health care, surveillance and security operations as well as for other areas involving resource allocation such as wireless communications and smart grid.
Project description:It is well established that individuals age differently. Yet the nature of these inter-individual differences is still largely unknown. For humans, two main hypotheses have been recently formulated: individuals may experience differences in aging rate or aging timing. This issue is central because it directly influences predictions for human lifespan and provides strong insights into the biological determinants of aging. In this article, we propose a model which lets population heterogeneity emerge from an evolutionary algorithm. We find that whether individuals differ in (i) aging rate or (ii) timing leads to different emerging population heterogeneity. Yet, in both cases, the same mortality patterns are observed at the population level. These patterns qualitatively reproduce those of yeasts, flies, worms and humans. Such findings, supported by an extensive parameter exploration, suggest that mortality patterns across species and their potential shapes belong to a limited and robust set of possible curves. In addition, we use our model to shed light on the notion of subpopulations, link population heterogeneity with the experimental results of stress induction experiments and provide predictions about the expected mortality patterns. As biology is moving towards the study of the distribution of individual-based measures, the model and framework we propose here paves the way for evolutionary interpretations of empirical and experimental data linking the individual level to the population level.
Project description:Considerable variation in feed efficiency (FE) has been observed in indigenous and selected meat-type chicken populations. Although this variation could be partially linked to extrinsic factors like diet, housing environment and microbiota, it further illustrates the existence of strong molecular mechanisms enabling the differential allocation of resources for various physiological processes. To further deepen the molecular basis of individual allocation capacity in male and female broilers, an RNA-seq experiment was conducted which based on a phenotyped chicken population divergent in FE. Transcriptional differences linked to FE were pronounced in intestinal and muscular tissue sites of male animals. Specifically, signalling pathways of farnesoid X receptor (FXR) and retinoid X receptor (RXR) might contribute to mediate individual FE. The transcriptional profiles suggested ACSBG2 (muscular lipid utilisation), ASBT (intestinal bile salt transport), CLEC2B (natural killer cell activation), HMGCS2 (jejunal, duodenal and muscular ketogenesis), and SCARB1 (jejunal lipid uptake) as potential mediators driving FE. Results indicate that improvements in FE exploit shifts in resource allocation which might occur at the expense of general immune responsiveness in high efficient male chickens. Consequently, to further improve FE traits and to explore causative molecular patterns, effects originating from sex-dimorphism in chickens need to be taken into consideration.
Project description:Large reductions in the global malaria burden have been achieved, but plateauing funding poses a challenge for progressing towards the ultimate goal of malaria eradication. Using previously published mathematical models of Plasmodium falciparum and Plasmodium vivax transmission incorporating insecticide-treated nets (ITNs) as an illustrative intervention, we sought to identify the global funding allocation that maximized impact under defined objectives and across a range of global funding budgets. The optimal strategy for case reduction mirrored an allocation framework that prioritizes funding for high-transmission settings, resulting in total case reductions of 76% and 66% at intermediate budget levels, respectively. Allocation strategies that had the greatest impact on case reductions were associated with lesser near-term impacts on the global population at risk. The optimal funding distribution prioritized high ITN coverage in high-transmission settings endemic for P. falciparum only, while maintaining lower levels in low-transmission settings. However, at high budgets, 62% of funding was targeted to low-transmission settings co-endemic for P. falciparum and P. vivax. These results support current global strategies to prioritize funding to high-burden P. falciparum-endemic settings in sub-Saharan Africa to minimize clinical malaria burden and progress towards elimination, but highlight a trade-off with 'shrinking the map' through a focus on near-elimination settings and addressing the burden of P. vivax.
Project description:Parthenium hysterophorus L. (Asteraceae) is a highly prevalent invasive species in subtropical regions across the world. It has recently been seen to shift from low (subtropical) to high (sub-temperate) elevations. Nevertheless, there is a dearth of research investigating the adaptive responses and the significance of leaf functional traits in promoting the expansion to high elevations. The current study investigated the variations and trade-offs among 14 leaf traits (structural, photosynthetic, and nutrient content) of P. hysterophorus across different elevations in the western Himalayas, India. Plots measuring 20 × 40 m were established at different elevations (700 m, 1100 m, 1400 m, and 1800 m) to collect leaf trait data for P. hysterophorus. Along the elevational gradient, significant variations were noticed in leaf morphological parameters, leaf nutrient content, and leaf photosynthetic parameters. Significant increases were observed in the specific leaf area, leaf thickness, and chlorophyll a, total chlorophyll and carotenoid content, as well as leaf nitrogen and phosphorus content with elevation. On the other hand, there were reductions in the amount of chlorophyll b, photosynthetic efficiency, leaf dry matter content, leaf mass per area, and leaf water content. The trait-trait relationships between leaf water content and dry weight and between leaf area and dry weight were stronger at higher elevations. The results show that leaf trait variability and trait-trait correlations are very important for sustaining plant fitness and growth rates in low-temperature, high-irradiance, resource-limited environments at relatively high elevations. To summarise, the findings suggest that P. hysterophorus can expand its range to higher elevations by broadening its functional niche through changes in leaf traits and resource utilisation strategies.
Project description:Hospitals and intensive care units are straining to provide care for a large surge of patients with coronavirus disease 19 (Covid-19). Contingency plans are being made for the possibility that resources for lifesaving care, including mechanical ventilators, will be in short supply. Covid-19 is more severe and more likely to be fatal in older persons. Dementia is one of the commonest severe comorbidities of aging. Persons with dementia are vulnerable and often need the support of others to make their voices heard. This commentary, created by a task force commissioned by the Alzheimer Society of Canada, provides guidance for triaging persons with dementia to scarce medical resources during the Covid-19 pandemic.
Project description:A central aim of cell biology is to understand the strategy of gene expression in response to the environment. Here we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector’s total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth-rate dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource-allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse-graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies.