Nuclear DNA in the determination of weighing factors to estimate exergy from organisms biomass

Computational Simulation of Colorectal Cancer Biomarker Particle Mobility in a 3D Model

Even though some methods for the detection of colorectal cancer have been used clinically, most of the techniques used do not consider the in situ detection of colorectal cancer (CRC) biomarkers, which would favor in vivo real-time monitoring of the carcinogenesis process and consequent studies of the disease. In order to give a scientific and computational framework ideal for the evaluation of diagnosis techniques based on the early detection of biomarker molecules modeled as spherical particles from the computational point of view, a computational representation of the rectum, stool and biomarker particles was developed. As consequence of the transport of stool, there was a displacement of CRC biomarker particles that entered the system as a result of the cellular apoptosis processes in polyps with a length lower than 1 cm, reaching a maximum velocity of 3.47×10-3 m/s. The biomarkers studied showed trajectories distant to regions of the polyp of origin in 1 min of simulation. The research results show that the biomarker particles for CRC respond to the variations in the movements of the stool with trajectories and speeds that depend on the location of the injury, which will allow locating the regions with the highest possibilities of catching particles through in situ measurement instruments in the future.

Dynamics of community structure and bio-thermodynamic health of soil organisms following subtropical forest succession

Soil organisms play essential roles in maintaining multiple ecosystem processes, but our understanding of the dynamics of these communities during forest succession remains limited. In this study, the dynamics of soil organism communities were measured along a 3-step succession sequence of subtropical forests (i.e., a conifer forest, CF; a mixed conifer and broad-leaved forest, MF; and a monsoon evergreen broad-leaved forest, BF). The eco-exergy evaluation method was used as a complement to the classic community structure index system to reveal the holistic dynamics of the bio-thermodynamic health of soil organism communities in a forest succession series. Association between the self-organization of soil organisms, soil properties, and plant factors were explored through redundancy analyses (RDA). The results indicated that the biomass of soil microbes progressively increased in the dry season, from 0.75 g m^-2 in CF to 1.75 g m^-2 in BF. Microbial eco-exergy showed a similar pattern, while the community structure and the specific eco-exergy remained constant. Different trends for the seasons were observed for the soil fauna community, where the community biomass increased from 0.72 g m^-2 to over 1.97 g m^-2 in the dry season, but decreased from 3.94 g m^-2 to 2.36 g m^-2 in the wet season. Faunal eco-exergies followed a similar pattern. Consequently, the average annual biomass of the soil faunal community remained constant (2.17-2.39 g m^-2) along the forest succession sequence, while the significant seasonal differences in both faunal biomass and eco-exergy observed at the early successional stage (CF) were insignificant in the middle and late forest successional stages (MF and BF). Both the dynamics of soil microbes and soil fauna were tightly correlated with tree biomass and with soil physicochemical properties, especially soil pH, moisture, total nitrogen, nitrate nitrogen, and organic matter content.

Analysis of the characteristics of Eco-Exergy-based indices and diversity indices in the Zhoushan archipelago, China

Anthropogenic disturbance of coastal ecosystems has increased the need for comprehensive methods and indicators to assess the health status of marine ecosystems. Biotic indices are important as they indicate different ecological states. In this study, Eco-Exergy-based indices (Exergy and Structural Exergy) and diversity indices (Shannon-Wiener index and Margalef index) were applied in the seas around the Zhoushan archipelago, and correlation analysis between biotic indices and environmental factors was used to test the robustness of these indices in capturing the environment changes, aimed to provide reference in selecting the indices for assessing marine eco-environment quality. Results showed that the benthic indices of Exergy, Shannon-Wiener, and Margalef increased with the distance from the mainland. The Eco-Exergy-based indices and Margalef index were significantly, negatively correlated with dissolved inorganic nitrogen and reactive phosphate, and significantly, positively correlated with the salinity of seawater. Overall, the marine ecosystem was more stable further away from the coast, where salinity was higher, and pollutants such as nutrients in seawater were lower. In addition, biodiversity and Eco-Exergy was also higher. Generally, Eco-Exergy-based indices were observed to be good indicators for detecting the environment changes in the study area.

Thermodynamics in Ecology-An Introductory Review

How to predict the evolution of ecosystems is one of the numerous questions asked of ecologists by managers and politicians. To answer this we will need to give a scientific definition to concepts like sustainability, integrity, resilience and ecosystem health. This is not an easy task, as modern ecosystem theory exemplifies. Ecosystems show a high degree of complexity, based upon a high number of compartments, interactions and regulations. The last two decades have offered proposals for interpretation of ecosystems within a framework of thermodynamics. The entrance point of such an understanding of ecosystems was delivered more than 50 years ago through Schrödinger's and Prigogine's interpretations of living systems as "negentropy feeders" and "dissipative structures", respectively. Combining these views from the far from equilibrium thermodynamics to traditional classical thermodynamics, and ecology is obviously not going to happen without problems. There seems little reason to doubt that far from equilibrium systems, such as organisms or ecosystems, also have to obey fundamental physical principles such as mass conservation, first and second law of thermodynamics. Both have been applied in ecology since the 1950s and lately the concepts of exergy and entropy have been introduced. Exergy has recently been proposed, from several directions, as a useful indicator of the state, structure and function of the ecosystem. The proposals take two main directions, one concerned with the exergy stored in the ecosystem, the other with the exergy degraded and entropy formation. The implementation of exergy in ecology has often been explained as a translation of the Darwinian principle of "survival of the fittest" into thermodynamics. The fittest ecosystem, being the one able to use and store fluxes of energy and materials in the most efficient manner. The major problem in the transfer to ecology is that thermodynamic properties can only be calculated and not measured. Most of the supportive evidence comes from aquatic ecosystems. Results show that natural and culturally induced changes in the ecosystems, are accompanied by a variations in exergy. In brief, ecological succession is followed by an increase of exergy. This paper aims to describe the state-of-the-art in implementation of thermodynamics into ecology. This includes a brief outline of the history and the derivation of the thermodynamic functions used today. Examples of applications and results achieved up to now are given, and the importance to management laid out. Some suggestions for essential future research agendas of issues that needs resolution are given.

Eco-exergy and emergy based self-organization of three forest plantations in lower subtropical China

The bio-thermodynamic structures of a mixed native species plantation, a conifer plantation and an Acacia mangium plantation in Southern China were quantified over a period of 15 years based on eco-exergy methods. The efficiencies of structural development and maintenance were quantified through an integrated application of eco-exergy and emergy methods. The results showed that the storage of eco-exergy increased over 3 times in all three plantations, as predicted by the maximum eco-exergy principle. This trend was primarily seen due to the accumulation of biomass, instead of an increase in the specific eco-exergy (eco-exergy per unit biomass), although species richness did increase. The eco-exergy to emergy and eco-exergy to empower ratios of the three plantations generally increased during the study period, but the rate of increase slowed down after 20 years. The dominant trees are the largest contributors to the eco-exergy stored in the plantations, and thus, the introduction of suitable indigenous tree species should be considered after the existing trees pass through their period of most rapid growth or around 20 years after planting. The combined application of C-values and suggested weighting factors in the eco-exergy calculation can imply opposite results, but may also supply useful information for forest management.

RNA:DNA ratio and other nucleic acid derived indices in marine ecology

Some of most used indicators in marine ecology are nucleic acid-derived indices. They can be divided by target levels in three groups: 1) at the organism level as ecophysiologic indicators, indicators such as RNA:DNA ratios, DNA:dry weight and RNA:protein, 2) at the population level, indicators such as growth rate, starvation incidence or fisheries impact indicators, and 3) at the community level, indicators such as trophic interactions, exergy indices and prey identification. The nucleic acids derived indices, especially RNA:DNA ratio, have been applied with success as indicators of nutritional condition, well been and growth in marine organisms. They are also useful as indicators of natural or anthropogenic impacts in marine population and communities, such as upwelling or dredge fisheries, respectively. They can help in understanding important issues of marine ecology such as trophic interactions in marine environment, fish and invertebrate recruitment failure and biodiversity changes, without laborious work of counting, measuring and identification of small marine organisms. Besides the objective of integrate nucleic acid derived indices across levels of organization, the paper will also include a general characterization of most used nucleic acid derived indices in marine ecology and also advantages and limitations of them. We can conclude that using indicators, such RNA:DNA ratios and other nucleic acids derived indices concomitantly with organism and ecosystems measures of responses to climate change (distribution, abundance, activity, metabolic rate, survival) will allow for the development of more rigorous and realistic predictions of the effects of anthropogenic climate change on marine systems.

Application of biotic indices and relationship with structural and functional features of macrobenthic community in the lagoon of Venice: an example over a long time series of data

In the context of the application of WFD, a scientific debate is growing about the applicability of biotic indices in coastal and transitional waters. In the present work, the question about the discriminating power of different biotic indices and the relationships with the structure and functioning of the macrobenthic community in a transitional environment is discussed. A time series of samples collected during the last 70 years in the lagoon of Venice, reflecting different environmental conditions (a sort of 'pristine state' in 1935, the distrophic crisis in 1988 and subsequent modifications in 1990, the invasion by an alien species and the developing of high impacting fishery in 1999) has been used. The comparison of results obtained by applying different biotic indices, such as AMBI, Bentix and BOPA, shows differences in the discriminating power of indices and a general overestimation of environmental conditions. Discrepancies between environmental status as indicated by biotic indices and the structure and functioning of the benthic community have been highlighted.

THIS ARTICLE HAS BEEN RETRACTED Exergy as an ecological application used in the recovery process of benthic communities

Exergy, the thermodynamic function that represents the distance of an open system from equilibrium, is proposed as an ecological indicator for summarizing the complex dynamics occurring in a disturbed community during its recovery processes. These complex dynamics can be difficult to capture by using classical indices. In this study, we sampled macrobenthos using the BACI scheme (before versus after; control versus impact) in tidal wetlands of west Chongming Island, China, an area that has been disturbed by ecological engineering measures. Exergy storage is estimated for benthic communities. The control area is proposed as dynamic reference for estimating local exergy storage of the benthic community. Three different methods were used for estimating exergy on the basis of coefficients: (a) taken for taxa groups; (b) estimated from coding genes given for broad taxonomic groups; and (c) estimated from genome size taken as close as possible to the taxonomic level of the species, providing a basis for inferring similarities. We found a decrease of local exergy content in the disturbed area 9 days after the disturbance. Subsequently, the reference exergy of the benthic community increased (i.e. in the surrounding control area) in accordance with the proposed hypothesis regarding the dynamics of exergy storage during a system's development. Estimates of local exergy arrived at using the three methods provided comparable results. Based on this, we then discuss the feasibility of using the more readily available genome size data for estimating exergy. This result may have important implications for broader application of this indicator to biological systems. Moreover, the adjacent control samples seem to represent an appropriate dynamic reference for estimating the local exergy of disturbed communities. We found that exergy was a useful indicator that integrates the processes underlying the recovery of the benthic community after disturbance.