Bioremediation of multi-metal contaminated soil using biosurfactant — a novel approach

An unconventional nutrient medium, distillery spent wash (1:3) diluted) was used to produce di-rhamnolipid biosurfactant by Pseudomonas aeruginosa strain BS2. This research further assessed the potential of the biosurfactant as a washing agent for metal removal from multimetal contaminated soil (Cr-940 ppm; Pb-900 ppm; Cd-430 ppm; Ni-880 ppm; Cu-480 ppm). Out of the treatments of contaminated soil with tap water and rhamnolipid biosurfactant, the latter was found to be potent in mobilization of metal and decontamination of contaminated soil. Within 36 hours of leaching study, di-rhamnolipid as compared to tap water facilitated 13 folds higher removal of Cr from the heavy metal spiked soil whereas removal of Pb and Cu was 9–10 and 14 folds higher respectively. Leaching of Cd and Ni was 25 folds higher from the spiked soil. This shows that leaching behavior of biosurfactant was different for different metals. The use of wastewater for production of biosurfactant and its efficient use in metal removal make it a strong applicant for bioremediation.     

A novel modeling approach for the “end-to-end” analysis of marine ecosystems

There is a growing demand for “end-to-end” models, which are modeling tools used to analyze and understand the fundamental complexities of marine ecosystems and processes emerging from the interaction of individuals from different trophic groups with respect to the physical environment and, even, human activity. These models are valuable quantitative tools for ecosystem-based management. To explore potential answers to complex questions regarding ecosystems using these models, it is necessary to incorporate classical ontogenic changes through the life cycle of target individuals, in addition to inherited behavioral strategies, as an additional differentiating aspect, particularly when the behavior has a direct impact on the ecosystem phenomena under study. However, it is difficult to combine different fine scale time and spatial granularities to infer animal behavior and ontogenic development. This complexity has kept these two levels of analysis separated, because most current tools do not have the required computational resources and advanced software architecture. To address this issue, we propose an individual-based modeling framework that is capable of handling and unifying the two experimental categories with a comprehensive biological and behavioral model that strictly adheres to the physiological functions of ingestion, growth, and metabolism of organisms. In addition, this model incorporates the exchange and transfer of mass and energy through local interactions at all trophic levels (lower to higher), the physical environment, and anthropogenic activity. For the framework to model short time events, such as classical predator–prey interactions, while also generating long-term ecosystem emergent properties, a special interleaving scheduling engine and physical space computer model was devised, which optimizes memory and processing resources. The framework was tested through several experiments with a three-population ecosystem containing up to 40 thousand organisms evolving inside a 200,000 m² simulation environment during 12,000 model-hours; yet, requiring only a few hours of program execution on a regular personal computer. The model included various environmental physical elements, such as several hundred shelters, the number of which can be easily modified in each experiment to simulate substrate degradation and its impact on populations. With the aid of the quantitative and qualitative tools provided by the model, it was possible to observe a coupling between prey and predator population dynamics. In conclusion, we confirmed that the end-to-end model developed here could successfully generate detailed specific hypotheses about fish behavior and quantify impacts on population dynamics.     

Cosmix-plexing®: a novel recombinatorial approach for evolutionary selection from combinatorial libraries

The efficiency of existing combinatorial biological library methods has been moderate in terms of the success rates, the affinities of the ligands selected and the time and effort involved in trying to optimize the initial leads. Although mimicking natural evolution, existing strategies take little notice of the importance of recombination within a selected population to generate increased diversity. We present an overview of our recent progress which has resulted in the successful development of such a strategy, which we designate cosmix-plexing^®. We incorporate recombination as a central feature in obtaining high success rates and high affinities, even for short monomer peptides, in a very short time. The method uses type II restriction enzymes to re-assort small hypervariable DNA cassettes from an intermediate pre-selected population (e.g. from a phagemid display library), while maintaining the original open-reading frame. Since, in the naive library, each cassette contains all possible combinations of the polypeptide sequences it encodes, much longer regions can be optimized than was possible with methods which depend on a simple selection from the naive library. Short peptides can now be rapidly selected, which exhibit the same, or higher, specificity and affinity for a defined target molecule, than (say) an antibody or even the natural ligand.     

Non-statistical isotope fractionation as a novel “retro-biosynthetic” approach to understanding alkaloid metabolic pathways

During the biosynthesis of natural products, isotope fractionation occurs due to the selectivity of enzymes for the heavier or lighter isotopomers. As only some of the positions in the molecule are implicated in a given reaction mechanism, position-specific fractionation occurs. Thus, the position-specific ¹³C/¹²C ratios in these compounds can be related to their known precursors and to the known isotope effects of enzymes involved in their biosynthesis, or similar reaction mechanisms. This can be accessed by isotope ratio monitoring NMR spectrometry. In this short review, how isotope fractionation occurs and when it is manifest is described. Then, the way that ¹³C NMR spectrometry has been applied to study certain aspects of the biosynthesis of the solanaceous alkaloids S-(−)-nicotine and tropine is outlined. Notably, it is shown how similar isotope fractionation is found in the steps of the pathway to the common intermediate, N-methyl-Δ¹-pyrrolinium, but that in the moieties derived from different origins no such similarity is found, the isotopic composition of these atoms reflecting their specific metabolic ancestry. In a second example, tramadol, it is shown how this technique can be used in retro-biosynthesis to give direction as to what precursors and pathway intermediates are probable. It is shown how the observed fractionation in the site-specific ¹³C/¹²C ratios can be effectively explained by known metabolism and the properties of enzymes proposed for the pathway. Furthermore, it can give indications of possible mechanisms of those enzymes that are as yet to be described for a number of key steps.     

Biotic wetland connectivity—supporting a new approach for wetland policy

Wetlands are key habitats connected physically and socially with processes occurring over a much wider territory. The biotic connection through dispersal mechanisms among wetlands is of primary importance to wetland management and policies. However, traditional wetland conservation approaches are based on the preservation of isolated sites considered to be of special importance (typically owing to their importance for concentrations of migratory waterbirds). Research linking local species richness and bird migration suggests that the effect of wetland loss on regional diversity might be much larger than what would be expected from direct habitat loss. Since the biotic connection among wetlands serviced by waterbirds appears to be more efficient within a limited range, the distribution of wetlands in space is a key aspect determining wetland connectedness even in the absence of direct hydrologic links. Protected areas should thus be defined with regard to waterfowl movements and waterbird migration as functional processes contributing to aquatic species migration and local species richness. This calls for a regional approach to wetland management within a continental context. This paper aims at defining an operational view of the dispersion function of wetlands and its implication for conservation policies. For this purpose, we examined the conservation policies of the Ramsar Convention (the international treaty that protects wetlands) and the European Union (as an example of relevant continental level policy-making) from the viewpoint of bird-mediated dispersal of aquatic organisms. We propose nine specific avenues for the inclusion of bird-mediated dispersal in the policy documents examined. Non-governmental organisations and other organisations working in waterbird conservation should also recognise the importance of their policies for aquatic biodiversity at broader levels and avoid compartmentalising their conservation activities.     

Independent information modules—a powerful approach for life cycle management

Background, aim, and scope

The term “information module” has been initially introduced by ISO 14025 (ISO 14025 2006) which specifies Type III environmental declarations. It comprises a set of predetermined parameters (PDPs) assigned to a process. Such a process can be part of a product system, i.e., a unit process or a combination of unit processes as, e.g., the production processes of a company. Independent information modules (IIMs) of processes within a system are modeled in a way that the predetermined parameters of the information modules related to these processes are identical and sufficiently independent so they can be added up to the predetermined parameters of such a system, typically after multiplication with specific factors based on the reference flow of the system.

Materials and methods

This paper shows how IIMs can be used as powerful approach in life cycle management and how operations, goods, and services of a company can be modeled efficiently with the help of IIMs. To define environmental objectives of their operations, organizations typically assess their foreground processes but do not apply system expansion for each of the foreground processes to include background processes. With the help of IIMs, background processes can be easily included, and the PDPs, therefore, also include both direct and indirect elementary flows, i.e., emissions and resources. In a “plant ecobalance” the PDPs of the different (foreground and background) processes of an organization can be determined and added up. This provides each process owner with important information about the environmental aspects which he or she can control and shows options for setting and implementing environmental objectives. For specific purposes, the number of PDPs can be restricted or even limited to one parameter, e.g., the carbon footprint. This paper illustrates the method with one example of the aluminum industry (carbon footprint of an automotive bumper beam) and shows how PDPs of product systems can be built up from IIMs which represent the different stages of a life cycle; how such results can show the influence of these stages in a transparent way, as required as a part of the life cycle interpretation phase.

Results and discussion

Life cycle assessments (LCAs) based on IIMs follow the principles and requirements of ISO 14040 (2006) and ISO 14044 (2006), as applicable. However, as a specific approach of life cycle management, they can obtain the required information with less effort than “conventional” LCAs where, following the guidance of ISO 14044, indicator results are calculated after the inventory data have been aggregated for the whole product system. Future efforts in ISO standardization should strengthen the role of LCA as a tool of environmental management.

     

Prodrugs for masking bitter taste of antibacterial drugs—a computational approach

DFT calculations for the acid-catalyzed hydrolysis of several maleamic acid amide derivatives revealed that the reaction rate-limiting step is determined on the nature of the amine leaving group. Further, it was established that when the amine leaving group was a secondary amine, acyclovir or cefuroxime moiety the tetrahedral intermediate formation was the rate-limiting step such as in the cases of acyclovir ProD 1- ProD 4 and cefuroxime ProD 1- ProD 4. In addition, the linear correlation between the calculated and experimental rates provided a credible basis for designing prodrugs for masking bitter taste of the corresponding parental drugs which have the potential to release the parent drug in a sustained release fashion. For example, based on the DFT calculated rates the predicted t_1/2 (a time needed for 50 % of the reactant to be hydrolyzed to products) for cefuroxime prodrugs, cefuroxime ProD 1- ProD 4, were 12 min, 18 min, 200 min and 123 min, respectively.

A novel approach to microbial breeding—low-energy ion implantation

Low-energy ions exist widely in the natural world. People had neglected the interaction between low-energy ions and material; it was even more out of the question to study the relation of low-energy ions and the complicated organism until the biological effects of low-energy ion implantation were discovered in 1989. Nowadays, the value of low-energy ion beam implantation, as a new breeding way, has drawn extensive attention of biologists and breeding experts. In this review, the understanding and utilization of microbial breeding by low-energy ion beam irradiation is summarized, including the characteristics of an ion beam bioengineering facility, present status of the technology of low-energy ions for microbial breeding, and new insights into microbial biotechnology.     

Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach

The majority of existing computational tools rely on sequence homology and/or structural similarity to identify novel microRNA (miRNA) genes. Recently supervised algorithms are utilized to address this problem, taking into account sequence, structure and comparative genomics information. In most of these studies miRNA gene predictions are rarely supported by experimental evidence and prediction accuracy remains uncertain. In this work we present a new computational tool (SSCprofiler) utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors. Via the simultaneous integration of biological features such as sequence, structure and conservation, SSCprofiler achieves a performance accuracy of 88.95% sensitivity and 84.16% specificity on a large set of human miRNA genes. The trained classifier is used to identify novel miRNA gene candidates located within cancer-associated genomic regions and rank the resulting predictions using expression information from a full genome tiling array. Finally, four of the top scoring predictions are verified experimentally using northern blot analysis. Our work combines both analytical and experimental techniques to show that SSCprofiler is a highly accurate tool which can be used to identify novel miRNA gene candidates in the human genome. SSCprofiler is freely available as a web service at http://www.imbb.forth.gr/SSCprofiler.html.     

Pyruvate — a novel substrate for growth and methane formation in Methanosarcina barkeri

Methanosarcina barkeri strain Fusaro was found to grow on pyruvate as sole carbon and energy source after an incubation period of 10–12 weeks in the presence of high pyruvate concentrations (100 mM). Growth studies, cell suspension experiments and enzymatic investigations were performed with pyruvate-utilizing M. barkeri. For comparison acetate-adapted cells of M. barkeri were analyzed.

1. Pyruvate-utilizing M. barkeri grew on pyruvate (100 mM) with an initial doubling time of about 25 h (37 °C, pH 6.5) up to cell densities of about 0.8 g cell dry weight/l. The specific growth rate was linearily dependent on the pyruvate concentration up to 100 mM indicating that pyruvate was taken up by passive diffusion. Only CO₂ and CH₄ were detected as fermentation products. As calculated from fermentation balances pyruvate was converted to CH₄ and CO₂ according to following equation: Pyruvate^-+H⁺+0.5 H₂O » 1.25 CH₄+1.75 CO₂. The molar growth yield (Ych ₄) was about 14 g dry weight cells/mol CH₄. In contrast the growth yield (Ych ₄) of M. barkeri during growth on acctate (Acetate^-+H⁺ » CH₄+CO₂) was about 3 g/mol CH₄.
2. Cell suspensions of pyruvate-grown M. barkeri catalyzed the conversion of pyruvate to CH₄, CO₂ and H₂ (5–15 nmol pyruvate consumed/min x mg protein). At low cell concentrations (0.5 mg protein/ml) 1 mol pyruvate was converted to 1 mol CH₄, 2 mol CO₂ and 1 mol H₂. At higher cell concentration less H₂ and CO₂ and more CH₄ were formed due to CH₄ formation from H₂/CO₂. The rate of pyruvate conversion was linearily dependent on the pyruvate concentration up to about 30 mM. Cell suspensions of acetate-grown M. barkeri also catalyzed the conversion of 1 mol pyruvate to 1 mol CH₄, 2 mol CO₂ and 1 mol H₂ at similar rates and with similar affinity for pyruvate as pyruvate-grown cells.
3. Cell extracts of both pyruvate-grown and acetate-grown M. barkeri contained pyruvate: ferredoxin oxidoreductase. The specific activity in pyruvate-grown cells (0.8 U/mg) was 8-fold higher than in acetate-grown cells (0.1 U/mg). Coenzyme F₄₂₀ was excluded as primary electron acceptor of pyruvate oxidoreductase. Cell extracts of pyruvate-grown M. barkeri contained carbon monoxide dehydrogenase activity and hydrogenase activity catalyzing the reduction by carbon monoxide and hydrogen of both methylviologen and ferredoxin (from Clostridium).

This is the first report on growth of a methanogen on pyruvate as sole carbon and energy source, i.e. on a substrate more complex than acetate.     

Coenzyme Q(10): a novel therapeutic approach for Fibromyalgia? case series with 5 patients

Coenzyme Q(10) (CoQ(10)) is an essential electron carrier in the mitochondrial respiratory chain and a strong antioxidant. Low CoQ(10) levels have been detected in patients with Fibromyalgia (FM). The purpose of the present work was to assess the effect of CoQ(10) on symptoms of five patients with FM. Patients were evaluated clinically with Visual Analogical Scale of pain (VAS), and Fibromyalgia Impact Questionnaire (FIQ). Patients with CoQ(10) deficiency showed a statistically significant reduction on symptoms after CoQ(10) treatment during 9 months (300 mg/day). Determination of deficiency and consequent supplementation in FM may result in clinical improvement. Further analysis involving more scientifically rigorous methodology will be required to confirm this observation.     

Glycosylase mediated polymorphism detection (GMPD)—a novel process for genetic analysis

A process for mutation and polymorphism detection is described here that offers significant advances over current mutation detection systems and that has the potential to significantly enhance molecular genetic analysis of human disease. This novel process is referred to as glycosylase mediated polymorphism detection (GMPD) and exploits the use of highly specific DNA glycosylase enzymes to excise substrate bases incorporated into amplified DNA. Action of the glycosylase leaves the DNA with one or more specific abasic sites which can be cleaved by enzymatic or chemical means. The GMPD process permits detection of polymorphisms and mutations using fragment size analysis or solid phase formats. GMPD is particularly suitable for genotyping of single nucleotide polymorphism (SNP) based markers and also permits efficient scanning of genes for unknown polymorphisms and mutations.