Genome Sequence of the Photoarsenotrophic Bacterium Ectothiorhodospira sp. Strain BSL-9, Isolated from a Hypersaline Alkaline Arsenic-Rich Extreme Environment.

The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out "photoarsenotrophy" anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content

Microbial transformation of elements: the case of arsenic and selenium

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as “essential toxins”, they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecularweight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements

Mobilisation of arsenic from bauxite residue (red mud) affected soils: effect of pH and redox conditions

The tailings dam breach at the Ajka alumina plant, western Hungary in 2010 introduced ~1 million m3 of red mud suspension into the surrounding area. Red mud (fine fraction bauxite residue) has a characteristically alkaline pH and contains several potentially toxic elements, including arsenic. Aerobic and anaerobic batch experiments were prepared using soils from near Ajka in order to investigate the effects of red mud addition on soil biogeochemistry and arsenic mobility in soil–water experiments representative of land affected by the red mud spill. XAS analysis showed that As was present in the red mud as As(V) in the form of arsenate. The remobilisation of red mud associated arsenate was highly pH dependent and the addition of phosphate to red mud suspensions greatly enhanced As release to solution. In aerobic batch experiments, where red mud was mixed with soils, As release to solution was highly dependent on pH. Carbonation of these alkaline solutions by dissolution of atmospheric CO2 reduced pH, which resulted in a decrease of aqueous As concentrations over time. However, this did not result in complete removal of aqueous As in any of the experiments. Carbonation did not occur in anaerobic experiments and pH remained high. Aqueous As concentrations initially increased in all the anaerobic red mud amended experiments, and then remained relatively constant as the systems became more reducing, both XANES and HPLC–ICP-MS showed that no As reduction processes occurred and that only As(V) species were present. These experiments show that there is the potential for increased As mobility in soil–water systems affected by red mud addition under both aerobic and anaerobic conditions

Bacterial Respiration of Arsenate and Its Significance in the Environment

Although arsenic is a trace element in terms of its natural abundance, it nonetheless has a common presence within the earth's crust. Because it is classified as a group VB element in the periodic table, it shares many chemical and biochemical properties in common with its neighbors phosphorus and nitrogen. Indeed, in the case of this element's most oxidized (+5) oxidation state, arsenate [HAsO_4^(2-) or As (V)], its toxicity is based on its action as an analog of phosphate. Hence, arsenate ions uncouple the oxidative phosphorylation normally associated with the enzyme glyceraldehyde 3-phosphate dehydrogenase, thereby preventing the formation ofphosphoglyceroyl phosphate, a key high-energy intermediate in glycolysis. To guard against this, a number of bacteria possess a detoxifying arsenate reductase pathway (the arsC system) whereby cytoplasmic enzymes remove internal pools of arsenate by achieving its reduction to arsenite [H_2AsO_3- or As (III)]. However, because the arsenite product binds with internal sulfhydryl groups that render it even more toxic than the original arsenate, efficient arsenite efflux from the cell is also required and is achieved by an active ion ''pumping'' system (1). The details of this bacterial arsenic detoxification phenomenon have been well established in the literature, and Chapter 10 in this volume provided a thorough review. Here, we discuss bacterial respiration of arsenate and its significance in the environment. As a biological phenomenon, respiratory growth on arsenate is quite remarkable, given the toxicity of the element. Moreover, the consequences of microbial arsenate respiration may, at times, have a significant impact on environmental chemistry

Mandibular fractures in short-finned pilot whales, \u3ci\u3eGlobicephala macrorhynchus\u3c/i\u3e

This study’s objective was to investigate mandibular fractures in 50 short-finned pilot whales, Globicephala macrorhynchus, from two mass strandings. Based on current theories that this species is sexually dimorphic and polygynous, hypotheses were: (1) males should suffer more frequent or more substantial mandibular fractures than should females, and (2) fracture occurrence should increase with male reproductive maturity and potential correlates of maturity, such as age and length. Fractures were described and correlated with physical characteristics to infer possible explanations for injuries. Mandibular fractures were surprisingly common in males and females, being found in more than half of the animals examined (27/50, or 54% overall; 17/36 or 47% of females and 10/14 or 71% of males). Length was the only correlate of fracture presence; the proportion of animals showing evidence of fracture increased with length. These results offer some support to initial hypotheses, but there must be another set of consequences that contribute to mandibular fractures in females. A combination of intra- and interspecific interactions and life history characteristics may be responsible for fractures. Further research from a larger sample of this and other cetacean species are suggested to help elucidate both the causes and implications of mandibular fractures

Acetylene Fuels TCE Reductive Dechlorination by Defined Dehalococcoides/Pelobacter Consortia.

Acetylene (C2H2) can be generated in contaminated groundwater sites as a consequence of chemical degradation of trichloroethene (TCE) by in situ minerals, and C2H2 is known to inhibit bacterial dechlorination. In this study, we show that while high C2H2 (1.3 mM) concentrations reversibly inhibit reductive dechlorination of TCE by Dehalococcoides mccartyi isolates as well as enrichment cultures containing D. mccartyi sp., low C2H2 (0.4 mM) concentrations do not inhibit growth or metabolism of D. mccartyi. Cocultures of Pelobacter SFB93, a C2H2-fermenting bacterium, with D. mccartyi strain 195 or with D. mccartyi strain BAV1 were actively sustained by providing acetylene as the electron donor and carbon source while TCE or cis-DCE served as the electron acceptor. Inhibition by acetylene of reductive dechlorination and methanogenesis in the enrichment culture ANAS was observed, and the inhibition was removed by adding Pelobacter SFB93 into the consortium. Transcriptomic analysis of D. mccartyi strain 195 showed genes encoding for reductive dehalogenases (e.g., tceA) were not affected during the C2H2-inhibition, while genes encoding for ATP synthase, biosynthesis, and Hym hydrogenase were down-regulated during C2H2 inhibition, consistent with the physiological observation of lower cell yields and reduced dechlorination rates in strain 195. These results will help facilitate the optimization of TCE-bioremediation at contaminated sites containing both TCE and C2H2

Optimization and Control of Agent-Based Models in Biology: A Perspective

Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of analyzing and using ABMs, due to the lack of the type of mathematical tools available for more traditional models, which leaves simulation as the primary approach. As models become large, simulation becomes challenging. This paper proposes a novel approach to two mathematical aspects of ABMs, optimization and control, and it presents a few first steps outlining how one might carry out this approach. Rather than viewing the ABM as a model, it is to be viewed as a surrogate for the actual system. For a given optimization or control problem (which may change over time), the surrogate system is modeled instead, using data from the ABM and a modeling framework for which ready-made mathematical tools exist, such as differential equations, or for which control strategies can explored more easily. Once the optimization problem is solved for the model of the surrogate, it is then lifted to the surrogate and tested. The final step is to lift the optimization solution from the surrogate system to the actual system. This program is illustrated with published work, using two relatively simple ABMs as a demonstration, Sugarscape and a consumer-resource ABM. Specific techniques discussed include dimension reduction and approximation of an ABM by difference equations as well systems of PDEs, related to certain specific control objectives. This demonstration illustrates the very challenging mathematical problems that need to be solved before this approach can be realistically applied to complex and large ABMs, current and future. The paper outlines a research program to address them

Avaliação experimental de um gerador de testes dirigidos para a verificação de memória compartilhada em multicore chips

TCC(graduação) - Universidade Federal de Santa Catarina. Centro Tecnológico. Ciências da Computação.No contexto de verificação de memória compartilhada em multicore chips, este trabalho propõe uma avaliação crítica da geração automática de testes dirigidos quando baseada em Programação Genética. A metodologia consiste na comparação do gerador McVerSi (que representa o estado da arte) com geradores de testes aleatórios (que representam a base de geradores dirigidos por cobertura). Dois geradores de testes aleatórios são utilizados: um deles (McVerSi_Rand) pressupõe uma restrição do espaço de endereçamento imposta estaticamente antes de disparar a geração, o outro (IRTG) admite a variação dinâmica de restrições impostas ao espaço de endereçamento. Os três geradores são comparados de acordo com duas métricas: cobertura estrutural dos controladores de cache e esforço requerido na detecção de erros de coerência de memória