Effect of DNA structural flexibility on promoter strength--molecular dynamics studies of E. coli promoter sequences

To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the -10 consensus region sequence and five variants forming the -10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength.     

Environmental control of clonal growth in Carex nigra: What can be masked under the name Carex nigra subsp. juncella in the Czech Republic?

Carex nigra plants forming elevated dense tussocks are often named C. nigra subsp. juncella, as opposed to rhizomatous C. nigra subsp. nigra. It is uncertain, however, whether the cespitose growth form is a hereditary trait useful for definition of the distinct taxon or a site modification of little taxonomic value. We used vegetation analyses (phytosociological relevés) to reveal main patterns in ecological demands of the cespitose C. nigra plants in the Czech Republic, and three cultivation experiments to assess changes in clonal growth of C. nigra under various environmental conditions. In the field the cespitose C. nigra plants were typically found in abandoned wet meadows near open water, whereas the rhizomatous morphotypes frequently occurred also in regularly mown wet meadows and in peat bogs. The cespitose growth form disappeared in the cultivations, and the rhizome system responded plastically to immediate environmental stimuli. Number of rhizome branches and mean rhizome length decreased after defoliation of aboveground parts and denudation of belowground parts, whereas increased due to inundation. In the population from a cold site in high altitude (Modrava, Šumava Mts.), however, the originally cespitose plants repeatedly produced shorter and less numerous rhizome branches than the rhizomatous plants cultivated in the same conditions. This suggests ecotypic (genetic) differentiation in some populations of C. nigra, driven by environmental selection for more compact growth form in climatically severe sites. The cespitose C. nigra plants thus arise polytopically, by different mechanisms. The growth form itself therefore cannot serve as the character reliably delimiting C. nigra subsp. juncella as the distinct taxon.     

A monolithic lipase reactor for biodiesel production by transesterification of triacylglycerides into fatty acid methyl esters

An enzymatic reactor with lipase immobilized on a monolithic polymer support has been prepared and used to catalyze the transesterification of triacylglycerides into the fatty acid methyl esters commonly used for biodiesel. A design of experiments procedure was used to optimize the monolithic reactor with variables including control of the surface polarity of the monolith via variations in the length of the hydrocarbon chain in alkyl methacrylate monomer, time of grafting of 1-vinyl-4,4-dimethylazlactone used to activate the monolith, and time used for the immobilization of porcine lipase. Optimal conditions involved the use of a poly(stearyl methacrylate-co-ethylene dimethacrylate) monolith, grafted first with vinylazlactone, then treated with lipase for 2 h to carry out the immobilization of the enzyme. Best conditions for the transesterification of glyceryl tributyrate included a temperature of 37°C and a 10 min residence time of the substrate in the bioreactor. The reactor did not lose its activity even after pumping through it a solution of substrate equaling 1,000 reactor volumes. This enzymatic reactor was also used for the transesterification of triacylglycerides from soybean oil to fatty acid methyl esters thus demonstrating the ability of the reactor to produce biodiesel.     

Predictive models for transient protein expression in tobacco (Nicotiana tabacum L.) can optimize process time, yield, and downstream costs

The transient expression of recombinant biopharmaceutical proteins in plants can suffer inter‐batch variation, which is considered a major drawback under the strict regulatory demands imposed by current good manufacturing practice (cGMP). However, we have achieved transient expression of the monoclonal antibody 2G12 and the fluorescent marker protein DsRed in tobacco leaves with ～15% intra‐batch coefficients of variation, which is within the range reported for transgenic plants. We developed models for the transient expression of both proteins that predicted quantitative expression levels based on five parameters: The OD_600nm of Agrobacterium tumefaciens (from 0.13 to 2.00), post‐inoculation incubation temperature (15–30°C), plant age (harvest at 40 or 47 days after seeding), leaf age, and position within the leaf. The expression models were combined with a model of plant biomass distribution and extraction, generating a yield model for each target protein that could predict the amount of protein in specific leaf parts, individual leaves, groups of leaves, and whole plants. When the yield model was combined with a cost function for the production process, we were able to perform calculations to optimize process time, yield, or downstream costs. We illustrate this procedure by transferring the cost function from a production process using transgenic plants to a hypothetical process for the transient expression of 2G12. Our models allow the economic evaluation of new plant‐based production processes and provide greater insight into the parameters that affect transient protein expression in plants. Biotechnol. Bioeng. 2012; 109: 2575–2588. © 2012 Wiley Periodicals, Inc.     

Effectiveness of TaqMan probes for detection of fish eggs and larvae in the stomach contents of a teleost predator

Experiments were conducted on the ability of TaqMan molecular probes to detect plaice Pleuronectes platessa DNA from eggs, and cod Gadus morhua DNA from eggs and larvae following ingestion by a teleost predator, whiting Merlangius merlangus. Estimated half-life detection rate (T50) for eggs was 31 h, and 26 h for larvae, with some positive detections occurring even after visual inspection indicated complete gut clearance. Because TaqMan probes are taxon specific, the results presented demonstrate that this technique can provide a means of rapid and unambiguous detection of predation by teleosts on fish eggs and larvae.     

Integrated versus stand-alone second generation ethanol production from sugarcane bagasse and trash

Ethanol production from lignocellulosic materials is often conceived considering independent, stand-alone production plants; in the Brazilian scenario, where part of the potential feedstock (sugarcane bagasse) for second generation ethanol production is already available at conventional first generation production plants, an integrated first and second generation production process seems to be the most obvious option. In this study stand-alone second generation ethanol production from surplus sugarcane bagasse and trash is compared with conventional first generation ethanol production from sugarcane and with integrated first and second generation; simulations were developed to represent the different technological scenarios, which provided data for economic and environmental analysis. Results show that the integrated first and second generation ethanol production process from sugarcane leads to better economic results when compared with the stand-alone plant, especially when advanced hydrolysis technologies and pentoses fermentation are included.     

Intraspecific variability in the response of bloom-forming marine microalgae to changed climate conditions

Phytoplankton populations can display high levels of genetic diversity that, when reflected by phenotypic variability, may stabilize a species response to environmental changes. We studied the effects of increased temperature and CO(2) availability as predicted consequences of global change, on 16 genetically different isolates of the diatom Skeletonema marinoi from the Adriatic Sea and the Skagerrak (North Sea), and on eight strains of the PST (paralytic shellfish toxin)-producing dinoflagellate Alexandrium ostenfeldii from the Baltic Sea. Maximum growth rates were estimated in batch cultures of acclimated isolates grown for five to 10 generations in a factorial design at 20 and 24°C, and present day and next century applied atmospheric pCO(2), respectively. In both species, individual strains were affected in different ways by increased temperature and pCO(2). The strongest response variability, buffering overall effects, was detected among Adriatic S. marinoi strains. Skagerrak strains showed a more uniform response, particularly to increased temperature, with an overall positive effect on growth. Increased temperature also caused a general growth stimulation in A. ostenfeldii, despite notable variability in strain-specific response patterns. Our data revealed a significant relationship between strain-specific growth rates and the impact of pCO(2) on growth-slow growing cultures were generally positively affected, while fast growing cultures showed no or negative responses to increased pCO(2). Toxin composition of A. ostenfeldii was consistently altered by elevated temperature and increased CO(2) supply in the tested strains, resulting in overall promotion of saxitoxin production by both treatments. Our findings suggest that phenotypic variability within populations plays an important role in the adaptation of phytoplankton to changing environments, potentially attenuating short-term effects and forming the basis for selection. In particular, A. ostenfeldii blooms may expand and increase in toxicity under increased water temperature and atmospheric pCO(2) conditions, with potentially severe consequences for the coastal ecosystem.     

Pollination efficiency of wild bees and hoverflies provided to oilseed rape

• 1 Declining numbers in honeybees and various wild bee species pose a threat to global pollination services. The identification and quantification of the pollination service provided by different taxa within the pollinator guild is a prerequisite for the successful establishment of nature conservation and crop management regimes.
• 2 Wild bees and hoverflies are considered to be valuable pollinators in agricultural and natural systems. Although some information on pollination efficiency of individual pollinator species is available, comparative studies of both taxa at different densities are rare. In the present study, the efficiency of the solitary mason bee Osmia rufa and two hoverfly species (Eristalis tenax and Episyrphus balteatus) as pollinators of oilseed rape Brassica napus was examined in a standardized caged plant breeding regime. Honeybee Apis mellifera colonies were used as a reference pollinator taxon.
• 3 Yield parameters responded differently to pollinator density and identity. Fruit set and number of seeds per pod increased with increasing pollinator density, although these were stronger in the mason bee than the hoverfly treatment. Weight per 1000 seeds did not respond to any pollinator treatment, indicating that seed quality was not affected. Oilseed rape yield in the highest tested densities of both pollinator taxa resulted in yield values close to the efficiency of small honeybee colonies.
• 4 Hoverflies required approximately five‐fold densities of the red mason bees to reach a similar fruit set and yield. Thus, mason bees are more efficient in plant breeding and managed pollination systems. Both natural pollinator taxa, however, are of potential value in open and closed crop production systems.

     

花颜色和花气味的量化研究方法

花颜色和花气味是花部构成的重要内容。在已开展的传粉生态学研究中对二者的报道主要是描述性的,而其量化研究可以为揭示传粉机制提供有力的实验证据。本文主要介绍了花颜色的测量和标定方法,包括比色卡、分光色差仪和便携式光谱仪等;花气味的采集方法,包括动态顶空套袋-吸附采集法、吸附-溶剂洗脱法和固相微萃取法等;花气味的检测和分析方法,包括气相色谱-质谱联用仪分析和电子鼻型超速气相色谱仪分析等;以及昆虫行为学实验方法,包括气相色谱-昆虫触角电位联用技术、Y型嗅觉仪和飞行箱实验等。科研人员可以根据实验材料的特点和实验目的选择适合的量化研究方法。     

The application of genetic algorithms in behavioural ecology, illustrated with a model of anti-predator vigilance

We develop a genetic algorithm (GA) approach to a well-known model of vigilance behaviour in a group of animals. We first demonstrate that the GA approach can provide a good match to analytic solutions to the original model. We demonstrate that a GA can be used to find the evolutionarily stable strategies in a model relevant to behavioural ecology where the fitness of each strategy is determined by the frequencies of different strategies in the population. We argue that the GA implementation demonstrates the combination of assumptions used to generate analytic solution to the original model can only be simultaneously satisfied under relatively restrictive conditions on the ecology of the species involved; specifically that group membership is very fluid but group size is conserved over timescales of individual foraging bouts. We further explore the sensitivity of model predictions to alternative choices in the implementation of the GA, and present advice for implementation and presentation of similar models. In particular, we emphasise the need for care in measuring the predictions of such models, so as to capture the intrinsic behaviour of the system and not the remnant of often arbitrarily chosen initial conditions. We also emphasise the potential for GA models to be more transparent about model assumptions regarding underlying biology than analytic models.