Genome sequencing: a grin without a cat

In some types of unicellular algae, the chloroplasts have their own nucleus — a legacy of the time when the chloroplast was a free-living cell. The sequence of the genome in one such nucleus is now revealed.

Researching a whole-year EE program: some methodological issues

A P-12 school in regional Victoria has an environmental theme throughout its Year Four program with classes located in a purpose- built Environmental Centre in a separate location within the school’s grounds. The authors report here on a one-year case study of the grade four thematic integrated curriculum at the school. They reflect on and describe some of the methodological issues that arose during the interviews, direct observations, photography and video-recording. Some of the practical considerations associated with case-study methodology are discussed. The paper concludes with a summary of emerging substantive issues and a prospective view to further research.

Eulerian superpath approach to correct sequencing error in shotgun assembly

This work describes an error correction method based on the Euler Superpath problem. Sequence data is mapped to an Euler Superpath dynamically by Merging Transformation. With restriction and guiding rules, data consistency is maintained and error paths are separated from correct data: Error edges are mapped to the correct ones and after substitution (of error edges with right paths), corresponding errors in the sequencing data are eliminated.

In vitro carbohydrate digestibility of whole-chickpea and chickpea bread products

Pulses such as the chickpea are generally considered to be valuable dietary sources of slowly digestible starch, a form of starch that is considered beneficial to health since it results in relatively low post-meal blood glucose levels compared with more rapidly digested starch. The development of novel chickpea-based foods is necessary to help expand the worldwide consumption of the chickpea. However, the effect of different processing methods on the starch digestibility of chickpea-based foods has not been widely investigated. This study used an in vitro method simulating human carbohydrate digestion to determine levels of slowly digestible starch, rapidly digestible starch (RDS), resistant starch, total starch and rapidly available glucose (RAG) of: (i) whole-chickpea products (domestically boiled, commercially canned and commercially precooked/vacuum-packaged); and (ii) standard white bread, chickpea flour bread (25% replacement of wheat flour by chickpea flour) and extruded chickpea flour bread (25% replacement of wheat flour by extruded chickpea flour). The RAG levels were then used to predict the relative in vivo glycaemic indices of the products. The commercially precooked/vacuum-packaged whole chickpeas demonstrated higher levels of RDS than the commercially canned and domestically boiled products (P<0.05). In addition, the domestically boiled product had lower levels of RAG (g/100 g available carbohydrate) compared with the canned and precooked/vacuum-packaged products (P<0.05). There were no significant differences between any of the carbohydrate digestibility measures of the white bread, chickpea flour bread and extruded chickpea flour bread (P>0.05) and all bread products demonstrated far higher RAG (g/100 g available carbohydrate) values than the whole-chickpea products. The findings suggest that the commercially precooked/vacuum-packaged whole chickpeas and the canned product may have higher and less beneficial glycaemic indices than the domestically boiled chickpeas. It appears unlikely that the use of chickpea flour or extruded chickpea flour, at the incorporation rate investigated in this study, would modify the glycaemic index of bread. It is probable, however, that the chickpea bread products investigated would demonstrate higher and potentially less beneficial glycaemic indices than the whole-chickpea products.

Fatty acid metabolism in the freshwater fish Murray cod (Maccullochella peelii peelii) deduced by the whole-body fatty acid balance method

The whole-body fatty acid balance method was used to investigate the fatty acid metabolism in Murray cod (Maccullochella peelii peelii) fed diets containing canola (CO) or linseed oil (LO). Murray cod were able to elongate and desaturate both 18 : 2n − 6 and 18 : 3n − 3. In fish fed the CO diet, 54.4% of the 18 : 2n − 6 consumed was accumulated, 38.5% oxidized and 6.4% elongated and desaturated to higher homologs. Fish fed the LO diet accumulated 52.9%, oxidized 37% and elongated and desaturated 8.6% of the consumed 18 : 3n − 3. The overall roles of n − 6 fatty acids appeared more important in Murray cod compared to other freshwater species. Murray cod also showed a preferential order of utilization of C18 fatty acid for energy production (18 : 3n − 3 > 18 : 2n − 6 > 18 : 1n − 9). Moreover, it is demonstrated that an increase in dietary 18 : 3n − 3 is directly responsible of increased desaturase activity and augmented saturated fatty acid accumulation in the fish body. The present study also suggests that, in the context of the possible maximization of the natural ability of fish to produce long chain polyunsaturated fatty acids, the whole-body approach can be considered well suited and informative and Murray cod is a suited candidate to fish oil replacement for its diets.

Modeling a just-in-time plant using sequencing algorithms

An Australian automotive component company plans to assemble and deliver seats to customer on just-in-time basis. The company management has decided to model operations of the seat plant to help them make decisions on capital investment and labour requirements. There are four different areas in seat assembly and delivery areas. Each area is modeled independently to optimise its operations. All four areas are then combined into one model called the plant model to model operations of seat plant from assembly to delivery. Discrete event simulation software is used to model the assembly operations of seat plant.

A parallel Euler approach for large-scale biological sequence assembly

Biological sequence assembly is an essential step for sequencing the genomes of organisms. Sequence assembly is very computing intensive especially for the large-scale sequence assembly. Parallel computing is an effective way to reduce the computing time and support the assembly for large amount of biological fragments. Euler sequence assembly algorithm is an innovative algorithm proposed recently. The advantage of this algorithm is that its computing complexity is polynomial and it provides a better solution to the notorious “repeat” problem. This paper introduces the parallelization of the Euler sequence assembly algorithm. All the Genome fragments generated by whole genome shotgun (WGS) will be assembled as a whole rather than dividing them into groups which may incurs errors due to the inaccurate group partition. The implemented system can be run on supercomputers, network of workstations or even network of PC computers. The experimental results have demonstrated the performance of our system.

A whole body, in vivo, fatty A\acid balance method to quantify PUFA metabolism (desaturation, elongation and beta-oxidation)

Currently there are several contrasting methods utilized for estimating elongation and desaturation of fatty acids and their general metabolism. The majority of these methods involve an ex vivo approach, requiring expensive and sophisticated equipment, likely to result in considerable variation in enzyme activity between and within species. In the present paper we introduce a further development of the whole-body fatty acid balance method for the estimation of the elongation and desaturation of fatty acids. This method though receiving considerable attention because of its simplicity and reliability has yet to be presented in detail. Theoretically, the whole-body fatty acid balance method can potentially be applied to any organism and requires little more than a gas chromatography unit for fatty acid analysis and elementary calculations. As such in this paper we attempt to spell out in detail the theoretical basis and the methods of application drawing specific examples. Using the present method it is possible to measure the fate of individual fatty acids towards desaturation, elongation and oxidation and calculate the elongase, Δ-6 desaturase and Δ-5 desaturase activities.

Using accelerated, whole-of-brain learning techniques in higher education: principles and practice

Accelerated learning is an integrative method of learning, combining both sides of the brain to strengthen a student's relationship with self, teacher, subject matter and other students, and so assists students to achieve deep, rather than surface, learning. While the approach has been used to teach school pupils and trainees in the corporate world, its use in marketing education in universities is limited, and there are no reports of studies focusing on its use in postgraduate coursework degrees. Thus this paper examines how accelerated learning could be used in teaching marketing at universities at the MBA level. Some techniques are synthesised from the literature that are particularly appropriate for the students and constraints of an MBA program in a university. We conclude that accelerated learning techniques can be used and are effective in a MBA program. Essentially, accelerated learning incorporate many, already known ideas but it is a useful comprehensive framework.