A hybrid genetic algorithm for the minimum interconnection cut problem

In the real world there are many problems in network of networks (NoNs) that can be abstracted to a so-called minimum interconnection cut problem, which is fundamentally different from those classical minimum cut problems in graph theory. Thus, it is desirable to propose an efficient and effective algorithm for the minimum interconnection cut problem. In this paper we formulate the problem in graph theory, transform it into a multi-objective and multi-constraint combinatorial optimization problem, and propose a hybrid genetic algorithm (HGA) for the problem. The HGA is a penalty-based genetic algorithm (GA) that incorporates an effective heuristic procedure to locally optimize the individuals in the population of the GA. The HGA has been implemented and evaluated by experiments. Experimental results have shown that the HGA is effective and efficient.

Genetic diversity of cultured and wild populations of the giant freshwater prawn Macrobrachium rosenbergii (de Man, 1879) based on microsatellite analysis

Freshwater prawn (Macrobrachium rosenbergii) culture in the Western Hemisphere is primarily, if not entirely, derived from 36 individual prawns originally introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding genetic variation within and among cultured prawn stocks worldwide. The goal of the current study was to characterize genetic diversity in various prawn populations with emphasis on those cultured in North America. Five microsatellite loci were screened to estimate genetic diversity in two wild (Myanmar and India-wild) and seven cultured (Hawaii-1, Hawaii-2, India-cultured, Israel, Kentucky, Mississippi and Texas) populations. Average allelic richness ranged from 3.96 (Israel) to 20.45 (Myanmar). Average expected heterozygosity ranged from 0.580 (Israel) to 0.935 (Myanmar). Many of the cultured populations exhibited reduced genetic diversity when compared with the Myanmar and the India-cultured populations. Significant deficiency in heterozygotes was detected in the India-cultured, Mississippi and Kentucky populations (overall Fis estimated of 0.053, 0.067 and 0.108 respectively) reflecting moderate levels of inbreeding. Overall estimate of fixation index (Fst = 0.1569) revealed moderately high levels of differentiation among the populations. Outcome of this study provide a baseline assessment of genetic diversity in some available strains that will be useful for the development of breeding programmes.

Population structure and patterns of genetic variation in a pearl oyster (Pinctada radiata) native to the Arabian Gulf

The study assessed natural levels and patterns of genetic variation in Arabian Gulf populations of a native pearl oyster to define wild population structure considering potential intrinsic and extrinsic factors that could influence any wild structure detected. The study was also the first attempt to develop microsatellite markers and to generate a genome survey sequence (GSS) dataset for the target species using next generation sequencing technology. The partial genome dataset generated has potential biotechnological applications and for pearl oyster farming in the future.

Quantitative genetic parameter estimates for body and carcass traits in a cultured stock of giant freshwater prawn (Macrobrachium rosenbergii) selected for harvest weight in Vietnam

We estimated the heritability and correlations between body and carcass weight traits in a cultured stock of giant freshwater prawn (GFP) (Macrobrachium rosenbergii) selected for harvest body weight in Vietnam. The data set consisted of 18,387 body and 1,730 carcass records, as well as full pedigree information collected over four generations. Variance and covariance components were estimated by restricted maximum likelihood fitting a multi-trait animal model. Across generations, estimates of heritability for body and carcass weight traits were moderate and ranged from 0.14 to 0.19 and 0.17 to 0.21, respectively. Body trait heritabilities estimated for females were significantly higher than for males whereas carcass weight trait heritabilities estimated for females and males were not significantly different (P>. 0.05). Maternal effects for body traits accounted for 4 to 5% of the total variance and were greater in females than in males. Genetic correlations among body traits were generally high in the mixed sexes. Genetic correlations between body and carcass weight traits were also high. Although some issues remain regarding the best statistical model to be fitted to GFP data, our results suggest that selection for high harvest body weight based on breeding values estimated by fitting an animal model to the data can significantly improve mean body and carcass weight in GFP.

Effect of pretreatment on saccharification of sugarcane bagasse by complex and simple enzyme mixtures

Saccharification of sugarcane bagasse pretreated at the pilot-scale with different processes (in combination with steam-explosion) was evaluated. Maximum glucan conversion with Celluclast 1.5 L (15–25 FPU/g glucan) was in the following order: glycerol/HCl > HCl > H2SO4 > NaOH, with the glycerol system achieving ∼100% conversion. Surprisingly, the NaOH substrate achieved optimum saccharification with only 8 FPU/g glucan. Glucan conversions (3.6–6%) obtained with mixtures of endo-1,4-β-glucanase (EG) and β-glucosidase (βG) for the NaOH substrate were 2–6 times that of acid substrates. However, glucan conversions (15–60%) obtained with mixtures of cellobiohydrolase (CBH I) and βG on acidified glycerol substrate were 10–30% higher than those obtained for NaOH and acid substrates. The susceptibility of the substrates to enzymatic saccharification was explained by their physical and chemical attributes. Acidified glycerol pretreatment offers the opportunity to simplify the complexity of enzyme mixtures required for saccharification of lignocellulosics.

Understanding the genetic basis of invasiveness

Invasive species provide excellent study systems to evaluate the ecological and evolutionary processes that contribute to the colonization of novel environments. While the ecological processes that contribute to the successful establishment of invasive plants have been studied in detail, investigation of the evolutionary processes involved in successful invasions has only recently received attention. In particular, studies investigating the genomic and gene expression differences between native and introduced populations of invasive species are just beginning and are required if we are to understand how plants become invasive. In the current issue of Molecular Ecology, Hodgins et al. () tackle this unresolved question, by examining gene expression differences between native and introduced populations of annual ragweed, Ambrosia artemisiifolia. The study identifies a number of potential candidate genes based on gene expression differences that may be responsible for the success of annual ragweed in its introduced range. Furthermore, genes involved in stress response are over-represented in the differentially expressed gene set. Future experiments could use functional studies to test whether changes in gene expression at these candidate genes do in fact underlie changes in growth characteristics and reproductive output observed in this and other invasive species.

Genetic response to combined family selection for improved mean harvest weight in giant freshwater prawn (Macrobrachium rosenbergii) in Vietnam

We estimated genetic changes in body and carcass weight traits in a giant freshwater prawn (GFP) (Macrobrachium rosenbergii) population selected for increased body weight at harvest in Vietnam. The data set consisted of 18,387 individual body and 1730 carcass weight records, as well as full pedigree information collected over four generations. Average selection response (per generation) in body weight at harvest (transformed to square root) estimated as the difference between the Selection line and the Control group was 7.4% calculated from least squares mean (LSMs), 7.0% from estimated breeding values (EBVs) and 4.4% calculated from EBVs between two consecutive generations. Favorable correlated selection responses (estimated from LSMs) were found for other body traits including: total length, cephalothorax length, abdominal length, cephalothorax width, and abdominal width (12.1%, 14.5%, 10.4%, 15.5% and 13.3% over three selection generations, respectively). Data in the second generation of selection showed positive correlated responses for carcass weight traits including: abdominal weight, exoskeleton-off weight, and telson-off weight of 8.8%, 8.6% and 8.8%, respectively. We conclude that body weight at harvest responded well to the application of combined (between and within) family selection and correlated responses in carcass weight traits were favorable.

Low temperature pretreatment of sugarcane bagasse at atmospheric pressure using mixtures of ethylene carbonate and ethylene glycol

A low temperature lignocellulose pretreatment process was developed using acid-catalysed mixtures of alkylene carbonate and alkylene glycol. Pretreatment of sugarcane bagasse with mixtures of ethylene carbonate (EC) and ethylene glycol (EG) was more effective than that with mixtures of propylene carbonate (PC) and propylene glycol (PG). These mixtures were more effective than the individual components in making bagasse cellulose more amenable to cellulase digestion. Glucan digestibilities of ≥87% could be achieved with a wide range of EC to EG ratios from 9:1 to 1:1 (w/w). Pretreatment of bagasse by the EC/EG mixture with a ratio of 4:1 in the presence of 1.2% H2SO4 at 90 °C for 30 min led to the highest glucan enzymatic digestibility of 93%. The high glucan digestibilities obtained under these acidic conditions were due to (a) the ability of alkylene carbonate to cause significant biomass size reduction, (b) the ability of alkylene glycol to cause biomass defibrillation, (c) the ability of alkylene carbonate and alkylene glycol to remove xylan and lignin, and (d) the magnified above attributes in the mixtures of alkylene carbonate and alkylene glycol.

Understanding mild acid pretreatment of sugarcane bagasse through particle scale modeling

Sugarcane bagasse is an abundant and sustainable resource, generated as a by-product of sugarcane milling. The cellulosic material within bagasse can be broken down into glucose molecules and fermented to produce ethanol, making it a promising feedstock for biofuel production. Mild acid pretreatment hydrolyses the hemicellulosic component of biomass, thus allowing enzymes greater access to the cellulosic substrate during saccharification. A particle-scale mathematical model describing the mild acid pretreatment of sugarcane bagasse has been developed, using a volume averaged framework. Discrete population-balance equations are used to characterise the polymer degradation kinetics, and diffusive effects account for mass transport within the cell wall of the bagasse. As the fibrous material hydrolyses over time, variations in the porosity of the cell wall and the downstream effects on the reaction kinetics are accounted for using conservation of volume arguments. Non-dimensionalization of the model equations reduces the number of parameters in the system to a set of four dimensionless ratios that compare the timescales of different reaction and diffusion events. Theoretical yield curves are compared to macroscopic experimental observations from the literature and inferences are made as to constraints on these “unknown” parameters. These results enable connections to be made between experimental data and the underlying thermodynamics of acid pretreatment. Consequently, the results suggest that data-fitting techniques used to obtain kinetic parameters should be carefully applied, with prudent consideration given to the chemical and physiological processes being modeled.

Rapid nutrient determination of sugarcane milling by-products using near infrared spectroscopy

This thesis investigates the use of near infrared (NIR) spectroscopic methods for rapid measurement of nutrient elements in mill mud and mill ash. Adoption of NIR-based analyses for carbon, nitrogen, phosphorus, potassium and silicon will allow Australian sugarcane farmers to comply with recent legislative changes, and act within recommended precision farming frameworks. For these analyses, NIR spectroscopic methods surpass several facets of traditional wet chemistry techniques, dramatically reducing costs, required expertise and chemical exposure, while increasing throughput and access to data. Further, this technology can be applied in various modes, including laboratory, at-line and on-line installations, allowing targeted measurement.

Pretreatment of sugarcane bagasse by acidified aqueous polyol solutions

Pretreatments of sugarcane bagasse by three high boiling-point polyol solutions were compared in acid-catalysed processes. Pretreatments by ethylene glycol (EG) and propylene glycol solutions containing 1.2 % H2SO4 and 10 % water at 130 °C for 30 min removed 89 % lignin from bagasse resulting in a glucan digestibility of 95 % with a cellulase loading of ~20 FPU/g glucan. Pretreatment by glycerol solution under the same conditions removed 57 % lignin with a glucan digestibility of 77 %. Further investigations with EG solutions showed that increases in acid content, pretreatment temperature and time, and decrease in water content improved pretreatment effectiveness. A good linear correlation of glucan digestibility with delignification was observed with R2 = 0.984. Bagasse samples pretreated with EG solutions were characterised by scanning electron microscopy, Fourier transform infrared spectroscopy and X-ray diffraction, which confirmed that improved glucan enzymatic digestibility is mainly due to delignification and defibrillation of bagasse. Pretreatment by acidified EG solutions likely led to the formation of EG-glycosides. Up to 36 % of the total lignin was recovered from pretreatment hydrolysate, which may improve the pretreatment efficiency of recycled EG solution.

Glycerol carbonate as green solvent for pretreatment of sugarcane bagasse

Background Pretreatment of lignocellulosic biomass is a prerequisite for effective saccharification to produce fermentable sugars. We have previously reported an effective low temperature (90 °C) process at atmospheric pressure for pretreatment of sugarcane bagasse with acidified mixtures of ethylene carbonate (EC) and ethylene glycol (EG). In this study, “greener” solvent systems based on acidified mixtures of glycerol carbonate (GC) and glycerol were used to treat sugarcane bagasse and the roles of each solvent in deconstructing biomass were determined. Results Pretreatment of sugarcane bagasse at 90 °C for only 30 min with acidified GC produced a solid residue having a glucan digestibility of 90% and a glucose yield of 80%, which were significantly higher than a glucan digestibility of 16% and a glucose yield of 15% obtained for bagasse pretreated with acidified EC. Biomass compositional analyses showed that GC pretreatment removed more lignin than EC pretreatment (84% vs 54%). Scanning electron microscopy (SEM) showed that fluffy and size-reduced fibres were produced from GC pretreatment whereas EC pretreatment produced compact particles of reduced size. The maximal glucan digestibility and glucose yield of GC/glycerol systems were about 7% lower than those of EC/ethylene glycol (EG) systems. Replacing up to 50 wt% of GC with glycerol did not negatively affect glucan digestibility and glucose yield. The results from pretreatment of microcrystalline cellulose (MCC) showed that (1) pretreatment with acidified alkylene glycol (AG) alone increased enzymatic digestibility compared to pretreatments with acidified alkylene carbonate (AC) alone and acidified mixtures of AC and AG, (2) pretreatment with acidified GC alone slightly increased, but with acidified EC alone significantly decreased, enzymatic digestibility compared to untreated MCC, and (3) there was a good positive linear correlation of enzymatic digestibility of treated and untreated MCC samples with congo red (CR) adsorption capacity. Conclusions Acidified GC alone was a more effective solvent for pretreatment of sugarcane bagasse than acidified EC alone. The higher glucose yield obtained with GC-pretreated bagasse is possibly due to the presence of one hydroxyl group in the GC molecular structure, resulting in more significant biomass delignification and defibrillation, though both solvent pretreatments reduced bagasse particles to a similar extent. The maximum glucan digestibility of GC/glycerol systems was less than that of EC/EG systems, which is likely attributed to glycerol being less effective than EG in biomass delignification and defibrillation. Acidified AC/AG solvent systems were more effective for pretreatment of lignin-containing biomass than MCC.

A hybrid genetic algorithm for the energy-efficient virtual machine placement problem in data centers

Server consolidation using virtualization technology has become an important technology to improve the energy efficiency of data centers. Virtual machine placement is the key in the server consolidation technology. In the past few years, many approaches to the virtual machine placement have been proposed. However, existing virtual machine placement approaches consider the energy consumption by physical machines only, but do not consider the energy consumption in communication network, in a data center. However, the energy consumption in the communication network in a data center is not trivial, and therefore should be considered in the virtual machine placement. In our preliminary research, we have proposed a genetic algorithm for a new virtual machine placement problem that considers the energy consumption in both physical machines and the communication network in a data center. Aiming at improving the performance and efficiency of the genetic algorithm, this paper presents a hybrid genetic algorithm for the energy-efficient virtual machine placement problem. Experimental results show that the hybrid genetic algorithm significantly outperforms the original genetic algorithm, and that the hybrid genetic algorithm is scalable.

QUT Library advances the use of open public tools to navigate genetic inventions and builds research networks

Many emerging economies are dangling the patent system to stimulate bio-technological innovations with the ultimate premise that these will improve their economic and social growth. The patent system mandates full disclosure of the patented invention in exchange of a temporary exclusive patent right. Recently, however, patent offices have fallen short of complying with such a mandate, especially for genetic inventions. Most patent offices provide only static information about disclosed patent sequences and even some do not keep track of the sequence listing data in their own database. The successful partnership of QUT Library and Cambia exemplifies advocacy in Open Access, Open Innovation and User Participation. The library extends its services to various departments within the university, builds and encourages research networks to complement skills needed to make a contribution in the real world.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16–45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.