The path to next generation biofuels: successes and challenges in the era of synthetic biology

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.     

Development and characterization of an oat TILLING-population and identification of mutations in lignin and β-glucan biosynthesis genes

Background  

Oat, Avena sativa is the sixth most important cereal in the world. Presently oat is mostly used as feed for animals. However, oat also has special properties that make it beneficial for human consumption and has seen a growing importance as a food crop in recent decades. Increased demand for novel oat products has also put pressure on oat breeders to produce new oat varieties with specific properties such as increased or improved β-glucan-, antioxidant- and omega-3 fatty acid levels, as well as modified starch and protein content. To facilitate this development we have produced a TILLING (Targeting Induced Local Lesions IN Genomes) population of the spring oat cultivar SW Belinda.     

Assessing the validity of impact pathways for child labour and well-being in social life cycle assessment

Background, aim and scope  

Assuming that the goal of social life cycle assessment (SLCA) is to assess damage and benefits on its ‘area of protection’ (AoP) as accurately as possible, it follows that the impact pathways, describing the cause effect relationship between indicator and the AoP, should have a consistent theoretical foundation so the inventory results can be associated with a predictable damage or benefit to the AoP. This article uses two concrete examples from the work on SLCA to analyse to what extent this is the case in current practice. One considers whether indicators included in SLCA approaches can validly assess impacts on the well-being of the stakeholder, whereas the other example addresses whether the ‘incidence of child labour’ is a valid measure for impacts on the AoPs.     

2′, 3′-<Emphasis Type="Italic">O</Emphasis>-(4-benzoylbenzoyl)–ATP-mediated calcium signaling in rat glioma C6 cells: role of the P2Y<Subscript>2</Subscript> nucleotide receptor

In this study, we examined the response of glioma C6 cells to 2′,3′-O-(4-benzoylbenzoyl)-ATP (BzATP) and showed that the BzATP-induced calcium signaling does not involve the P2X₇ receptor activity. We show here that in the absence of extracellular Ca²⁺, BzATP-generated increase in [Ca²⁺]_i via Ca²⁺ release from intracellular stores. In the presence of calcium ions, BzATP established a biphasic Ca²⁺ response, in a manner typical for P2Y receptors. Brilliant Blue G, a selective antagonist of the rat P2X₇ receptor, did not reduce any of the two components of the Ca²⁺ response elicited by BzATP. Periodate-oxidized ATP blocked not only BzATP- but also UTP-induced Ca²⁺ elevation. Moreover, BzATP did not open large transmembrane pores. What is more, a cross-desensitization between UTP and BzATP occurred, which clearly shows that in glioma C6 cells BzATP activates most likely the P2Y₂ but not the P2X₇ receptors.     

Incompatibility behavior of a symbiotic plasmid pMH7653Rb in <Emphasis Type="Italic">Mesorhizobium huakuii</Emphasis> 7653R

Mesorhizobium huakuii strain 7653R harbored two indigenous plasmids named pMH7653Ra and pMH7653Rb. The larger plasmid pMH7653Rb (symbiotic plasmid) was transferred to M. huakuii HN308SR harboring three plasmids: pMHHN308a, pMHHN308b and pMHHN308c, and HN3015SR harboring three plasmids: pMHHN3015a, pMHHN3015b and pMHHN3015c by tri-parent mating. Two stable indigenous plasmids, pMHHN308b and pMHHN308c of HN308SR, were co-eliminated due to the introduction of pMH7653Rb, and the transconjugant was named HN308SRN14. The results implied that pMH7653Rb and pMHHN308b, pMHHN308c were incompatible and might have been ascribed to the same incompatible group. The plasmid profiles of transconjugant HN3015SRN14 showed that the second largest plasmid pMHHN3015b of HN3015SR was cured due to the introduction of pMH7653Rb. The results also implied that pMH7653Rb and pMHHN3015b were incompatible. Results from plant nodulation tests showed that pMH7653Rb could only maintain the nodulation ability in transconjugant HN308SRN14 and its nodule number was more than that of wild strain HN308SR, but could not replace the nitrogen fixation effect of pMHHN308b and pMHHN308c. The plasmid cured mutant HN308SRN14D harboring only pMHHN308a formed null nodules that demonstrated pMHHN308a was relevant to nodulation ability. HN3015SRN14 harboring pMH7653Rb, pMHHN3015a and pMHHN3015c formed null nodules while HN3015SRN14D containing pMHHN3015a and pMHHN3015c lost the nodulation ability. The plasmid replication repC-like gene sequences were detected by a polymerase chain reaction from 7653R, HN308, HN3015, HN308SRN14 and HN3015SRN14. The repC gene sequence similarities of the strains tested attained 99%.     

Expression of human growth hormone gene in <Emphasis Type="Italic">Pleurotus eryngii</Emphasis>

Recombinant human growth hormone (rhGH) has been widely used in many medical applications. Large scale production of rhGH is important for a wider application of this molecule in the field of proteomics. This investigation reports a modified Agrobacterium-mediated method for transfer and expression of human growth hormone gene in the popular edible mushroom Pleurotus eryngii. A binary vector pCAMBIA1304 containing the hGH2 gene was constructed and introduced into Pleurotus eryngii via Agrobacterium tumefaciens-mediated transformation. Integration of hGH2 into mushroom genome was detected by PCR and expression was confirmed by Western blot assay. The successful expression of the human growth hormone gene in mushroom suggests that the proposed modified transformation system is probably useful for the production of transgenic mushrooms.     

Comparative evaluation of hydro-, chemo- , and hormonal-priming methods for imparting salt and PEG stress tolerance in Indian mustard (<Emphasis Type="Italic">Brassica</Emphasis><Emphasis Type="Italic">juncea</Emphasis> L.)

The present study was aimed to evaluate the effect of different seed priming methods to enhance the sodium chloride (NaCl) and polyethylene glycol-8000 (PEG-8000) stress tolerance in Indian mustard (Brassica juncea L.). Seeds subjected to different priming treatments such as water (hydro-priming), calcium chloride (CaCl₂) (chemo-priming), and abscisic acid (ABA) (hormonal-priming) showed increased rate of germination as compared to non-primed seeds. The primed and non-primed seeds were grown for 15 days and then the seedlings were independently subjected to iso-osmotic salt (150 mM NaCl) or PEG-8000 (20%) stress. The different biochemical responses were studied 10 days after treatment. Under NaCl and PEG stress, the dry weight and total chlorophyll content were higher in primed sets as compared to non-primed treatment which was also evident by the phenotype of the seedlings. In general, the higher activities of superoxide dismutase and glutathione reductase resulted in lower oxidative damage, in terms of malondialdehyde content, under NaCl and PEG stress in hydro-primed set as compared to non-primed, ABA-, and CaCl₂-primed treatments. Besides, the level of total phenolics and accumulation of osmolytes such as free proline, glycine betaine, and total soluble sugars was also lower in hydro-primed set as compared to other primed and non-primed treatments. The study thus suggests the use of hydro-priming as a simple and cost-effective strategy to alleviate the NaCl and PEG induced stress in B. juncea.     

Early activation of wheat polyamine biosynthesis during Fusarium head blight implicates putrescine as an inducer of trichothecene mycotoxin production

Background  

The fungal pathogen Fusarium graminearum causes Fusarium Head Blight (FHB) disease on wheat which can lead to trichothecene mycotoxin (e.g. deoxynivalenol, DON) contamination of grain, harmful to mammalian health. DON is produced at low levels under standard culture conditions when compared to plant infection but specific polyamines (e.g. putrescine and agmatine) and amino acids (e.g. arginine and ornithine) are potent inducers of DON by F. graminearum in axenic culture. Currently, host factors that promote mycotoxin synthesis during FHB are unknown, but plant derived polyamines could contribute to DON induction in infected heads. However, the temporal and spatial accumulation of polyamines and amino acids in relation to that of DON has not been studied.     

Large scale comparison of global gene expression patterns in human and mouse

Background  

It is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms. However, the level of conservation of gene expression patterns of the orthologous genes in different species has been unclear. To address the issue, we compared gene expression of orthologous genes based on 2,557 human and 1,267 mouse samples with high quality gene expression data, selected from experiments stored in the public microarray repository ArrayExpress.