A gene’s eye view of Darwinian populations

Biologists and philosophers differ on whether selection should be analyzed at the level of the gene or of the individual. In Peter Godfrey-Smith’s book, Darwinian Populations and Natural Selection, he argues that individuals can be good members of Darwinian populations, whereas genes rarely can. I take issue with parts of this view, and suggest that Godfrey-Smith’s scheme for thinking about Darwinian populations is also applicable to populations of genes.     

Metabolic Basis for the Self-Referential Genetic Code

An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine—this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.     

Protoplast formation and regeneration in <Emphasis Type="Italic">Lactobacillus delbrueckii</Emphasis>

Method for production and regeneration of Lactobacillus delbrueckii protoplasts are described. The protoplasts were obtained by treatment with a mixture of lysozyme and mutanolysin in protoplast buffer at pH 6.5 with different osmotic stabilizers. The protoplasts were regenerated on deMan, Rogosa and Sharpe (MRS) with various osmotic stabilizers. Maximum protoplast formation was obtained in protoplast buffer with sucrose as an osmotic stabilizer using a combination of lysozyme (1 mg/ml) and mutanolysin (10 μg/ml). Maximum protoplast regeneration was obtained on MRS medium with sucrose (0.5 M) as an osmotic stabilizer. The regeneration medium was also applicable to other species of lactobacilli as well. This is, to our knowledge, the first report on protoplast formation and efficient regeneration in case of L. delbrueckii.     

Systems genetics analyses predict a transcription role for P2P-R: Molecular confirmation that P2P-R is a transcriptional co-repressor

Background  

The 250 kDa P2P-R protein (also known as PACT and Rbbp6) was cloned over a decade ago and was found to bind both the p53 and Rb1 tumor suppressor proteins. In addition, P2P-R has been associated with multiple biological functions, such as mitosis, mRNA processing, translation and ubiquitination. In the current studies, the online GeneNetwork system was employed to further probe P2P-R biological functions. Molecular studies were then performed to confirm the GeneNetwork evaluations.     

Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis

Background  

Recent studies point to a great diversity of non-ribosomal peptide synthesis systems with major roles in amino acid and co-factor biosynthesis, secondary metabolism, and post-translational modifications of proteins by peptide tags. The least studied of these systems are those utilizing tRNAs or aminoacyl-tRNA synthetases (AAtRS) in non-ribosomal peptide ligation.     

Great-granny’s Garden: a living archive and a sensory garden

Since 2003, the Botanical Garden in Oslo has been involved in a project coordinated by the Norwegian Genetic Resource Centre. The wide range of work supervised by this centre includes conservation of ornamental plants. Our garden has been responsible for the registration and collecting of ornamentals in Southeast-Norway and has a special responsibility for the conservation of Paeonia species and cultivars. As a result of the project, Great-granny’s Garden was opened to the public in 2008. It has two objectives. Firstly, it shall be a living archive of Norway’s horticultural heritage. Although proven hardy, easy to grow, and long-lived, old varieties of traditional ornamentals are rapidly disappearing. We aim to keep these old-fashioned varieties for sustainable use in future horticulture and encourage people to use them in present day gardening, both in new gardens and in the restoration of old ones. Secondly, the garden is designed as a sensory garden for people with dementia, in cooperation with Oslo’s Resource Centre for Dementia and Psychiatric Care of the Elderly. It is enclosed by a picked fence and by shrubs, offers rest on several benches, and has a paved and easy to follow round-walk among traditional garden elements and plants with a lush variety of colours, forms, and scents. A sensory garden stimulates many senses, evokes pleasant emotions, brings out long-forgotten memories, and stimulates communication. Sensory gardens are therefore considered an important tool in the therapy of dementia.     

White-rot fungal conversion of wheat straw to energy rich cattle feed

In order to improve the digestibility and nutrient availability in rumen, wheat straw was subjected to solid state fermentation (SSF) with white-rot fungi (i.e. Pleurotus ostreatus and Trametes versicolor) and the fermented biomass (called myco-straw) was evaluated for biochemical, enzymatic and nutritional parameters. The fungal treatment after 30 days led to significant decrease (P < 0.05) in cell wall constituents viz, acid detergent fiber (ADF), neutral detergent fiber (NDF), hemicellulose, lignin and cellulose to the extent of 35.00, 38.88, 45.00, 37.48 and 37.86%, respectively in P. ostreatus fermented straw, while 30.04, 33.85, 39.90, 31.29 and 34.00%, respectively in T. versicolor fermented straw. However, maximum efficiency of fermentation in terms of low carbohydrate consumption per unit of lignin degradation, favoring cattle feed production was observed for P. ostreatus on the 10th day (17.12%) as compared with T. versicolor on the 30th day (16.91%). The myco-straw was found to contain significantly high (P < 0.05) crude protein (CP; 4.77% T. versicolor, 5.08% P. ostreatus) as compared to control straw (3.37%). Metabolizable energy (ME, MJ/kg DM), percent organic matter digestibility (OMD) and short chain fatty acids (SCFAs; mmol) production also increased considerably from control straw (4.40, 29.91 and 0.292) to a maximum up to P. ostreatus fermented straw (4.92, 33.39 and 0.376 on 20th day) and T. versicolor fermented straw (4.66, 31.74 and 0.334 on 10th day), respectively. Moreover, the myco-straw had lower organic carbon and was rich in nitrogen with lower C/N ratio as compared to control wheat straw. Results suggest that the fungal fermentation of wheat straw effectively improved CP content, OM digestibility, SCFAs production, ME value and simultaneously lowered the C/N ratio, thus showing potential for bioconversion of lignin rich wheat straw into high energy cattle feed.     

Germination responses of three grassland species differ between native and invasive origins

The germination stage is critical in plant life-history and is also a key process during the expansion of species’ ranges into new environments. In this study we investigated the germination patterns of three plant species (Achillea millefolium, Hieracium pilosella and Hypericum perforatum) that are invasive to New Zealand (NZ) and native to Central Europe. We asked whether the species show differences in germination temperature requirements, germination speed and maximum germination rates, and thus, whether they display evidence of adaptation to different conditions in the invasive range. Seeds from three populations per species and region were subjected to three different temperature regimes to compare germination rates among origins and across temperature conditions. For Achillea millefolium and Hypericum perforatum, germination rates were significantly higher for invasive NZ provenances than for native German ones. Seeds from invasive populations of all three species displayed increased maximum germination at medium temperature conditions when compared to native populations, which indicates altered germination strategies in the invaded range. Changes in temporal development patterns were most conspicuous for invasive Hieracium pilosella and Hypericum perforatum populations. These findings imply that adaptation in germination patterns towards different climatic conditions in invasive populations has occurred. Our study emphasises the importance of the germination stage during plant invasion and its role in explaining range expansion of these species.