Number of natively unfolded proteins scales with genome size

Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in important cellular processes. In this work we used from three indicators of folding status, derived from the analysis of mean packing and mean contact energy of a protein sequence as well as from VSL2, a disorder predictor, and we combined them into a consensus score to identify natively unfolded proteins in several genomes from Archaea, Bacteria and Eukarya. We found a high correlation among the number of predicted natively unfolded proteins and the number of proteins in the genomes. More specifically, the number of natively unfolded proteins scaled with the number of proteins in the genomes, with exponent 1.81 +- 0.10. This scaling law may be important to understand the relation between the number of natively unfolded proteins and their roles in cellular processes.Comment: Submitted to Biophysics and Bioengineering Letters http://padis2.uniroma1.it:81/ojs/index.php/CISB-BB

Codon Bias Patterns of E.coliE.coli's Interacting Proteins

Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, $CompAI$, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for $E.coli$, comparing $CompAI$ with other widely used indices: $tAI$, $CAI$, and $Nc$. We show that $CompAI$ and $tAI$ capture similar information by being positively correlated with gene conservation, measured by ERI, and essentiality, whereas, $CAI$ and $Nc$ appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of $tAI$ and $CompAI$ with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in $E.coli$. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by $CompAI$ and $tAI$). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, $CompAI$ turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation

Sediment features and heavy metal levels in four areas of Sardinia devoted to bivalve culture = Caratteristiche dei sedimenti e livelli di metalli pesanti in quattro aree della Sardegna idonee all’allevamento dei bivalvi

Sediment characteristics and Cd, Cu, Mn, Pb and Zn concentrations were assessed in the lagoons of Marceddì, Calich and Porto Pozzo, and in the inner part of the Gulf of Olbia. Sediment of the zones examined were quite similar, except for the Calich lagoon that showed the higher content of total organic carbon. High values of Cd, Pb and Zn were detected in the sediments of the Marceddì lagoon, while remarkable levels of Cu and Mn were found in the Calich lagoon and in the Gulf of Olbia

L'Invecchiamento biologico del Cannonau di Oliena

Accelerated ageing trials were carried out on « Cannonau di Oliena» under production conditions. Yeast «Flor» strains of the species Saccharomyces prostoserdovii were used as ageing agents. Results showed that wines produced using these yeasts were superior to those produced normally specially when Sacch. Prostoserdovii was added to the musts as «pied de cuve», thus reducing maturing times considerably

Produzione di anidride solforosa da parte dei lieviti nel corso della fermentazione alcolica

SO2 production by yeast during alcoholic fermentation. Determinations were made of SO2 produced during must fermentation by 29 strains of Saccharomyces cerevisiae. After 2 days of fermentation, only 4 reached a 50 - 70 mg/l SO2 production; on the 4th day only 2; and on the 7th day only 1. All proved to belong to the low SO2 producer category

Aerobic and anaerobic spore-forming bacteria in Sardinian honey.

Apart from an ubiquitous microflora, this investigation into 52 samples of honey revealed some undesirable spore-forming bacteria, Bacillus alvei and B. larvae which are bee pathogens. Bacillus cereus can cause spoilage and food poisoning. It is, therefore, considered essential that every country includes microbiological standards in its Food Safety Regulations for honey, so that the consumer is guaranteed as to the wholesomeness as well as the quality of the product

I Lieviti del tubo digerente dell'<i>Apis inellifica ligustica</i> Spinola

The results of microbiological surveis of apis mellifica lingustica Spinola intestinal tacts are givenhere. From 100 samples 54 yeast strains were isolated. The yeast specie identified are: H. anomala var. schneggii, C. guilliermondii var. guilliermondii, T. apicola, T. candida, T. glabrata, T. haemulonii. The yeast species isolated were not so different from those discovered by other authors in similar environments