The significance of nitrogen cost minimization in proteomes of marine microorganisms

Marine microorganisms thrive under low levels of nitrogen (N). N cost minimization is a major selective pressure imprinted on open-ocean microorganism genomes. Here we show that amino-acid sequences from the open ocean are reduced in N, but increased in average mass compared with coastal-ocean microorganisms. Nutrient limitation exerts significant pressure on organisms supporting the trade-off between N cost minimization and increased average mass of amino acids that is a function of increased A+T codon usage. N cost minimization, especially of highly expressed proteins, reduces the total cellular N budget by 2.7–10% this minimization in combination with reduction in genome size and cell size is an evolutionary adaptation to nutrient limitation. The biogeochemical and evolutionary precedent for these findings suggests that N limitation is a stronger selective force in the ocean than biosynthetic costs and is an important evolutionary strategy in resource-limited ecosystems

Synchronization in graph analysis algorithms on the Partially Ordered Event-Triggered Systems many-core architecture

Abstract: One of the key problems in designing and implementing graph analysis algorithms for distributed platforms is to find an optimal way of managing communication flows in the massively parallel processing network. Message‐passing and global synchronization are powerful abstractions in this regard, especially when used in combination. This paper studies the use of a hardware‐implemented refutable global barrier as a design optimization technique aimed at unifying these abstractions at the API level. The paper explores the trade‐offs between the related overheads and performance factors on a message‐passing prototype machine with 49,152 RISC‐V threads distributed over 48 FPGAs (called the Partially Ordered Event‐Triggered Systems platform). Our experiments show that some graph applications favour synchronized communication, but the effect is hard to predict in general because of the interplay between multiple hardware and software factors. A classifier model is therefore proposed and implemented to perform such a prediction based on the application graph topology parameters: graph diameter, degree of connectivity, and reconvergence metric. The presented experimental results demonstrate that the correct choice of communication mode, granted by the new model‐driven approach, helps to achieve 3.22 times faster computation time on average compared to the baseline platform operation

An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease

Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 3′ end of cyanophage psbA genes, implying that this potential mechanism of regulating marine ‘viral’ photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes

Digital food marketing to children: Exploitation, surveillace and rights violations

Unhealthy food marketing has long been identified as a systems factor with negative health effects on children. The data-driven, personal data extraction and behavioural design practices of 21st century media advertising in digital technology systems mean that food marketing now sits at the intersection of multiple harms, infringing not only children’s rights to health and to food, but also their rights to privacy and to be free from exploitation. This further sharpens the need for State regulation to protect children and their rights effectively