Cocrystal structure of a class-I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

Riboswitches are mRNA domains that bind metabolites and modulate gene expression in cis. We report cocrystal structures of a remarkably compact riboswitch (34 nucleotides suffice for ligand recognition) from Bacillus subtilis selective for the essential nucleobase preQ1 (7-aminomethyl-7-deazaguanine). These reveal a previously unrecognized pseudoknot fold, and suggest a conserved gene-regulatory mechanism whereby ligand binding promotes sequestration of an RNA segment that otherwise assembles into a transcriptional anti-terminator

Migration, Seafarers and the Humanitarian-Security-Economic Regimes Complex at Sea

Undocumented migration across the maritime space poses different challenges to the maritime industry. By focusing on a hitherto overlooked group, seafarers, the chapter attempts to set their experiences in the maritime security research agenda by using the Mediterranean scene as a demonstrative case study. The chapter highlights the normative dilemma and conceptual limitation of reading undocumented migration at sea through a security lens alone. Instead, by focusing on the experiences of seafarers in relation to migrants at sea, the chapter draws from the literature on international regime complexity to frame the socio-legal, political and economic environment seafarers inhabit and operate in vis-à-vis migrants as a ‘humanitarian-security-economic regimes complex’. Using examples from the Mediterranean Sea, the chapter argues that the humanitarian, security and economic regimes within the complex place contradicting expectations on seafarers which entail significant tensions and lead to trade-offs such as instances of non-rescue. The chapter, thus, calls for more research into the experiences of seafarers which takes into account the nuances of the humanitarian, security and economic challenges they face when encountering migrants at sea

Visualizing codon usage within and across genomes : concepts and tools

Cost and time of genome sequencing have plummeted over the last decade. This leads to explosive growth of genetic databases and development of novel sequencing-based approaches to study various biological phenomena. The database growth was particularly beneficial for investigation of protein-coding sequences at the codon level, requiring the access to large sets of related genomes. Such studies are expected to illuminate biological forces that shape primary structure of coding sequences and predict their evolutionary trajectories more precisely. In addition to fundamental interest, codon usage studies are of ample practical value, for example, in drug discovery and genomic medicine areas. Nevertheless, the depth of our understanding of codon-related issues is currently shallower as compared to what we know about nucleotide and amino acid sequences. Besides the lack of adequate datasets in the early days of molecular biology, codon usage studies, in our opinion, suffer from underdevelopment of easy-to-use tools to analyze and visualize how codon sequence changes along the gene and across the homologous genes in course of evolution. In this review, we aim to describe main areas of codon usage studies with an emphasis on the tools that allow visual interpretation of the data. We discuss underlying principles of different approaches, what kind of statistics lends confidence in their results and what has to be done to further boost the field of codon usage research