Association mapping of cold‐induced sweetening in potato using historical phenotypic data

In this study, historical phenotypic data from a potato breeding programme were used with an association mapping approach to identify alleles of candidate genes associated with cold‐induced sweetening of potato. Molecular marker analysis was used to determine allelic variation of candidate genes potentially involved in cold‐induced sweetening. Variations in the UDP‐glucose pyrophosphorylase (UGPase, EC 2.7.7.9) and apoplastic invertase genes (EC 3.2.1.26) were significantly associated with cold‐induced sweetening, and a possible interaction of apoplastic invertase and apoplastic invertase inhibitor was identified. This demonstrates that breeding programme phenotypic data collected over multiple years and environments can be used successfully with pedigree information for association mapping. It also confirms that the UGPase and apoplastic invertase markers are transferable across breeding programmes with distinct germplasm.     

A Framework for Development and Communication of Absolute Environmental Sustainability Assessment Methods

An absolute environmental sustainability assessment (AESA) addresses whether a production or consumption activity can be considered environmentally sustainable in an absolute sense. This involves a comparison of its environmental pressure to its allocated environmental carrying capacity. AESA methods have been developed in multiple academic fields, each using their own set of concepts and terms with little communication across the fields. A recent growing interest in using AESA methods for decision support calls for a better common understanding of the constituents of an AESA method and how it can be communicated to scientific peers and to potential users. With this aim, we develop a framework for AESA methods, composed of a succession of four assessment steps and involving six methodological choices that must be made by the method developer or the user. We then use the framework to analyze and compare five selected AESA methods that focus on the release of phosphorus and nitrogen to the environment. In this manner, we show that the framework is able to systematically differentiate AESA methods that initially appear to be similar. Intended users of the framework include (1) method developers communicating new AESA methods to academic peers or potential method users and (2) researchers comparing a group of existing AESA methods and communicating their differences to their peers and to potential users looking for guidance on method selection.     

John Kendrew and myoglobin: Protein structure determination in the 1950s

The essay reviews John Kendrew's pioneering work on the structure of myoglobin for which he shared the Nobel Prize for Chemistry in 1962. It reconstructs the status of protein X‐ray crystallography at the time Kendrew entered the field in 1945, after distinctive service in operational research during the war. It reflects on the choice of sperm whale myoglobin as research material. In particular, it highlights Kendrew's early use of digital electronic computers for crystallographic computations and the marshaling of other tools and approaches that made it possible to solve the structure at increasing resolution. The essay further discusses the role of models in structure resolution and their broader reception. It ends by briefly reviewing Kendrew's other contributions in the formation and institutionalization of molecular biology.     

Phosphatidylinositol‐4 kinase III beta and oxysterol‐binding protein accumulate unesterified cholesterol on poliovirus‐induced membrane structure

Studies on anti‐picornavirus compounds have revealed an essential role of a novel cellular pathway via host phosphatidylinositol‐4 kinase III beta (PI4KB) and oxysterol‐binding protein (OSBP) family I in poliovirus (PV) replication. However, the molecular role for this pathway in PV replication has yet to be determined. Here, viral and host proteins modulating production of phosphatidylinositol 4‐phosphate (PI4P) and accumulation of unesterified cholesterol (UC) in cells were analyzed and the role of the PI4KB/OSBP pathway in PV replication characterized. Virus protein 2BC was identified as a novel interactant of PI4KB. PI4KB and VCP/p97 bind to a partially overlapped region of 2BC with different sensitivity to a 2C inhibitor. Production of PI4P and accumulation of UC were enhanced by virus protein 2BC, but suppressed by virus proteins 3A and 3AB. In PV‐infected cells, a PI4KB inhibitor suppressed production of PI4P, and both a PI4KB inhibitor and an OSBP ligand suppressed accumulation of UC on virus‐induced membrane structure. Inhibition of PI4KB activity caused dissociation of OSBP from virus‐induced membrane structure in PV‐infected cells. Synthesis of viral nascent RNA in PV‐infected cells was not affected in the presence of PI4KB inhibitor and OSBP ligand; however, transient pre‐treatment of PV‐infected cells with these inhibitors suppressed viral RNA synthesis. These results suggest that virus proteins modulate PI4KB activity and provide PI4P for recruitment of OSBP to accumulate UC on virus‐induced membrane structure for formation of a virus replication complex.     

Sequence and structure space of RNA-binding peptides

Studies of RNA-binding peptides, and recent combinatorial library experiments in particular, have demonstrated that diverse peptide sequences and structures can be used to recognize specific RNA sites. The identification of large numbers of sequences capable of binding to a particular site has provided extensive phylogenetic information used to deduce basic principles of recognition. The high frequency at which RNA-binding peptides are found in large sequence libraries suggests plausible routes to evolve sequence-specific binders, facilitating the design of new binding molecules and perhaps reflecting characteristics of natural evolution.     

Modulation of immunogenicity of poly(sarcosine) displayed on various nanoparticle surfaces due to different physical properties

Poly(sarcosine) displayed on polymeric micelle is reported to trigger a T cell‐independent type2 reaction with B1a cells in the mice to produce IgM and IgG3 antibodies. In addition to polymeric micelle, three kinds of vesicles displaying poly(sarcosine) on surface were prepared here to evaluate the amounts and avidities of IgM and IgG3, which were produced in mice, to correlate them with physical properties of the molecular assemblies. The largest amount of IgM was produced after twice administrations of a polymeric micelle of 35 nm diameter ( G1 ). On the other hand, the production amount of IgG3 became the largest after twice administrations of G3 (vesicle of 229 nm diameter) or G4 (vesicle of 85 nm diameter). The augmented avidity of IgG3 after the twice administrations compared with that at the single administration was the highest with G3 . These differences in immune responses are discussed in terms of surface density of poly(sarcosine) chains, nanoparticle size, hydrophobic component of poly(L‐lactic acid) or (Leu‐ or Val‐Aib)_n, and membrane elasticity of the nanoparticles. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

High sequence coverage by in-capillary proteolysis of native proteins and simultaneous analysis of the resulting peptides by nanoelectrospray ionization-mass spectrometry and tandem mass spectrometry

Losses of proteolytic peptides during extraction and/or purification procedures succeeding in-gel or in-solution digests of proteins frequently occur in the course of protein identification investigations. In order to overcome this disadvantage, the method of in-capillary digest was developed: native proteins were incubated in the presence of endoproteases in the electrospray capillary and the resulting peptides were analyzed by nanoelectrospray-mass spectrometry during the ongoing proteolysis. In-capillary digest of apomyglobin by use of trypsin in a molar ratio of 25:1 yielded complete degradation already after 15 min. The sequence coverage based on formation of molecular ions was 100% and peptide ions could be fragmented by collision-induced dissociation and sequenced. When myoglobin was incubated in the electrospray capillary with trypsin in a molar ratio of 500:1, a clear shift from molecular ions and miscleaved peptide ions to the expected final tryptic peptide ions was observed over a 2 h period. The peptide spectra obtained from tryptic in-capillary proteolysis of bovine serum albumin and apotransferrin, respectively, gave rise to sequence coverages of more than 40% for both proteins. The data obtained from the peptide maps as well as from collision-induced dissociation (CID) of selected peptides were more than sufficient for protein identification by database searches. An elephant milk protein preparation was used to demonstrate the application of in-capillary proteolysis on protein mixtures. Tryptic digest, simultaneous analysis of the proteolytic peptides by use of CID, and subsequent sequencing allowed the identification of lactoferrin, alphas1-casein, beta-casein, delta-casein, and kappa-casein by homology search.