The involvement of ethylene in liatris corm dormancy

Corms of liatris (L. spicata, cv. Callilepsis) show a seasonal dormancy, being most active in the November harvest and least active in June. Storage of dormant corms at 3 °C for about 9 weeks resulted in a complete break of dormancy. This was accompanied by a sharp temporal increase in their rate of ethylene production, which was more pronounced in the buds than in the parenchyma tissue. Application of ethylene to the corms in the form of ethrel solution increased both ethylene production rate and sprouting. The ethylene-forming activity from ACC, measured both in vivo and in vitro, was higher in corms producing more ethylene. However, the content of 1-aminocyclopropane-1-carboxylic acid (ACC) of the corms was inversely related to their ethylene production rate. Ethylene thus seems to be involved in the dormancy control of liatris corms, and its production is apparently regulated mainly by the activity of the membranous ethylene-forming system.     

Spatial determinants of specificity in insulin action

Insulin is a potent stimulator of intermediary metabolism, however the basis for the remarkable specificity of insulin's stimulation of these pathways remains largely unknown. This review focuses on the role compartmentalization plays in insulin action, both in signal initiation and in signal reception. Two examples are discussed: (1) a novel signalling pathway leading to the phosphorylation of the caveolar coat protein caveolin, and (2) a recently identified scaffolding protein, PTG, involved directly in the regulation of enzymes controlling glycogen metabolism.     

Conformation of parathyroid hormone antagonists by CD,nmr, and molecular dynamics simulations

The conformation of two highly potent parathyroid hormone (PTH) antagonists was investigated in water/2, 2, 2-trifluoroethanol mixtures. The two peptides are derived from the sequence (7-34) of PTH and of PTH-related protein (PTHrP) and have a D -Trp replacing Gly in position 12. In the analogue derived from PTHrP, Lys¹¹ was replaced by Leu to remove the residual agonist activity. The study was conducted by CD and two-dimensional proton magnetic resonance spectroscopy, and the nuclear Overhauser effects found were utilized in restrained distance geometry and molecular dynamics simulations. Both peptides adopt a helical C-terminal conformation, which seems more stable in the case of the PTHrP analogue. A type II′ β-turn centered around D -Trp¹² and Lys¹³ is present inboth structures. © 1995 John Wiley & Sons, Inc.     

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a “reverse mapping” approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper’s utility for recovering depth of coverage, and accurate genotyping of SNP sites across the human genome. We show that genotyping unmapped reads can correctly inform a sample’s population, sex, and relatedness in a family setting. Detection of pathogen sequences within RNA-seq data was sensitive and accurate, performing comparably to existing methods, but with increased flexibility. We present two examples of ways in which this flexibility allows the analysis of genome features not well-represented in a linear reference. First, we analyze contigs from African genome sequencing studies, showing how they distribute across families from three distinct populations. Second, we show how gene-marking k-mers for the killer immune receptor locus allow allele detection in a region that is challenging for standard read mapping pipelines. The future adoption of the reverse mapping approach represented by FlexTyper will be enabled by more efficient methods for FM-index generation and biology-informed collections of reference queries. In the long-term, selection of population-specific references or weighting of edges in pan-population reference genome graphs will be possible using the FlexTyper approach. FlexTyper is available at https://github.com/wassermanlab/OpenFlexTyper.     

Bacterial chemoreceptors of different length classes signal independently

Bacterial chemoreceptors sense environmental stimuli and govern cell movement by transmitting the information to the flagellar motors. The highly conserved cytoplasmic domain of chemoreceptors consists in an alpha‐helical hairpin that forms in the homodimer a coiled‐coil four‐helix bundle. Several classes of chemoreceptors that differ in the length of the coiled‐coil structure were characterized. Many bacterial species code for chemoreceptors that belong to different classes, but how these receptors are organized and function in the same cell remains an open question. E. coli cells normally code for single class chemoreceptors that form extended arrays based on trimers of dimers interconnected by the coupling protein CheW and the kinase CheA. This structure promotes effective coupling between the different receptors in the modulation of the kinase activity. In this work, we engineered functional derivatives of the Tsr chemoreceptor of E. coli that mimic receptors whose cytoplasmic domain is longer by two heptads. We found that these long Tsr receptors did not efficiently mix with the native receptors and appeared to function independently. Our results suggest that the assembly of membrane‐bound receptors of different specificities into mixed clusters is dictated by the length‐class to which the receptors belong, ensuring cooperative function only between receptors of the same class.