If the loop fits..

The structure of the yeast L30 ribosomal protein bound to its autoregulatory RNA site has been determined by NMR spectroscopy. The intricate architecture of the RNA internal loop and the structure of the binding region of the protein both are stabilized in the complex, highlighting the importance of mutually-induced fit in RNA-protein interactions.     

Biological wastewater treatment model building fits and misfits

The modeling of biological wastewater treatment processes has received much attention over the past ten years. Efforts are underway to develop a unified model for these processes which will greatly aid in the design and operation of wastewater treatment facilities. This paper presents a philosophical discussion of model building strategies augmented by a discussion of statistical problems associated with model parameter estimation and model discrimination. This discussion further illustrates with actual data, that goodness of fit is not a sufficient condition for model acceptance. Numerous rival models are examined to illustrate this point. In order to verify a model or to discriminate between rival models, they must be “Put in jeopardy.” If this attitude is not employed in model building efforts, important discrepancies in the proposed model may go undetected.     

The impact of hissy fits in primary care

BACKGROUND: Hissy fits are experienced by physicians and patients alike, yet their full impact has never been studied before. METHODS: Specially trained researchers observed hissy fits at a clinic over 12 months. They interviewed perpetrators, victims and witnesses and recorded their comments because they had to. RESULTS: Hissy fits were common at the clinic and sometimes escalated to riots. Seasonal variations were endured. INTERPRETATION: Nobody likes this behaviour. Efforts should be made to counsel hissy fitters in channeling their angst in other, more positive ways.     

RAGE: a single receptor fits multiple ligands

The receptor for advanced glycation end products (RAGE) is a central signaling molecule in the innate immune system and is involved in the onset and sustainment of the inflammatory response. RAGE belongs to a class of pattern recognition receptors that recognize common features rather than a specific ligand. Recent structural information on the extracellular portion (ectodomain) of RAGE shed new light on this unusual ability. X-ray crystallographic, NMR and biochemical data suggest that ligand binding is driven largely by electrostatic interactions between the positively charged surface of the ectodomain and negatively charged ligands. In this article, I propose a putative mechanism of RAGE ligand recognition of receptor activation.     

Synapse fits neuron: joint reduction by model inversion

In this paper, we introduce a novel simplification method for dealing with physical systems that can be thought to consist of two subsystems connected in series, such as a neuron and a synapse. The aim of our method is to help find a simple, yet convincing model of the full cascade-connected system, assuming that a satisfactory model of one of the subsystems, e.g., the neuron, is already given. Our method allows us to validate a candidate model of the full cascade against data at a finer scale. In our main example, we apply our method to part of the squid’s giant fiber system. We first postulate a simple, hypothetical model of cell-to-cell signaling based on the squid’s escape response. Then, given a FitzHugh-type neuron model, we derive the verifiable model of the squid giant synapse that this hypothesis implies. We show that the derived synapse model accurately reproduces synaptic recordings, hence lending support to the postulated, simple model of cell-to-cell signaling, which thus, in turn, can be used as a basic building block for network models.     

An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding

Key message

The innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding.

Abstract

The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Our proposed GWAS procedure is characterized as a novel restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS, https://github.com/njau-sri/rtm-gwas). The Chinese soybean germplasm population (CSGP) composed of 1024 accessions with 36,952 SNPLDBs (generated from 145,558 SNPs, with reduced linkage disequilibrium decay distance) was used to demonstrate the power and efficiency of RTM-GWAS. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. A relatively thorough detection of QTL with their multiple alleles was achieved by RTM-GWAS compared with the linear mixed model method on 100-seed weight in CSGP. A QTL-allele matrix (402 alleles of 139 QTL × 1024 accessions) was established as a compact form of the population genetic constitution. The 100-seed weight QTL-allele matrix was used for genetic characterization, candidate gene prediction, and genomic selection for optimal crosses in the germplasm population.