Possible consequences of an inability of plants to control manganese uptake

Plant and Soil - This commentary presents several thoughts elicited by the observation of Lambers et al. (Plant Soil, 2021) in this Special Issue that the release of carboxylates by roots increases...     

High-throughput protein production – Lessons from scaling up from 10 to 288 recombinant proteins per week

The demand for high-throughput recombinant protein production has markedly increased with the increased activity in the field of proteomics. Within the Human Protein Atlas project recombinantly produced human protein fragments are used for antibody production. Here we describe how the protein expression and purification protocol has been optimized in the project to allow for handling of nearly 300 different proteins per week. The number of manual handling steps has been significantly reduced (from 18 to 9) and the protein purification has been completely automated.     

Integrating force-sensing and signaling pathways in a model for the regulation of wing imaginal disc size

The regulation of organ size constitutes a major unsolved question in developmental biology. The wing imaginal disc of Drosophila serves as a widely used model system to study this question. Several mechanisms have been proposed to have an impact on final size, but they are either contradicted by experimental data or they cannot explain a number of key experimental observations and may thus be missing crucial elements. We have modeled a regulatory network that integrates the experimentally confirmed molecular interactions underlying other available models. Furthermore, the network includes hypothetical interactions between mechanical forces and specific growth regulators, leading to a size regulation mechanism that conceptually combines elements of existing models, and can be understood in terms of a compression gradient model. According to this model, compression increases in the center of the disc during growth. Growth stops once compression levels in the disc center reach a certain threshold and the compression gradient drops below a certain level in the rest of the disc. Our model can account for growth termination as well as for the paradoxical observation that growth occurs uniformly in the presence of a growth factor gradient and non-uniformly in the presence of a uniform growth factor distribution. Furthermore, it can account for other experimental observations that argue either in favor or against other models. The model also makes specific predictions about the distribution of cell shape and size in the developing disc, which we were able to confirm experimentally.     

Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis

The cactophilic fly Drosophila mojavensis exhibits considerable intraspecific genetic structure across allopatric geographic regions and shows associations with different host cactus species across its range. The divergence between these populations has been studied for more than 60years, yet their exact historical relationships have not been resolved. We analysed sequence data from 15 intronic X-linked loci across populations from Baja California, mainland Sonora-Arizona and Mojave Desert regions under an isolation-with-migration model to assess multiple scenarios of divergence. We also compared the results with a pre-existing sequence data set of eight autosomal loci. We derived a population tree with Baja California placed at its base and link their isolation to Pleistocene climatic oscillations. Our estimates suggest the Baja California population diverged from an ancestral Mojave Desert/mainland Sonora-Arizona group around 230,000-270,000years ago, while the split between the Mojave Desert and mainland Sonora-Arizona populations occurred one glacial cycle later, 117,000-135,000years ago. Although we found these three populations to be effectively allopatric, model ranking could not rule out the possibility of a low level of gene flow between two of them. Finally, the Mojave Desert population showed a small effective population size, consistent with a historical population bottleneck. We show that model-based inference from multiple loci can provide accurate information on the historical relationships of closely related groups allowing us to set into historical context a classic system of incipient ecological speciation.     

Temporal integration of olfactory perceptual evidence in human orbitofrontal cortex

Given a noisy sensory world, the nervous system integrates perceptual evidence over time to optimize decision-making. Neurophysiological accumulation of sensory information is well-documented in the animal visual system, but how such mechanisms are instantiated in the human brain remains poorly understood. Here we combined psychophysical techniques, drift-diffusion modeling, and functional magnetic resonance imaging (fMRI) to establish that odor evidence integration in the human olfactory system enhances discrimination on a two-alternative forced-choice task. Model-based measures of fMRI brain activity highlighted a ramp-like increase in orbitofrontal cortex (OFC) that peaked at the time of decision, conforming to predictions derived from an integrator model. Combined behavioral and fMRI data further suggest that decision bounds are not fixed but collapse over time, facilitating choice behavior in the presence of low-quality evidence. These data highlight a key role for the orbitofrontal cortex in resolving sensory uncertainty and provide substantiation for accumulator models of human perceptual decision-making.     

Identification of fused bicyclic heterocycles as potent and selective 5-HT(2A) receptor antagonists for the treatment of insomnia

A series of fused bicyclic heterocycles was identified as potent and selective 5-HT(2A) receptor antagonists. Optimization of the series resulted in compounds that had improved PK properties, favorable CNS partitioning, good pharmacokinetic properties, and significant improvements on deep sleep (delta power) and sleep consolidation.     

The perichromatin region of the plant cell nucleus is the area with the strongest co-localisation of snRNA and SR proteins

The spatial organisation of the splicing system in plant cells containing either reticular (Allium cepa) or chromocentric (Lupinus luteus) nuclei was studied by immunolabelling of SR proteins, snRNA, and the PANA antigen, known markers for interchromatin granule clusters in mammalian cells. Electron microscope results allowed us to determine the distribution of these molecules within the structural domains of the nucleus. Similar to animal cells, in both plant species SR proteins were localised in interchromatin granules, but contrary to animal cells contained very small amounts of snRNA. The area with the strongest snRNA and SR protein co-localisation was the perichromatin region, which may be the location of pre-mRNA splicing in the plant cell nuclei. The only observable differences in the organisation of reticular and chromocentric nuclei were the size of the speckles and the number of snRNA pools in the condensed chromatin. We conclude that, despite remarkable changes in the nuclear architecture, the organisation of the splicing system is remarkably similar in both types of plant cell nuclei.     

Fast Isogenic Mapping-by-Sequencing of Ethyl Methanesulfonate-Induced Mutant Bulks

Mapping-by-sequencing (or SHOREmapping) has revitalized the powerful concept of forward genetic screens in plants. However, as in conventional genetic mapping approaches, mapping-by-sequencing requires phenotyping of mapping populations established from crosses between two diverged accessions. In addition to the segregation of the focal phenotype, this introduces natural phenotypic variation, which can interfere with the recognition of quantitative phenotypes. Here, we demonstrate how mapping-by-sequencing and candidate gene identification can be performed within the same genetic background using only mutagen-induced changes as segregating markers. Using a previously unknown suppressor of mutants of like heterochromatin protein1 (lhp1), which in its functional form is involved in chromatin-mediated gene repression, we identified three closely linked ethyl methanesulfonate-induced changes as putative candidates. In order to assess allele frequency differences between such closely linked mutations, we introduced deep candidate resequencing using the new Ion Torrent Personal Genome Machine sequencing platform to our mutant identification pipeline and thereby reduced the number of causal candidate mutations to only one. Genetic analysis of two independent additional alleles confirmed that this mutation was causal for the suppression of lhp1.In Arabidopsis (Arabidopsis thaliana) research, ethyl methanesulfonate (EMS) mutagenesis is a powerful tool that has been widely explored to uncover the functionality of many genes in a broad spectrum of pathways (Page and Grossniklaus, 2002). Recent advances in sequencing technology have greatly reduced the time required to pinpoint induced mutations. In a proof-of-principle experiment, mapping-by-sequencing (SHOREmapping) was first demonstrated on a mutant in the background of the Arabidopsis reference accession Columbia (Col-0) crossed to the diverged accession Landsberg erecta. A pool of DNA isolated from bulked segregants was sequenced and used for the simultaneous mapping and mutant identification (Schneeberger et al., 2009b). This first application was followed by other studies successfully applying similar methods (Cuperus et al., 2010; Austin et al., 2011).Although all described approaches are straightforward and extremely fast, their application is hindered by the requirement for interaccession crosses that impedes the success rate of screens based on quantitative traits, such as screens for genetic modifiers. The major obstacle is that the considerable phenotypic variation in F2 populations from crosses between diverged accessions impairs the recognition of mutants with subtle phenotypic alterations. In addition, if genetic screens involve modifiers of a preexisting mutant, the mapping depends on the availability of the primary mutant in another suitable accession, the introgression of the mutation in such a background, or the laborious additional genotyping for the presence of the first-site mutation.Avoiding these disadvantages, Ashelford et al. (2011) have demonstrated that the isolation of a causative EMS-induced change is possible by direct resequencing of a complete mutant genome. However, their approach initially resulted in 103 putative causal mutations that had the potential to change the amino acid sequences of 48 putative proteins. In addition, the mutations were clustered in two separate regions of the genome, even though the mutant had been backcrossed four times to the parental line.Recently, Abe et al. (2012) reduced the large number of candidate mutations by backcrossing mutant genomes to their nonmutagenized progenitor, followed by sequencing bulk segregants from these crosses. This drastically reduced the number of causal candidates, although it was not possible to pinpoint the causal change from the sequencing data alone. The main problem remains the short-read coverage at each of the candidate mutations, which is typically lower than the number of individuals combined within the bulked DNA. This hinders accurate allele frequency estimations based on the whole-genome sequencing data alone and thus makes it impossible to distinguish between causal and closely linked mutations.In this study, we combined isogenic bulk segregant analysis with deep candidate resequencing (dCARE) to facilitate the mutation identification of genetic modifiers based on bulked DNA and sequencing data alone. Our approach relies on the assumption that in pools of bulked segregants, the causative change occurs with the highest frequency among all EMS-induced changes (Fig. 1). Using resequencing data alone, it is not possible to distinguish between the subtle allele frequencies of EMS changes that are closely linked. However, dCARE of all candidate mutations using the new Ion Torrent sequencing technology enables quick and cost-effective detection of subtle allele frequency differences between closely linked mutations and thus allows the identification of causal candidates.Open in a separate windowFigure 1.Schematic illustration of the fast isogenic mapping approach. Chemical mutagens typically introduce hundreds of novel mutations. Within the M2 generation, mutants are screened for phenotypes. Selected plants are backcrossed to the nonmutagenized progenitor. The F2 offspring of such a cross forms an isogenic mapping population, as only novel mutations are segregating. Backcrossed individuals that display the mutant phenotype are selected, bulked, and their DNA is prepared as a pool and whole-genome sequenced. If the parental line is genetically different from the reference line Col-0, it needs to be resequenced in order to control for naturally occurring differences that need to be differentiated from novel mutations. Thus, all novel EMS-induced mutations can be selected for SHOREmap analysis by filtering for mutations that do not reside in the parental line. Candidate mutations (gray box) that show high mutant allele frequencies and linkage are selected for dCARE to pinpoint the causal mutation.The mutant identified by this fast isogenic mapping approach was isolated as a suppressor of developmental aberrations caused by defects in LIKE HETEROCHROMATIN PROTEIN1 (LHP1), which participates in the Polycomb Group (PcG) gene regulatory pathway in Arabidopsis. Enhancer/suppressor screens have been successfully used to identify genes that play a role in chromatin-mediated gene repression and activation in Drosophila melanogaster. For example, many components of the repressive PcG pathway were isolated as genetic enhancers or suppressors of homeotic mutations, whereas components of the Trithorax Group protein pathway were originally identified as suppressors of PcG-related mutations (Landecker et al., 1994; Gildea et al., 2000; Alonso et al., 2007).