Epigenetic cues modulating the generation of cell‐type diversity in the cerebral cortex

The cerebral cortex is composed of a large variety of distinct cell‐types including projection neurons, interneurons, and glial cells which emerge from distinct neural stem cell lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that neural stem cell and radial glial progenitor lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell‐type diversity during cortical development.     

Genome‐wide association study identifies variation of glucosidase being linked to natural variation of the maximal quantum yield of photosystem II

The maximum quantum yield of photosystem II (as reflected by variable to maximum chlorophyll a fluorescence, F_v/F_m) is regarded as one of the most important photosynthetic parameters. The genetic basis underlying natural variation in F_v/F_m, which shows low level of variations in plants under non‐stress conditions, is not easy to be exploited using the conventional gene cloning approaches. Thus, in order to answer this question, we have followed another strategy: we used genome‐wide association study (GWAS) and transgenic analysis in a rice mini‐core collection. We report here that four single‐nucleotide polymorphisms, located in the promoter region of β‐glucosidase 5 (BGlu‐5), are associated with observed variation in F_v/F_m. Indeed, our transgenic analysis showed a good correlation between BGlu‐5 and F_v/F_m. Thus, our work demonstrates the feasibility of using GWAS to study natural variation in F_v/F_m, suggesting that cis‐element polymorphism, affecting the BGlu‐5 expression level, may, indirectly, contribute to F_v/F_m variation in rice through the gibberellin signaling pathway. Further research is needed to understand the mechanism of our novel observation.     

Paecilomyces variotii extracts (ZNC) enhance plant immunity and promote plant growth

Plant and Soil - There are growing concerns regarding the restoration of karst rocky desertification (KRD) areas. However, the soil conditions and its residing microorganisms, which are essential...     

Legume nodulation: The host controls the party

Global demand to increase food production and simultaneously reduce synthetic nitrogen fertilizer inputs in agriculture are underpinning the need to intensify the use of legume crops. The symbiotic relationship that legume plants establish with nitrogen‐fixing rhizobia bacteria is central to their advantage. This plant–microbe interaction results in newly developed root organs, called nodules, where the rhizobia convert atmospheric nitrogen gas into forms of nitrogen the plant can use. However, the process of developing and maintaining nodules is resource intensive; hence, the plant tightly controls the number of nodules forming. A variety of molecular mechanisms are used to regulate nodule numbers under both favourable and stressful growing conditions, enabling the plant to conserve resources and optimize development in response to a range of circumstances. Using genetic and genomic approaches, many components acting in the regulation of nodulation have now been identified. Discovering and functionally characterizing these components can provide genetic targets and polymorphic markers that aid in the selection of superior legume cultivars and rhizobia strains that benefit agricultural sustainability and food security. This review addresses recent findings in nodulation control, presents detailed models of the molecular mechanisms driving these processes, and identifies gaps in these processes that are not yet fully explained.     

Microbially Induced Calcite Precipitation for Seepage Control in Sandy Soil

Microbially induced calcite precipitation (MICP) can reduce the permeability of soil by reducing the pore volumes. A MICP-based soil improvement method to control water leakage in irrigation channels and reservoirs built on sandy soil grounds is presented in this article. Using this method, a low-permeable hard crust can be formed at the soil surfaces. An experimental study was carried out to evaluate the effect of this method. Sandy soil samples were treated using four different schemes, namely, (1) surface spray, (2) surface spray with the addition of fibers, (3) surface spray and bulk stabilization, and (4) immersion stabilization. By applying around 2.6?L treatment liquid (consisting of ureolytic bacteria, 0.5?mol/L calcium chloride and 0.5?mol/L urea) to the top 2-cm thick soil, the seepage rates of the samples treated by the four different schemes could be reduced by up to 379 times. The conversion rates of calcium source in the tests were up to 89.7%. The results showed that a method of treating the soil in bulk before the formation of a crust on top of the soil layer was effective in reducing the seepage rates. After the bio-treatment, the formed low-permeable hard crust layer was 10 to 20?mm thick with a calcite content higher than 5%. Below the hard crusts, the calcite content was less than 5% and the soil was not properly cemented. Using the mercury intrusion test, it was found that both pore volumes and pore sizes of the bio-treated soil reduced significantly as compared with the untreated soil. Penetration tests using a flat-bottom penetrometer were used to assess the mechanical behavior of the bio-treated soil. The results indicated that the penetration resistance of the bio-treated soil layer was much higher than that of the untreated soil.     

Site-directed mutagenesis of two amino acid residues in cytochrome b559 α subunit that interact with a phosphatidylglycerol molecule (PG772) induces quinone-dependent inhibition of photosystem II activity

Photosynthesis Research - X-ray crystallographic analysis (1.9-Å resolution) of the cyanobacterial photosystem II (PSII) dimer showed the presence of five phosphatidylglycerol (PG) molecules...     

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.     

MolMod – an open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de and contains intermolecular force fields for over 150 pure fluids at present. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programmes ms2 and ls1 mardyn, GROMACS, and LAMMPS. To characterise the semantics associated with the numerical database content, a force field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the database were generally optimised such as to yield good representations of experimental data of the vapour–liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.     

A biogeographic reversal in sexual size dimorphism along a continental temperature gradient

The magnitude and direction of sexual size dimorphism (SSD) varies greatly across the animal kingdom, reflecting differential selection pressures on the reproductive and/or ecological roles of males and females. If the selection pressures and constraints imposed on body size change along environmental gradients, then SSD will vary geographically in a predictable way. Here, we uncover a biogeographical reversal in SSD of lizards from Central and North America: in warm, low latitude environments, males are larger than females, but at colder, high latitudes, females are larger than males. Comparisons to expectations under a Brownian motion model of SSD evolution indicate that this pattern reflects differences in the evolutionary rates and/or trajectories of sex‐specific body sizes. The SSD gradient we found is strongly related to mean annual temperature, but is independent of species richness and body size differences among species within grid cells, suggesting that the biogeography of SSD reflects gradients in sexual and/or fecundity selection, rather than intersexual niche divergence to minimize intraspecific competition. We demonstrate that the SSD gradient is driven by stronger variation in male size than in female size and is independent of clutch mass. This suggests that gradients in sexual selection and male–male competition, rather than fecundity selection to maximize reproductive output by females in seasonal environments, are predominantly responsible for the gradient.