Interactive regulation of root exudation and rhizosphere denitrification by plant metabolite content and soil properties

Plant and Soil - Cyperaceae are common on nutrient-poor soils, including in western Japan. We examined the ability of the native Cyperaceae from western Japan to form dauciform roots and assessed...     

Dinucleotides as simple models of the base stacking-unstacking component of DNA ‘breathing’ mechanisms

Regulatory protein access to the DNA duplex ‘interior’ depends on local DNA ‘breathing’ fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson–Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.     

Evaluating the Mechanisms of Landscape Change on White-Tailed Deer Populations

Understanding how landscape change influences the distribution and densities of species, and the consequences of these changes, is a central question in modern ecology. The distribution of white-tailed deer (Odocoileus virginianus) is expanding across North America, and in some areas, this pattern has led to an increase in predators and consequently higher predation rates on woodland caribou (Rangifer tarandus caribou)—an alternate prey species that is declining across western Canada. Understanding the factors influencing deer distribution has therefore become important for effective conservation of caribou in Canada. Changing climate and anthropogenic landscape alteration are hypothesized to facilitate white-tailed deer expansion. Yet, climate and habitat alteration are spatiotemporally correlated, making these factors difficult to isolate. Our study evaluates the relative effects of snow conditions and human-modified habitat (habitat alteration) across space on white-tailed deer presence and relative density. We modeled deer response to snow depth and anthropogenic habitat alteration across a large latitudinal gradient (49° to 60°) in Alberta, Canada, using motion-sensitive camera data collected in winter and spring from 2015 to 2019. Deer distribution in winter and spring were best explained by models including both snow depth and habitat alteration. Sites with shallower snow had higher deer presence regardless of latitude. Increased habitat alteration increased deer presence in the northern portion of the study area only. Winter deer density was best explained by snow depth only, whereas spring density was best explained by both habitat alteration and the previous winter's snow depth. Our results suggest that limiting future habitat alteration or restoring habitat can alter deer distribution, thereby potentially slowing or reversing expansion, but that climate plays a significant role beyond what managers can influence. © 2020 The Wildlife Society.     

MyD88 oligomer size functions as a physical threshold to trigger IL1R Myddosome signaling

A recurring feature of innate immune receptor signaling is the self-assembly of signaling proteins into oligomeric complexes. The Myddosome is an oligomeric complex that is required to transmit inflammatory signals from TLR/IL1Rs and consists of MyD88 and IRAK family kinases. However, the molecular basis for how Myddosome proteins self-assemble and regulate intracellular signaling remains poorly understood. Here, we developed a novel assay to analyze the spatiotemporal dynamics of IL1R and Myddosome signaling in live cells. We found that MyD88 oligomerization is inducible and initially reversible. Moreover, the formation of larger, stable oligomers consisting of more than four MyD88s triggers the sequential recruitment of IRAK4 and IRAK1. Notably, genetic knockout of IRAK4 enhanced MyD88 oligomerization, indicating that IRAK4 controls MyD88 oligomer size and growth. MyD88 oligomer size thus functions as a physical threshold to trigger downstream signaling. These results provide a mechanistic basis for how protein oligomerization might function in cell signaling pathways.     

PEtab—Interoperable specification of parameter estimation problems in systems biology

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.     

Next Generation Semiconductor Based-Sequencing of a Nutrigenetics Target Gene (GPR120) and Association with Growth Rate in Italian Large White Pigs

The GPR120 gene (also known as FFAR4 or O3FAR1) encodes for a functional omega-3 fatty acid receptor/sensor that mediates potent insulin sensitizing effects by repressing macrophage-induced tissue inflammation. For its functional role, GPR120 could be considered a potential target gene in animal nutrigenetics. In this work we resequenced the porcine GPR120 gene by high throughput Ion Torrent semiconductor sequencing of amplified fragments obtained from 8 DNA pools derived, on the whole, from 153 pigs of different breeds/populations (two Italian Large White pools, Italian Duroc, Italian Landrace, Casertana, Pietrain, Meishan, and wild boars). Three single nucleotide polymorphisms (SNPs), two synonymous substitutions and one in the putative 3′-untranslated region (g.114765469C > T), were identified and their allele frequencies were estimated by sequencing reads count. The g.114765469C > T SNP was also genotyped by PCR-RFLP confirming estimated frequency in Italian Large White pools. Then, this SNP was analyzed in two Italian Large White cohorts using a selective genotyping approach based on extreme and divergent pigs for back fat thickness (BFT) estimated breeding value (EBV) and average daily gain (ADG) EBV. Significant differences of allele and genotype frequencies distribution was observed between the extreme ADG-EBV groups (P < 0.001) whereas this marker was not associated with BFT-EBV.