A major goal of community genetics is to understand the influence of genetic variation within a species on ecological communities. Although well-documented for some organisms, additional research is ...necessary to understand the relative and interactive effects of genotype and environment on biodiversity, identify mechanisms through which tree genotype influences communities, and connect this emerging field with existing themes in ecology. We employ an underutilized but ecologically significant group of organisms, epiphytic bark lichens, to understand the relative importance of
Populus angustifolia
(narrowleaf cottonwood) genotype and environment on associated organisms within the context of community assembly and host ontogeny. Several key findings emerged. (1) In a single common garden, tree genotype explained 18-33% and 51% of the variation in lichen community variables and rough bark cover, respectively. (2) Across replicated common gardens, tree genotype affected lichen species richness, total lichen cover, lichen species composition, and rough bark cover, whereas environment only influenced composition and there were no genotype by environment interactions. (3) Rough bark cover was positively correlated with total lichen cover and richness, and was associated with a shift in species composition; these patterns occurred with variation in rough bark cover among tree genotypes of the same age in common gardens and with increasing rough bark cover along a ~40 year tree age gradient in a natural riparian stand. (4) In a common garden, 20-year-old parent trees with smooth bark had poorly developed lichen communities, similar to their 10-year-old ramets (root suckers) growing in close proximity, while parent trees with high rough bark cover had more developed communities than their ramets. These findings indicate that epiphytic lichens are influenced by host genotype, an effect that is robust across divergent environments. Furthermore, the response to tree genotype is likely the result of genetic variation in the timing of the ontogenetic shift from smooth to rough bark allowing communities on some genotypes to assemble faster than those on other genotypes. Organisms outside the typical sphere of community genetics, such as lichens, can help address critical issues and connect plant genotype effects to long-established streams of biological research, such as ontogeny and community assembly.
Food safety is vital in everyday life. Food toxins are small peptides or proteins that can cause disease by disrupting biological macromolecules such as enzymes or cellular receptors. Toxins are ...introduced either externally or from internal, spoilage-related pathogens. To keep these unsafe foods off the market, detection techniques for various toxins have been devised. Although many techniques serve this purpose well, challenges remain regarding sensitivity, specificity, and cost, especially for trace amounts of highly lethal proteinaceous toxins.
Atomic force microscopy (AFM) is a widely used nanotechnology for imaging and force measurement in biophysics and biology. Its high sensitivity in probing specific, single-molecule binding between molecules is applicable to food toxin detection. In this review, after a summary of the development of AFM, different detection operation modes are introduced along with examples of their applications.
Cantilever sensing and recognition imaging are found to be the appropriate AFM techniques for detection. Their shared functionalization approaches are outlined for two categories of surfaces: silicon and gold. Recent progress in AFM biosensors and their applications to food toxin detection are discussed. Single-molecule sensitivity and ease of designing sensing schemes make these AFM techniques excellent candidates for real-world application. Existing challenges in designing sensing molecules and preventing the food matrix from confounding signals are not only applicable to AFM techniques but to most current biosensors. Through the collaboration among materials science, chemistry, and molecular biology, solving these issues will promote significant advancement in AFM-based food toxin detection.
Besides different detection operation modes of AFM, a recognition element can be coupled to an AFM to produce an instrument that is capable of providing extraordinarily high sensitivity, high selectivity, and a cost-effective path toward recognizing these contaminants and securing the safety of the food supply. Display omitted
•Accurate, trace detection of food toxins is critical for securing the food supply.•AFM's biosensing capabilities can sensitively and reliably detect food toxins.•Chemical functionalization of the AFM probe tip is straight-forward and flexible.
To predict the future contributions of the Antarctic ice sheets to sea-level rise, numerical models use reconstructions of past ice-sheet retreat after the Last Glacial Maximum to tune model ...parameters
. Reconstructions of the West Antarctic Ice Sheet have assumed that it retreated progressively throughout the Holocene epoch (the past 11,500 years or so)
. Here we show, however, that over this period the grounding line of the West Antarctic Ice Sheet (which marks the point at which it is no longer in contact with the ground and becomes a floating ice shelf) retreated several hundred kilometres inland of today's grounding line, before isostatic rebound caused it to re-advance to its present position. Our evidence includes, first, radiocarbon dating of sediment cores recovered from beneath the ice streams of the Ross Sea sector, indicating widespread Holocene marine exposure; and second, ice-penetrating radar observations of englacial structure in the Weddell Sea sector, indicating ice-shelf grounding. We explore the implications of these findings with an ice-sheet model. Modelled re-advance of the grounding line in the Holocene requires ice-shelf grounding caused by isostatic rebound. Our findings overturn the assumption of progressive retreat of the grounding line during the Holocene in West Antarctica, and corroborate previous suggestions of ice-sheet re-advance
. Rebound-driven stabilizing processes were apparently able to halt and reverse climate-initiated ice loss. Whether these processes can reverse present-day ice loss
on millennial timescales will depend on bedrock topography and mantle viscosity-parameters that are difficult to measure and to incorporate into ice-sheet models.
Food safety is vital in everyday life. Food toxins are small peptides or proteins that can cause disease by disrupting biological macromolecules such as enzymes or cellular receptors. Toxins are ...introduced either externally or from internal, spoilage-related pathogens. To keep these unsafe foods off the market, detection techniques for various toxins have been devised. Although many techniques serve this purpose well, challenges remain regarding sensitivity, specificity, and cost, especially for trace amounts of highly lethal proteinaceous toxins.
Atomic force microscopy (AFM) is a widely used nanotechnology for imaging and force measurement in biophysics and biology. Its high sensitivity in probing specific, single-molecule binding between molecules is applicable to food toxin detection. In this review, after a summary of the development of AFM, different detection operation modes are introduced along with examples of their applications.
Cantilever sensing and recognition imaging are found to be the appropriate AFM techniques for detection. Their shared functionalization approaches are outlined for two categories of surfaces: silicon and gold. Recent progress in AFM biosensors and their applications to food toxin detection are discussed. Single-molecule sensitivity and ease of designing sensing schemes make these AFM techniques excellent candidates for real-world application. Existing challenges in designing sensing molecules and preventing the food matrix from confounding signals are not only applicable to AFM techniques but to most current biosensors. Through the collaboration among materials science, chemistry, and molecular biology, solving these issues will promote significant advancement in AFM-based food toxin detection.
Besides different detection operation modes of AFM, a recognition element can be coupled to an AFM to produce an instrument that is capable of providing extraordinarily high sensitivity, high selectivity, and a cost-effective path toward recognizing these contaminants and securing the safety of the food supply. Display omitted
•Accurate, trace detection of food toxins is critical for securing the food supply.•AFM's biosensing capabilities can sensitively and reliably detect food toxins.•Chemical functionalization of the AFM probe tip is straight-forward and flexible.
Context.
Fast rotation is responsible for important changes in the structure and evolution of stars and the way we see them. Optical long baseline interferometry now allows for the study of its ...effects on the stellar surface, mainly gravity darkening and flattening.
Aims.
We aim to determine the fundamental parameters of the fast-rotating star Altair, in particular its evolutionary stage (represented here by the core hydrogen mass fraction
X
c
), mass, and differential rotation, using state-of-the-art stellar interior and atmosphere models together with interferometric (ESO-VLTI), spectroscopic, and asteroseismic observations.
Methods.
We use ESTER two-dimensional stellar models to produce the relevant surface parameters needed to create intensity maps from atmosphere models. Interferometric and spectroscopic observables are computed from these intensity maps and several stellar parameters are then adjusted using the publicly available MCMC algorithm Emcee.
Results.
We determined Altair’s equatorial radius to be
R
eq
= 2.008 ± 0.006
R
⊙
, the position angle PA = 301.1 ± 0.3°, the inclination
i
= 50.7 ± 1.2°, and the equatorial angular velocity Ω = 0.74 ± 0.01 times the Keplerian angular velocity at equator. This angular velocity leads to a flattening of
ε
= 0.220 ± 0.003. We also deduce from the spectroscopically derived
v
sin
i
≃ 243 km s
−1
, a true equatorial velocity of ∼314 km s
−1
corresponding to a rotation period of 7h46m (∼3 cycles/day). The data also impose a strong correlation between mass, metallicity, hydrogen abundance, and core evolution. Thanks to asteroseismic data, and provided our frequencies identification is correct, we constrain the mass of Altair to 1.86 ± 0.03
M
⊙
and further deduce its metallicity
Z
= 0.019 and its core hydrogen mass fraction
X
c
= 0.71, assuming an initial solar hydrogen mass fraction
X
= 0.739. These values suggest that Altair is a young star ∼100 Myr old. Finally, the 2D ESTER model also gives the internal differential rotation of Altair, showing that its core rotates approximately 50% faster than the envelope, while the surface differential rotation does not exceed 6%.
The measurement of antioxidant capacity in fruits differs from that of other biological samples due to their low pH and very low lipophilic antioxidant capacity. In this report, we present a modified ...2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) method for fruits and compare its performance with the other commonly used antioxidant methods of 2,2‘-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP). The antioxidant capacity and reaction kinetics of four phenolic compounds, two antioxidant standards, and five fruits were also investigated. The modified ABTS method prepared at a pH of 4.5 with sodium acetate buffer is highly stable and easily applied to fruit samples as compared to the standard (pH 7.4) version. The measured antioxidant capacity of samples varied with the assay method used, pH, and time of reaction. Traditional antioxidant standards (trolox, ascorbic acid) displayed stable, simple reaction kinetics, which allowed end point analysis with all of assays. Of the phenolic compounds examined, chlorogenic and caffeic acids exhibited the most complex reaction kinetics and reaction rates that precluded end point analysis while gallic acid and quercetin reached stable end points. All fruit extracts exhibited complex and varied kinetics and required long reaction times to approach an end point. Because the antioxidant capacity of fruit extracts is a function of the array of individual antioxidants present, accurate comparisons among fruit samples require that reaction times be standardized and of sufficient length to reach steady state conditions and that more than one assay be used to describe the total antioxidant activity of fruit samples. Keywords: Natural antioxidants; polyphenols; phenolics; ABTS; phytonutrients; phytochemicals; oxidative stress; berries; black raspberry; red raspberry; blackberry; strawberry; grape; free radicals; antioxidant assay; dietary antioxidants
A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY ...family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement.
We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors.
The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.
PrP-lipid membrane interactions are critical to PrP structural conversion and neurotoxicity, but its molecular mechanism remains unclear. A two-dimensional histogram of force-distance curves and a ...worm-like chain model revealed three binding regions at the PrP N-terminal, providing the molecular basis for understanding the interactions between full-length PrP and lipid membranes.
Obesity is associated with increased risk for infections and poor responses to vaccinations, which may be due to compromised B cell function. However, there is limited information about the influence ...of obesity on B cell function and underlying factors that modulate B cell responses. Therefore, we studied B cell cytokine secretion and/or Ab production across obesity models. In obese humans, B cell IL-6 secretion was lowered and IgM levels were elevated upon ex vivo anti-BCR/TLR9 stimulation. In murine obesity induced by a high fat diet, ex vivo IgM and IgG were elevated with unstimulated B cells. Furthermore, the high fat diet lowered bone marrow B cell frequency accompanied by diminished transcripts of early lymphoid commitment markers. Murine B cell responses were subsequently investigated upon influenza A/Puerto Rico/8/34 infection using a Western diet model in the absence or presence of docosahexaenoic acid (DHA). DHA, an essential fatty acid with immunomodulatory properties, was tested because its plasma levels are lowered in obesity. Relative to controls, mice consuming the Western diet had diminished Ab titers whereas the Western diet plus DHA improved titers. Mechanistically, DHA did not directly target B cells to elevate Ab levels. Instead, DHA increased the concentration of the downstream specialized proresolving lipid mediators (SPMs) 14-hydroxydocosahexaenoic acid, 17-hydroxydocosahexaenoic acid, and protectin DX. All three SPMs were found to be effective in elevating murine Ab levels upon influenza infection. Collectively, the results demonstrate that B cell responses are impaired across human and mouse obesity models and show that essential fatty acid status is a factor influencing humoral immunity, potentially through an SPM-mediated mechanism.
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