Versatile Solid Supports for Oligonucleotide Synthesis that Incorporate Urea Bridge

The universal solid support, USIII, representing a new and improved version of commercial USII, as well as 2 ′-deoxynucleoside and 2 ′-deoxy-2 ′-fluoronucleoside bound supports, incorporating a labile phenoxyacetyl fragment, was synthesized by an aminomethyl polystyrene carbamoylation with corresponding azides in the presence of aqueous triethylammonium bicarbonate. All three solid phases incorporate a stable urea tether, thus bridging the polymer and functional linker. These new matrices proved to be potent solid phases for the synthesis of DNA, RNA, or modified oligonucleotides as well as randomized mixed 2 ′-ribo/2 ′-deoxy-2 ′-fluoro-RNA libraries and/or DNA libraries, randomized with trinucleotides (codons).     

Effect of membrane stiffness and cytoskeletal element density on mechanical stimuli within cells: an analysis of the consequences of ageing in cells

A finite element model of a single cell was created and used to compute the biophysical stimuli generated within a cell under mechanical loading. Major cellular components were incorporated in the model: the membrane, cytoplasm, nucleus, microtubules, actin filaments, intermediate filaments, nuclear lamina and chromatin. The model used multiple sets of tensegrity structures. Viscoelastic properties were assigned to the continuum components. To corroborate the model, a simulation of atomic force microscopy indentation was performed and results showed a force/indentation simulation with the range of experimental results. A parametric analysis of both increasing membrane stiffness (thereby modelling membrane peroxidation with age) and decreasing density of cytoskeletal elements (thereby modelling reduced actin density with age) was performed. Comparing normal and aged cells under indentation predicts that aged cells have a lower membrane area subjected to high strain as compared with young cells, but the difference, surprisingly, is very small and may not be measurable experimentally. Ageing is predicted to have a more significant effect on strain deep in the nucleus. These results show that computation of biophysical stimuli within cells are achievable with single-cell computational models; correspondence between computed and measured force/displacement behaviours provides a high-level validation of the model. Regarding the effect of ageing, the models suggest only small, although possibly physiologically significant, differences in internal biophysical stimuli between normal and aged cells.     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.     

Plasticity in thermal tolerance has limited potential to buffer ectotherms from global warming

Global warming is increasing the overheating risk for many organisms, though the potential for plasticity in thermal tolerance to mitigate this risk is largely unknown. In part, this shortcoming stems from a lack of knowledge about global and taxonomic patterns of variation in tolerance plasticity. To address this critical issue, we test leading hypotheses for broad-scale variation in ectotherm tolerance plasticity using a dataset that includes vertebrate and invertebrate taxa from terrestrial, freshwater and marine habitats. Contrary to expectation, plasticity in heat tolerance was unrelated to latitude or thermal seasonality. However, plasticity in cold tolerance is associated with thermal seasonality in some habitat types. In addition, aquatic taxa have approximately twice the plasticity of terrestrial taxa. Based on the observed patterns of variation in tolerance plasticity, we propose that limited potential for behavioural plasticity (i.e. behavioural thermoregulation) favours the evolution of greater plasticity in physiological traits, consistent with the ‘Bogert effect’. Finally, we find that all ectotherms have relatively low acclimation in thermal tolerance and demonstrate that overheating risk will be minimally reduced by acclimation in even the most plastic groups. Our analysis indicates that behavioural and evolutionary mechanisms will be critical in allowing ectotherms to buffer themselves from extreme temperatures.     

Seasonal dynamics of δ13C of C‐rich fractions from Picea abies (Norway spruce) and Fagus sylvatica (European beech) fine roots

The ^13/12C ratio in plant roots is likely dynamic depending on root function (storage versus uptake), but to date, little is known about the effect of season and root order (an indicator of root function) on the isotopic composition of C‐rich fractions in roots. To address this, we monitored the stable isotopic composition of one evergreen (Picea abies) and one deciduous (Fagus sylvatica), tree species' roots by measuring δ¹³C of bulk, respired and labile C, and starch from first/second and third/fourth order roots during spring and fall root production periods. In both species, root order differences in δ¹³C were observed in bulk organic matter, labile, and respired C fractions. Beech exhibited distinct seasonal trends in δ¹³C of respired C, while spruce did not. In fall, first/second order beech roots were significantly depleted in ¹³C, whereas spruce roots were enriched compared to higher order roots. Species variation in δ ¹³C of respired C may be partially explained by seasonal shifts from enriched to depleted C substrates in deciduous beech roots. Regardless of species identity, differences in stable C isotopic composition of at least two root order groupings (first/second, third/fourth) were apparent, and should hereafter be separated in belowground C‐supply‐chain inquiry.     

Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy

The development of cryo-focused ion beam (cryo-FIB) for the thinning of frozen-hydrated biological specimens enabled cryo-electron tomography (cryo-ET) analysis in unperturbed cells and tissues. However, the volume represented within a typical FIB lamella constitutes a small fraction of the biological specimen. Retaining low-abundance and dynamic subcellular structures or macromolecular assemblies within such limited volumes requires precise targeting of the FIB milling process. In this study, we present the development of a cryo-stage allowing for spinning-disk confocal light microscopy at cryogenic temperatures and describe the incorporation of the new hardware into existing workflows for cellular sample preparation by cryo-FIB. Introduction of fiducial markers and subsequent computation of three-dimensional coordinate transformations provide correlation between light microscopy and scanning electron microscopy/FIB. The correlative approach is employed to guide the FIB milling process of vitrified cellular samples and to capture specific structures, namely fluorescently labeled lipid droplets, in lamellas that are 300 nm thick. The correlation procedure is then applied to localize the fluorescently labeled structures in the transmission electron microscopy image of the lamella. This approach can be employed to navigate the acquisition of cryo-ET data within FIB-lamellas at specific locations, unambiguously identified by fluorescence microscopy.     

MinC spatially controls bacterial cytokinesis by antagonizing the scaffolding function of FtsZ

BACKGROUND: Cytokinesis in bacteria is mediated by a cytokinetic ring, termed the Z ring, which forms a scaffold for recruitment of other cell-division proteins. The Z ring is composed of FtsZ filaments, but their organization in the Z ring is poorly understood. In Escherichia coli, the Min system contributes to the spatial regulation of cytokinesis by preventing the assembly of the Z ring away from midcell. The effector of the Min system, MinC, inhibits Z ring assembly by a mechanism that is not clear. RESULTS: Here, we report that MinC controls the scaffolding function of FtsZ by antagonizing the mechanical integrity of FtsZ structures. Specifically, MinC antagonizes the ability of FtsZ filaments to be in a solid-like gel state. MinC is a modular protein whose two domains (MinC(C) and MinC(N)) synergize to inhibit FtsZ function. MinC(C) interacts directly with FtsZ polymers to target MinC to Z rings. MinC(C) also prevents lateral interactions between FtsZ filaments, an activity that seems to be unique among cytoskeletal proteins. Because MinC(C) is inhibitory in vivo, it suggests that lateral interactions between FtsZ filaments are important for the structural integrity of the Z ring. MinC(N) contributes to MinC activity by weakening the longitudinal bonds between FtsZ molecules in a filament leading to a loss of polymer rigidity and consequent polymer shortening. On the basis of our results, we develop the first computational model of the Z ring and study the effects of MinC. CONCLUSIONS: Control over the scaffolding activity of FtsZ probably represents a universal regulatory mechanism of bacterial cytokinesis.