Search

Magnetotactic bacteria orient in magnetic fields with the help of their magnetosome chain, a linear structure of membrane enclosed magnetic nanoparticles (magnetosomes) anchored to a cytoskeletal filament. Here, we use simulations to study the assembly and the stability of magnetosome chains. We introduce a computational model describing the attachment of the magnetosomes to the filament and their magnetic interactions. We show that the filamentous backbone is crucial for the robust assembly of the magnetic particles into a linear chain, which in turn is key for the functionality of the chain in cellular orientation and magnetically directed swimming. In addition, we simulate the response to an external magnetic field that is rotated away from the axis of the filament, an experimental method used to probe the mechanical stability of the chain. The competition between alignment along the filament and alignment with the external fields leads to the rupture of a chain if the applied field exceeeds a threshold value. These observations are in agreement with previous experiments at the population level. Beyond that, our simulations provide a detailed picture of chain rupture at the single cell level, which is found to happen through two abrupt events, which both depend on the field strength and orientation. The re-formation of the chain structure after such rupture is found to be strongly sped up in the presence of a magnetic field parallel to the filament, an observation that may also be of interest for the design of self-healing materials. Our simulations underline the dynamic nature of the magnetosome chain. More generally, they show the rich complexity of self-assembly in systems with competing driving forces for alignment. [ABSTRACT FROM AUTHOR]

Expression quantitative trait (eQTL) studies are a powerful tool for identifying genetic variants that affect levels of messenger RNA. Since gene expression is controlled by a complex network of gene-regulating factors, one way to identify these factors is to search for interaction effects between genetic variants and mRNA levels of transcription factors (TFs) and their respective target genes. However, identification of interaction effects in gene expression data pose a variety of methodological challenges, and it has become clear that such analyses should be conducted and interpreted with caution. Investigating the validity and interpretability of several interaction tests when screening for eQTL SNPs whose effect on the target gene expression is modified by the expression level of a transcription factor, we characterized two important methodological issues. First, we stress the scale-dependency of interaction effects and highlight that commonly applied transformation of gene expression data can induce or remove interactions, making interpretation of results more challenging. We then demonstrate that, in the setting of moderate to strong interaction effects on the order of what may be reasonably expected for eQTL studies, standard interaction screening can be biased due to heteroscedasticity induced by true interactions. Using simulation and real data analysis, we outline a set of reasonable minimum conditions and sample size requirements for reliable detection of variant-by-environment and variant-by-TF interactions using the heteroscedasticity consistent covariance-based approach. [ABSTRACT FROM AUTHOR]

Objective: To enable early prediction of strong traction force vacuum extraction. Design: Observational cohort. Setting: Karolinska University Hospital delivery ward, tertiary unit. Population and sample size: Term mid and low metal cup vacuum extraction deliveries June 2012—February 2015, n = 277. Methods: Traction forces during vacuum extraction were collected prospectively using an intelligent handle. Levels of traction force were analysed pairwise by subjective category strong versus non-strong extraction, in order to define an objective predictive value for strong extraction. Statistical analysis: A logistic regression model based on the shrinkage and selection method lasso was used to identify the predictive capacity of the different traction force variables. Predictors: Total (time force integral, Newton minutes) and peak traction (Newton) force in the first to third pull; difference in traction force between the second and first pull, as well as the third and first pull respectively. Accumulated traction force at the second and third pull. Outcome: Subjectively categorized extraction as strong versus non-strong. Results: The prevalence of strong extraction was 26%. Prediction including the first and second pull: AUC 0,85 (CI 0,80–0,90); specificity 0,76; sensitivity 0,87; PPV 0,56; NPV 0,94. Prediction including the first to third pull: AUC 0,86 (CI 0,80–0,91); specificity 0,87; sensitivity 0,70; PPV 0,65; NPV 0,89. Conclusion: Traction force measurement during vacuum extraction can help exclude strong category extraction from the second pull. From the third pull, two-thirds of strong extractions can be predicted. [ABSTRACT FROM AUTHOR]

Ecological theory has uncovered dynamical differences between food web modules (i.e. low species food web configurations) with only species-level links and food web modules that include within-species links (e.g. non-feeding links between mature and immature individuals) and has argued that these differences ought to cause food web theory that includes within-species links to contrast with classical food web theory. It is unclear, however, if life-history will affect the observed connection between interaction strength and stability in species-level theory. We show that when the predator in a species-level food chain is split into juvenile and adult stages using a simple nested approach, stage-structure can mute potentially strong interactions through the transfer of biomass within a species. Within-species biomass transfer distributes energy away from strong interactions promoting increased system stability consistent with classical food web theory. [ABSTRACT FROM AUTHOR]

In this study, the ground state energies of face-centered cubic Hubbard clusters are analyzed using the Lanczos method. Examination of the ground state energy as a function of the number of particle per site n showed an energy minimum for face-centered cubic structures. This energy minimum decreased in n with increasing coulombic interaction parameter U. We found that the ground state energy had a minimum at n = 0.6, when U = 3W, where W denotes the non-interacting energy bandwidth and the face-centered cubic structure was ferromagnetic. These results, when compared with the properties of nickel, shows strong similarity with other finite temperature analyses in the literature and supports the Hirsh’s conjecture that the interatomic direct exchange interaction dominates in driving the system into a ferromagnetic phase. [ABSTRACT FROM AUTHOR]

The septins are a conserved family of GTP-binding proteins that, in the baker's yeast, assemble into a highly ordered array of filaments at the mother bud neck. These filaments undergo significant structural rearrangements during the cell cycle. We aimed at identifying key components that are involved in or regulate the transitions of the septins. By combining cell synchronization and quantitative affinity-purification mass-spectrometry, we performed a screen for specific interaction partners of the septins at three distinct stages of the cell cycle. A total of 83 interaction partners of the septins were assigned. Surprisingly, we detected DNA-interacting/nuclear proteins and proteins involved in ribosome biogenesis and protein synthesis predominantly present in alpha-factor arrested that do not display an assembled septin structure. Furthermore, two distinct sets of regulatory proteins that are specific for cells at S-phase with a stable septin collar or at mitosis with split septin rings were identified. Complementary methods like SPLIFF and immunoprecipitation allowed us to more exactly define the spatial and temporal characteristics of selected hits of the AP-MS screen. [ABSTRACT FROM AUTHOR]