Magnetic forces and DNA mechanics in multiplexed magnetic tweezers

Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization where large numbers of molecules (say 10³) are addressed in the same amount of time required by a single-molecule measurement. We apply offline analysis of recorded images and show that this approach provides a scalable solution for parallel tracking of the xyz-positions of many beads simultaneously. We employ a large field-of-view imaging system to address many DNA-bead tethers in parallel. We model the 3D magnetic field generated by the magnets and derive the magnetic force experienced by DNA-bead tethers across the large field of view from first principles. We furthermore experimentally demonstrate that a DNA-bead tether subject to a rotating magnetic field describes a bicircular, Limaçon rotation pattern and that an analysis of this pattern simultaneously yields information about the force angle and the position of attachment of the DNA on the bead. Finally, we apply MMT in the high-throughput investigation of the distribution of the induced magnetic moment, the position of attachment of DNA on the beads, and DNA flexibility. The methods described herein pave the way to kilo-molecule level magnetic tweezers experiments.     

Validation of exposure visualization and audible distance emission for navigated temporal bone drilling in phantoms

Background

A neuronavigation interface with extended function as compared with current systems was developed to aid during temporal bone surgery. The interface, named EVADE, updates the prior anatomical image and visualizes the bone drilling process virtually in real-time without need for intra-operative imaging. Furthermore, EVADE continuously calculates the distance from the drill tip to segmented temporal bone critical structures (e.g. the sigmoid sinus and facial nerve) and produces audiovisual warnings if the surgeon drills in too close vicinity. The aim of this study was to evaluate the accuracy and surgical utility of EVADE in physical phantoms.

Methodology/Principal Findings

We performed 228 measurements assessing the position accuracy of tracking a navigated drill in the operating theatre. A mean target registration error of 1.33±0.61 mm with a maximum error of 3.04 mm was found. Five neurosurgeons each drilled two temporal bone phantoms, once using EVADE, and once using a standard neuronavigation interface. While using standard neuronavigation the surgeons damaged three modeled temporal bone critical structures. No structure was hit by surgeons utilizing EVADE. Surgeons felt better orientated and thought they had improved tumor exposure with EVADE. Furthermore, we compared the distances between surface meshes of the virtual drill cavities created by EVADE to actual drill cavities: average maximum errors of 2.54±0.49 mm and −2.70±0.48 mm were found.

Conclusions/Significance

These results demonstrate that EVADE gives accurate feedback which reduces risks of harming modeled critical structures compared to a standard neuronavigation interface during temporal bone phantom drilling.     

DNA methylation-based biomarkers in serum of patients with breast cancer

Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.     

Soil Nutrient Depletion and Tree Functional Composition Shift Following Repeated Clearing in Secondary Forests of the Congo Basin

Ecosystems - The Congo Basin's rapidly growing population still largely depends on shifting cultivation for both energy and food security. This nexus of population growth and ecological impact...     

Systemic Suppression of the Shoot Metabolism upon Rice Root Nematode Infection

Hirschmanniella oryzae is the most common plant-parasitic nematode in flooded rice cultivation systems. These migratory animals penetrate the plant roots and feed on the root cells, creating large cavities, extensive root necrosis and rotting. The objective of this study was to investigate the systemic response of the rice plant upon root infection by this nematode. RNA sequencing was applied on the above-ground parts of the rice plants at 3 and 7 days post inoculation. The data revealed significant modifications in the primary metabolism of the plant shoot, with a general suppression of for instance chlorophyll biosynthesis, the brassinosteroid pathway, and amino acid production. In the secondary metabolism, we detected a repression of the isoprenoid and shikimate pathways. These molecular changes can have dramatic consequences for the growth and yield of the rice plants, and could potentially change their susceptibility to above-ground pathogens and pests.     

Neuronal Autophagy Regulates Presynaptic Neurotransmission by Controlling the Axonal Endoplasmic Reticulum

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