Amplitude dependence of image quality in atomically-resolved bimodal atomic microscopy

In bimodal FM-AFM, two flexural modes are excited simultaneously. The total vertical oscillation deflection range of the tip is the sum of the peak-to-peak amplitudes of both flexural modes (sum amplitude). We show atomically resolved images of KBr(100) in ambient conditions in bimodal AFM that display a strong correlation between image quality and sum amplitude. When the sum amplitude becomes larger than about 200 pm, the signal-to-noise ratio (SNR) is drastically decreased. We propose this is caused by the temporary presence of one or more water layers in the tip-sample gap. These water layers screen the short range interaction and must be displaced with each oscillation cycle. Further decreasing the sum amplitude, however, causes a decrease in SNR. Therefore, the highest SNR in ambient conditions is achieved when the sum amplitude is slightly less than the thickness of the primary hydration layer.Comment: 3000 words, 3 Figures, 3 supplimentary figure

The role of a disulfide bridge in the stability and folding kinetics of Arabidopsis thaliana cytochrome c6A

Cytochrome c 6A is a eukaryotic member of the Class I cytochrome c family possessing a high structural homology with photosynthetic cytochrome c 6 from cyanobacteria, but structurally and functionally distinct through the presence of a disulfide bond and a heme mid-point redox potential of + 71 mV (vs normal hydrogen electrode). The disulfide bond is part of a loop insertion peptide that forms a cap-like structure on top of the core α-helical fold. We have investigated the contribution of the disulfide bond to thermodynamic stability and (un)folding kinetics in cytochrome c 6A from Arabidopsis thaliana by making comparison with a photosynthetic cytochrome c 6 from Phormidium laminosum and through a mutant in which the Cys residues have been replaced with Ser residues (C67/73S). We find that the disulfide bond makes a significant contribution to overall stability in both the ferric and ferrous heme states. Both cytochromes c 6A and c 6 fold rapidly at neutral pH through an on-pathway intermediate. The unfolding rate for the C67/73S variant is significantly increased indicating that the formation of this region occurs late in the folding pathway. We conclude that the disulfide bridge in cytochrome c 6A acts as a conformational restraint in both the folding intermediate and native state of the protein and that it likely serves a structural rather than a previously proposed catalytic role. © 2011 Elsevier B.V. All rights reserved

A Chaperonin Subunit with Unique Structures Is Essential for Folding of a Specific Substrate

Type I chaperonins are large, double-ring complexes present in bacteria (GroEL), mitochondria (Hsp60), and chloroplasts (Cpn60), which are involved in mediating the folding of newly synthesized, translocated, or stress-denatured proteins. In Escherichia coli, GroEL comprises 14 identical subunits and has been exquisitely optimized to fold its broad range of substrates. However, multiple Cpn60 subunits with different expression profiles have evolved in chloroplasts. Here, we show that, in Arabidopsis thaliana, the minor subunit Cpn60β4 forms a heterooligomeric Cpn60 complex with Cpn60α1 and Cpn60β1–β3 and is specifically required for the folding of NdhH, a subunit of the chloroplast NADH dehydrogenase-like complex (NDH). Other Cpn60β subunits cannot complement the function of Cpn60β4. Furthermore, the unique C-terminus of Cpn60β4 is required for the full activity of the unique Cpn60 complex containing Cpn60β4 for folding of NdhH. Our findings suggest that this unusual kind of subunit enables the Cpn60 complex to assist the folding of some particular substrates, whereas other dominant Cpn60 subunits maintain a housekeeping chaperonin function by facilitating the folding of other obligate substrates

Border collapse and boundary maintenance: militarisation and the micro-geographies of violence in Israel–Palestine

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Drawing upon subaltern geopolitics and feminist geography, this article explores how militarisation shapes micro-geographies of violence and occupation in Israel–Palestine. While accounts of spectacular and large-scale political violence dominate popular imaginaries and academic analyses in/of the region, a shift to the micro-scale foregrounds the relationship between power, politics and space at the level of everyday life. In the context of Israel–Palestine, micro-geographies have revealed dynamic strategies for ‘getting by’ or ‘dealing with’ the occupation, as practiced by Palestinian populations in the face of spatialised violence. However, this article considers how Jewish Israelis actively shape the spatial micro-politics of power within and along the borders of the Israeli state. Based on 12 months of ethnographic research in Tel Aviv and West Jerusalem during 2010–2011, an analysis of everyday narratives illustrates how relations of violence, occupation and domination rely upon gendered dynamics of border collapse and boundary maintenance. Here, the borders between home front and battlefield break down at the same time as communal boundaries are reproduced, generating conditions of ‘total militarism’ wherein military interests and agendas are both actively and passively diffused. Through gendering the militarised micro-geographies of violence among Jewish Israelis, this article reveals how individuals construct, navigate and regulate the everyday spaces of occupation, detailing more precisely how macro political power endures.This work was supported by the SOAS, University of London; University of London Central Research Fund

DNA G-segment bending is not the sole determinant of topology simplification by type II DNA topoisomerases

DNA topoisomerases control the topology of DNA. Type II topoisomerases exhibit topology simplification, whereby products of their reactions are simplified beyond that expected based on thermodynamic equilibrium. The molecular basis for this process is unknown, although DNA bending has been implicated. To investigate the role of bending in topology simplification, the DNA bend angles of four enzymes of different types (IIA and IIB) were measured using atomic force microscopy (AFM). The enzymes tested were Escherichia coli topo IV and yeast topo II (type IIA enzymes that exhibit topology simplification), and Methanosarcina mazei topo VI and Sulfolobus shibatae topo VI (type IIB enzymes, which do not). Bend angles were measured using the manual tangent method from topographical AFM images taken with a novel amplitude-modulated imaging mode: small amplitude small set-point (SASS), which optimises resolution for a given AFM tip size and minimises tip convolution with the sample. This gave improved accuracy and reliability and revealed that all 4 topoisomerases bend DNA by a similar amount: ~120° between the DNA entering and exiting the enzyme complex. These data indicate that DNA bending alone is insufficient to explain topology simplification and that the ‘exit gate’ may be an important determinant of this process

Forschungsinformationssysteme: Not oder Tugend?

Cambridge University decided to implement a research information system (CRIS) to collect and validate meta-data in order to comply with the UK REF requirements. This marked the foundation of a tool primarily based on publication meta-data. It assists to inform not only REF but other mandatory reporting requirements (e.g. RCUK via Researchfish or other Funder reporting requests). Due to the increased level of interoperability, the Cambridge CRIS is now capable of not only reporting retrospectively, but also to aid and inform academics and administrators in their day-to-day business. This paper exploits some examples based around interconnectivity, application of data standards and network analysis to showcase the increase in efficiency and sustainability in research information matters

qPlus magnetic force microscopy in frequency-modulation mode with millihertz resolution

Magnetic force microscopy (MFM) allows one to image the domain structure of ferromagnetic samples by probing the dipole forces between a magnetic probe tip and a magnetic sample. The magnetic domain structure of the sample depends on the alignment of the individual atomic magnetic moments. It is desirable to be able to image both individual atoms and domain structures with a single probe. However, the force gradients of the interactions responsible for atomic contrast and those causing domain contrast are orders of magnitude apart, ranging from up to 100 Nm−1 for atomic interactions down to 0.0001 Nm−1 for magnetic dipole interactions. Here, we show that this gap can be bridged with a qPlus sensor, with a stiffness of 1800 Nm−1 (optimized for atomic interaction), which is sensitive enough to measure millihertz frequency contrast caused by magnetic dipole–dipole interactions. Thus we have succeeded in establishing a sensing technique that performs scanning tunneling microscopy, atomic force microscopy and MFM with a single probe