Exploring atomic-scale lateral forces in the attractive regime: a case study on graphite (0001)

Cataloged from PDF version of article.A non-contact atomic force microscopy-based method has been used to map the static lateral forces exerted on an atomically sharp Pt/Ir probe tip by a graphite surface. With measurements carried out at low temperatures and in the attractive regime, where the atomic sharpness of the tip can be maintained over extended time periods, the method allows the quantification and directional analysis of lateral forces with piconewton and picometer resolution as a function of both the in-plane tip position and the vertical tip-sample distance, without limitations due to a finite contact area or to stick-slip-related sudden jumps of tip apex atoms. After reviewing the measurement principle, the data obtained in this case study are utilized to illustrate the unique insight that the method offers. In particular, the local lateral forces that are expected to determine frictional resistance in the attractive regime are found to depend linearly on the normal force for small tip-sample distances

Interdisciplinary Training in Mathematical Biology through Team-based Undergraduate Research and Courses

Inspired by BIO2010 and leveraging institutional and external funding, Truman State University built an undergraduate program in mathematical biology with high-quality, faculty-mentored interdisciplinary research experiences at its core. These experiences taught faculty and students to bridge the epistemological gap between the mathematical and life sciences. Together they created the infrastructure that currently supports several interdisciplinary courses, an innovative minor degree, and long-term interdepartmental research collaborations. This article describes how the program was built with support from the National Science Foundation's Interdisciplinary Training for Undergraduates in Biology and Mathematics program, and it shares lessons learned that will help other undergraduate institutions build their own program

Interface and electronic characterization of thin epitaxial Co3O4 films

The interface and electronic structure of thin (~20-74 nm) Co3O4(110) epitaxial films grown by oxygen-assisted molecular beam epitaxy on MgAl2O4(110) single crystal substrates have been investigated by means of real and reciprocal space techniques. As-grown film surfaces are found to be relatively disordered and exhibit an oblique low energy electron diffraction (LEED) pattern associated with the O-rich CoO2 bulk termination of the (110) surface. Interface and bulk film structure are found to improve significantly with post-growth annealing at 820 K in air and display sharp rectangular LEED patterns, suggesting a surface stoichiometry of the alternative Co2O2 bulk termination of the (110) surface. Non-contact atomic force microscopy demonstrates the presence of wide terraces separated by atomic steps in the annealed films that are not present in the as-grown structures; the step height of ~ 2.7 A corresponds to two atomic layers and confirms a single termination for the annealed films, consistent with the LEED results. A model of the (1 * 1) surfaces that allows for compensation of the polar surfaces is presented.Comment: 8 pages, 7 figure

Functional conservation of the Drosophila hybrid incompatibility gene Lhr

<p>Abstract</p> <p>Background</p> <p>Hybrid incompatibilities such as sterility and lethality are commonly modeled as being caused by interactions between two genes, each of which has diverged separately in one of the hybridizing lineages. The gene <it>Lethal hybrid rescue </it>(<it>Lhr</it>) encodes a rapidly evolving heterochromatin protein that causes lethality of hybrid males in crosses between <it>Drosophila melanogaster </it>females and <it>D. simulans </it>males. Previous genetic analyses showed that hybrid lethality is caused by <it>D. simulans Lhr </it>but not by <it>D. melanogaster Lhr</it>, confirming a critical prediction of asymmetry in the evolution of a hybrid incompatibility gene.</p> <p>Results</p> <p>Here we have examined the functional properties of <it>Lhr </it>orthologs from multiple Drosophila species, including interactions with other heterochromatin proteins, localization to heterochromatin, and ability to complement hybrid rescue in <it>D. melanogaster</it>/<it>D. simulans </it>hybrids. We find that these properties are conserved among most <it>Lhr </it>orthologs, including <it>Lhr </it>from <it>D. melanogaster</it>, <it>D. simulans </it>and the outgroup species <it>D. yakuba</it>.</p> <p>Conclusions</p> <p>We conclude that evolution of the hybrid lethality properties of <it>Lhr </it>between <it>D. melanogaster </it>and <it>D. simulans </it>did not involve extensive loss or gain of functions associated with protein interactions or localization to heterochromatin.</p

The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex

Dosage compensation in male Drosophila relies on the X chromosome–specific recruitment of a chromatin-modifying machinery, the dosage compensation complex (DCC). The principles that assure selective targeting of the DCC are unknown. According to a prevalent model, X chromosome targeting is initiated by recruitment of the DCC core components, MSL1 and MSL2, to a limited number of so-called “high-affinity sites” (HAS). Only very few such sites are known at the DNA sequence level, which has precluded the definition of DCC targeting principles. Combining RNA interference against DCC subunits, limited crosslinking, and chromatin immunoprecipitation coupled to probing high-resolution DNA microarrays, we identified a set of 131 HAS for MSL1 and MSL2 and confirmed their properties by various means. The HAS sites are distributed all over the X chromosome and are functionally important, since the extent of dosage compensation of a given gene and its proximity to a HAS are positively correlated. The sites are mainly located on non-coding parts of genes and predominantly map to regions that are devoid of nucleosomes. In contrast, the bulk of DCC binding is in coding regions and is marked by histone H3K36 methylation. Within the HAS, repetitive DNA sequences mainly based on GA and CA dinucleotides are enriched. Interestingly, DCC subcomplexes bind a small number of autosomal locations with similar features

Perturbation Analysis of Heterochromatin-Mediated Gene Silencing and Somatic Inheritance

Repetitive sequences in eukaryotic genomes induce chromatin-mediated gene-silencing of juxtaposed genes. Many components that promote or antagonize silencing have been identified, but how heterochromatin causes variegated and heritable changes in gene expression remains mysterious. We have used inducible mis-expression in the Drosophila eye to recover new factors that alter silencing caused by the bwD allele, an insertion of repetitive satellite DNA that silences a bw+ allele on the homologous chromosome. Inducible modifiers allow perturbation of silencing at different times in development, and distinguish factors that affect establishment or maintenance of silencing. We find that diverse chromatin and RNA processing factors can de-repress silencing. Most factors are effective even in differentiated cells, implying that silent chromatin remains plastic. However, over-expression of the bantam microRNA or the crooked-legs (crol) zinc-finger protein only de-repress silencing when expressed in cycling cells. Over-expression of crol accelerates the cell cycle, and this is required for de-repression of silencing. Strikingly, continual over-expression of crol converts the speckled variegation pattern of bwD into sectored variegation, where de-repression is stably inherited through mitotic divisions. Over-expression of crol establishes an open chromatin state, but the factor is not needed to maintain this state. Our analysis reveals that active chromatin states can be efficiently inherited through cell divisions, with implications for the stable maintenance of gene expression patterns through development

Alanine Zipper-Like Coiled-Coil Domains Are Necessary for Homotypic Dimerization of Plant GAGA-Factors in the Nucleus and Nucleolus

GAGA-motif binding proteins control transcriptional activation or repression of homeotic genes. Interestingly, there are no sequence similarities between animal and plant proteins. Plant BBR/BPC-proteins can be classified into two distinct groups: Previous studies have elaborated on group I members only and so little is known about group II proteins. Here, we focused on the initial characterization of AtBPC6, a group II protein from Arabidopsis thaliana. Comparison of orthologous BBR/BPC sequences disclosed two conserved signatures besides the DNA binding domain. A first peptide signature is essential and sufficient to target AtBPC6-GFP to the nucleus and nucleolus. A second domain is predicted to form a zipper-like coiled-coil structure. This novel type of domain is similar to Leucine zippers, but contains invariant alanine residues with a heptad spacing of 7 amino acids. By yeast-2-hybrid and BiFC-assays we could show that this Alanine zipper domain is essential for homotypic dimerization of group II proteins in vivo. Interhelical salt bridges and charge-stabilized hydrogen bonds between acidic and basic residues of the two monomers are predicted to form an interaction domain, which does not follow the classical knobs-into-holes zipper model. FRET-FLIM analysis of GFP/RFP-hybrid fusion proteins validates the formation of parallel dimers in planta. Sequence comparison uncovered that this type of domain is not restricted to BBR/BPC proteins, but is found in all kingdoms