First-Principles Study of the Band Gap Structure of Oxygen-Passivated Silicon Nanonets

A net-like nanostructure of silicon named silicon nanonet was designed and oxygen atoms were used to passivate the dangling bonds. First-principles calculation based on density functional theory with the generalized gradient approximation (GGA) were carried out to investigate the energy band gap structure of this special structure. The calculation results show that the indirect–direct band gap transition occurs when the nanonets are properly designed. This band gap transition is dominated by the passivation bonds, porosities as well as pore array distributions. It is also proved that Si–O–Si is an effective passivation bond which can change the band gap structure of the nanonets. These results provide another way to achieve a practical silicon-based light source

Transition-metal dimers and physical limits on magnetic anisotropy

Recent advances in nanoscience have raised interest in the minimum bit size required for classical information storage, i.e. for bistability with suppressed quantum tunnelling and energy barriers that exceed ambient temperatures. In the case of magnetic information storage much attention has centred on molecular magnets[1] with bits consisting of ~ 100 atoms, magnetic uniaxial anisotropy energy barriers ~ 50 K, and very slow relaxation at low temperatures. In this article we draw attention to the remarkable magnetic properties of some transition metal dimers which have energy barriers approaching ~ 500 K with only two atoms. The spin dynamics of these ultra small nanomagnets is strongly affected by a Berry phase which arises from quasi-degeneracies at the electronic Highest Occupied Molecular Orbital (HOMO) energy. In a giant spin-approximation, this Berry phase makes the effective reversal barrier thicker. [1] Gatteschi, D., Sessoli, R. & Villain, J. Molecular Nanomagnets. (Oxford, New York 2006).Comment: 14 pages, 1 figur

Tuning fulleride electronic structure and molecular ordering via variable layer index

C60 fullerides are uniquely flexible molecular materials that exhibit a rich variety of behavior, including superconductivity and magnetism in bulk compounds, novel electronic and orientational phases in thin films, and quantum transport in a single-C60 transistor. The complexity of fulleride properties stems from the existence of many competing interactions, such as electron-electron correlations, electron-vibration coupling, and intermolecular hopping. The exact role of each interaction is controversial due to the difficulty of experimentally isolating the effects of a single interaction in the intricate fulleride materials. Here we report a unique level of control of the material properties of KxC60 ultra-thin films through well-controlled atomic layer indexing and accurate doping concentrations. Using STM techniques, we observe a series of electronic and structural phase transitions as the fullerides evolve from two-dimensional monolayers to quasi-threedimensional multilayers in the early stages of layer-by-layer growth. These results demonstrate the systematic evolution of fulleride electronic structure and molecular ordering with variable KxC60 film layer index, and shed new light on creating novel molecular structures and devices.Comment: 16 pages, 4 figures, to appear in Nature Material

Tunneling Spectra of Individual Magnetic Endofullerene Molecules

The manipulation of single magnetic molecules may enable new strategies for high-density information storage and quantum-state control. However, progress in these areas depends on developing techniques for addressing individual molecules and controlling their spin. Here we report success in making electrical contact to individual magnetic N@C60 molecules and measuring spin excitations in their electron tunneling spectra. We verify that the molecules remain magnetic by observing a transition as a function of magnetic field which changes the spin quantum number and also the existence of nonequilibrium tunneling originating from low-energy excited states. From the tunneling spectra, we identify the charge and spin states of the molecule. The measured spectra can be reproduced theoretically by accounting for the exchange interaction between the nitrogen spin and electron(s) on the C60 cage.Comment: 7 pages, 4 figures. Typeset in LaTeX, updated text of previous versio

Polymorphism of the Tryptophan Hydroxylase 2 (TPH2) Gene Is Associated with Chimpanzee Neuroticism

In the brain, serotonin production is controlled by tryptophan hydroxylase 2 (TPH2), a genotype. Previous studies found that mutations on the TPH2 locus in humans were associated with depression and studies of mice and studies of rhesus macaques have shown that the TPH2 locus was involved with aggressive behavior. We previously reported a functional single nucleotide polymorphism (SNP) in the form of an amino acid substitution, Q468R, in the chimpanzee TPH2 gene coding region. In the present study we tested whether this SNP was associated with neuroticism in captive and wild-born chimpanzees living in Japan and Guinea, respectively. Even after correcting for multiple tests (Bonferroni p = 0.05/6 = 0.008), Q468R was significantly related to higher neuroticism (β = 0.372, p = 0.005). This study is the first to identify a genotype linked to a personality trait in chimpanzees. In light of the prior studies on humans, mice, and rhesus macaques, these findings suggest that the relationship between neuroticism and TPH2 has deep phylogenetic roots

The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16–61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95–98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3′ end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes

Bone regeneration: current concepts and future directions

Bone regeneration is a complex, well-orchestrated physiological process of bone formation, which can be seen during normal fracture healing, and is involved in continuous remodelling throughout adult life. However, there are complex clinical conditions in which bone regeneration is required in large quantity, such as for skeletal reconstruction of large bone defects created by trauma, infection, tumour resection and skeletal abnormalities, or cases in which the regenerative process is compromised, including avascular necrosis, atrophic non-unions and osteoporosis. Currently, there is a plethora of different strategies to augment the impaired or 'insufficient' bone-regeneration process, including the 'gold standard' autologous bone graft, free fibula vascularised graft, allograft implantation, and use of growth factors, osteoconductive scaffolds, osteoprogenitor cells and distraction osteogenesis. Improved 'local' strategies in terms of tissue engineering and gene therapy, or even 'systemic' enhancement of bone repair, are under intense investigation, in an effort to overcome the limitations of the current methods, to produce bone-graft substitutes with biomechanical properties that are as identical to normal bone as possible, to accelerate the overall regeneration process, or even to address systemic conditions, such as skeletal disorders and osteoporosis

Identification of Small Molecule Inhibitors of Pseudomonas aeruginosa Exoenzyme S Using a Yeast Phenotypic Screen

Pseudomonas aeruginosa is an opportunistic human pathogen that is a key factor in the mortality of cystic fibrosis patients, and infection represents an increased threat for human health worldwide. Because resistance of Pseudomonas aeruginosa to antibiotics is increasing, new inhibitors of pharmacologically validated targets of this bacterium are needed. Here we demonstrate that a cell-based yeast phenotypic assay, combined with a large-scale inhibitor screen, identified small molecule inhibitors that can suppress the toxicity caused by heterologous expression of selected Pseudomonas aeruginosa ORFs. We identified the first small molecule inhibitor of Exoenzyme S (ExoS), a toxin involved in Type III secretion. We show that this inhibitor, exosin, modulates ExoS ADP-ribosyltransferase activity in vitro, suggesting the inhibition is direct. Moreover, exosin and two of its analogues display a significant protective effect against Pseudomonas infection in vivo. Furthermore, because the assay was performed in yeast, we were able to demonstrate that several yeast homologues of the known human ExoS targets are likely ADP-ribosylated by the toxin. For example, using an in vitro enzymatic assay, we demonstrate that yeast Ras2p is directly modified by ExoS. Lastly, by surveying a collection of yeast deletion mutants, we identified Bmh1p, a yeast homologue of the human FAS, as an ExoS cofactor, revealing that portions of the bacterial toxin mode of action are conserved from yeast to human. Taken together, our integrated cell-based, chemical-genetic approach demonstrates that such screens can augment traditional drug screening approaches and facilitate the discovery of new compounds against a broad range of human pathogens

A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis

Transcriptional enhancers integrate the contributions of multiple classes of transcription factors (TFs) to orchestrate the myriad spatio-temporal gene expression programs that occur during development. A molecular understanding of enhancers with similar activities requires the identification of both their unique and their shared sequence features. To address this problem, we combined phylogenetic profiling with a DNA–based enhancer sequence classifier that analyzes the TF binding sites (TFBSs) governing the transcription of a co-expressed gene set. We first assembled a small number of enhancers that are active in Drosophila melanogaster muscle founder cells (FCs) and other mesodermal cell types. Using phylogenetic profiling, we increased the number of enhancers by incorporating orthologous but divergent sequences from other Drosophila species. Functional assays revealed that the diverged enhancer orthologs were active in largely similar patterns as their D. melanogaster counterparts, although there was extensive evolutionary shuffling of known TFBSs. We then built and trained a classifier using this enhancer set and identified additional related enhancers based on the presence or absence of known and putative TFBSs. Predicted FC enhancers were over-represented in proximity to known FC genes; and many of the TFBSs learned by the classifier were found to be critical for enhancer activity, including POU homeodomain, Myb, Ets, Forkhead, and T-box motifs. Empirical testing also revealed that the T-box TF encoded by org-1 is a previously uncharacterized regulator of muscle cell identity. Finally, we found extensive diversity in the composition of TFBSs within known FC enhancers, suggesting that motif combinatorics plays an essential role in the cellular specificity exhibited by such enhancers. In summary, machine learning combined with evolutionary sequence analysis is useful for recognizing novel TFBSs and for facilitating the identification of cognate TFs that coordinate cell type–specific developmental gene expression patterns