Dynamics of the silicon (111) surface phase transition

The manner in which phase transformations occur in solids determines important structural and physical properties of many materials. The main problem in characterizing the kinetic processes that occur during phase transformations is the difficulty of observing directly, in real time, the growth of one phase at the expense of another. Here we use low-energy electron microscopy to study the real-time kinetics of a phase transformation confined to the silicon (111) surface. We show that the transformation is governed by the rate at which material is exchanged between the first layer of the crystal and the surface. In bulk phase transformations, the dynamics are usually governed either by the rate of diffusion of material to the phase boundaries or by the structural rearrangement of atoms at the phase boundary. The kinetic process that we have identified here has no bulk analogue and leads to domain dynamics that are qualitatively different from those expected for bulk systems.     

The influence of the surface migration of gold on the growth of silicon nanowires

Interest in nanowires continues to grow, fuelled in part by applications in nanotechnology. The ability to engineer nanowire properties makes them especially promising in nanoelectronics. Most silicon nanowires are grown using the vapour-liquid-solid (VLS) mechanism, in which the nanowire grows from a gold/silicon catalyst droplet during silicon chemical vapour deposition. Despite over 40 years of study, many aspects of VLS growth are not well understood. For example, in the conventional picture the catalyst droplet does not change during growth, and the nanowire sidewalls consist of clean silicon facets. Here we demonstrate that these assumptions are false for silicon nanowires grown on Si(111) under conditions where all of the experimental parameters (surface structure, gas cleanliness, and background contaminants) are carefully controlled. We show that gold diffusion during growth determines the length, shape, and sidewall properties of the nanowires. Gold from the catalyst droplets wets the nanowire sidewalls, eventually consuming the droplets and terminating VLS growth. Gold diffusion from the smaller droplets to the larger ones (Ostwald ripening) leads to nanowire diameters that change during growth. These results show that the silicon nanowire growth is fundamentally limited by gold diffusion: smooth, arbitrarily long nanowires cannot be grown without eliminating gold migration.     

Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities

The spindle checkpoint prevents chromosome mis-segregation by delaying sister chromatid separation until all chromosomes have achieved bipolar attachment to the mitotic spindle. Its operation is essential for accurate chromosome segregation, whereas its dysregulation can contribute to birth defects and tumorigenesis. The target of the spindle checkpoint is the anaphase-promoting complex (APC), a ubiquitin ligase that promotes sister chromatid separation and progression to anaphase. Using a short hairpin RNA screen targeting components of the ubiquitin-proteasome pathway in human cells, we identified the deubiquitinating enzyme USP44 (ubiquitin-specific protease 44) as a critical regulator of the spindle checkpoint. USP44 is not required for the initial recognition of unattached kinetochores and the subsequent recruitment of checkpoint components. Instead, it prevents the premature activation of the APC by stabilizing the APC-inhibitory Mad2-Cdc20 complex. USP44 deubiquitinates the APC coactivator Cdc20 both in vitro and in vivo, and thereby directly counteracts the APC-driven disassembly of Mad2-Cdc20 complexes (discussed in an accompanying paper). Our findings suggest that a dynamic balance of ubiquitination by the APC and deubiquitination by USP44 contributes to the generation of the switch-like transition controlling anaphase entry, analogous to the way that phosphorylation and dephosphorylation of Cdk1 by Wee1 and Cdc25 controls entry into mitosis.     

Genome-wide in situ exon capture for selective resequencing

Increasingly powerful sequencing technologies are ushering in an era of personal genome sequences and raising the possibility of using such information to guide medical decisions. Genome resequencing also promises to accelerate the identification of disease-associated mutations. Roughly 98% of the human genome is composed of repeats and intergenic or non-protein-coding sequences. Thus, it is crucial to focus resequencing on high-value genomic regions. Protein-coding exons represent one such type of high-value target. We have developed a method of using flexible, high-density microarrays to capture any desired fraction of the human genome, in this case corresponding to more than 200,000 protein-coding exons. Depending on the precise protocol, up to 55-85% of the captured fragments are associated with targeted regions and up to 98% of intended exons can be recovered. This methodology provides an adaptable route toward rapid and efficient resequencing of any sizeable, non-repeat portion of the human genome.     

A germline-specific class of small RNAs binds mammalian Piwi proteins

Small RNAs associate with Argonaute proteins and serve as sequence-specific guides to regulate messenger RNA stability, protein synthesis, chromatin organization and genome structure. In animals, Argonaute proteins segregate into two subfamilies. The Argonaute subfamily acts in RNA interference and in microRNA-mediated gene regulation using 21-22-nucleotide RNAs as guides. The Piwi subfamily is involved in germline-specific events such as germline stem cell maintenance and meiosis. However, neither the biochemical function of Piwi proteins nor the nature of their small RNA guides is known. Here we show that MIWI, a murine Piwi protein, binds a previously uncharacterized class of approximately 29-30-nucleotide RNAs that are highly abundant in testes. We have therefore named these Piwi-interacting RNAs (piRNAs). piRNAs show distinctive localization patterns in the genome, being predominantly grouped into 20-90-kilobase clusters, wherein long stretches of small RNAs are derived from only one strand. Similar piRNAs are also found in human and rat, with major clusters occurring in syntenic locations. Although their function must still be resolved, the abundance of piRNAs in germline cells and the male sterility of Miwi mutants suggest a role in gametogenesis.     

A micrococcal nuclease homologue in RNAi effector complexes

RNA interference (RNAi) regulates gene expression by the cleavage of messenger RNA, by mRNA degradation and by preventing protein synthesis. These effects are mediated by a ribonucleoprotein complex known as RISC (RNA-induced silencing complex). We have previously identified four Drosophila components (short interfering RNAs, Argonaute 2 (ref. 2), VIG and FXR) of a RISC enzyme that degrades specific mRNAs in response to a double-stranded-RNA trigger. Here we show that Tudor-SN (tudor staphylococcal nuclease)--a protein containing five staphylococcal/micrococcal nuclease domains and a tudor domain--is a component of the RISC enzyme in Caenorhabditis elegans, Drosophila and mammals. Although Tudor-SN contains non-canonical active-site sequences, we show that purified Tudor-SN exhibits nuclease activity similar to that of other staphylococcal nucleases. Notably, both purified Tudor-SN and RISC are inhibited by a specific competitive inhibitor of micrococcal nuclease. Tudor-SN is the first RISC subunit to be identified that contains a recognizable nuclease domain, and could therefore contribute to the RNA degradation observed in RNAi.