Crystalline and oxide phases revealed and formed on InSb(111)B

Oxidation treatment creating a well-ordered crystalline structure has been shown to provide a major improvement for III–V semiconductor/oxide interfaces in electronics. We present this treatment’s effects on InSb(111)B surface and its electronic properties with scanning tunneling microscopy and spectroscopy. Possibility to oxidize (111)B surface with parameters similar to the ones used for (100) surface is found, indicating a generality of the crystalline oxidation among different crystal planes, crucial for utilization in nanotechnology. The outcome is strongly dependent on surface conditions and remarkably, the (111) plane can oxidize without changes in surface lattice symmetry, or alternatively, resulting in a complex, semicommensurate quasicrystal-like structure. The findings are of major significance for passivation via oxide termination for nano-structured III–V/oxide devices containing several crystal plane surfaces. As a proof-of-principle, we present a procedure where InSb(111)B surface is cleaned by simple HCl-etching, transferred via air, and post-annealed and oxidized in ultrahigh vacuum

Cell cycle profiling reveals protein oscillation, phosphorylation, and localization dynamics

The cell cycle is a highly conserved process involving the coordinated separation of a single cell into two daughter cells. To relate transcriptional regulation across the cell cycle with oscillatory changes in protein abundance and activity, we carried out a proteome- and phospho-proteome-wide mass spectrometry profiling. We compared protein dynamics with gene transcription, revealing many transcriptionally regulated G2 mRNAs that only produce a protein shift after mitosis. Integration of CRISPR/Cas9 survivability studies further highlighted proteins essential for cell viability. Analyzing the dynamics of phosphorylation events and protein solubility dynamics over the cell cycle, we characterize predicted phospho-peptide motif distributions and predict cell cycle-dependent translocating proteins, as exemplified by the S-adenosylmethionine synthase MAT2A. Our study implicates this enzyme in translocating to the nucleus after the G1/S-checkpoint, which enables epigenetic histone methylation maintenance during DNA replication. Taken together, this data set provides a unique integrated resource with novel insights on cell cycle dynamics

Imaging empty states on the Ge(100) surface at 12 K

Our understanding of bias-dependent scanning-tunneling-microscopy (STM) images is complicated not only by the multiplicity of the surface electronic structure, but also the manifold tunneling effects in probing semiconductor surfaces having directional dangling- and covalent-bond orbitals. Here we present a refined interpretation of empty-state STM images from the model semiconductor surface, Ge(100), on the basis of measurements at low temperature (12 K) combined with density-functional-theory calculations. In the lower-bias regime (<= 1.6 V), the electron tunneling is found to occur predominantly in antibonding dangling-bond or/and dimer-bond states (pi*(1)pi*(2) and sigma*) of Ge(100) at the surface-parallel wave vector k(parallel to) = 0, leading to the tunneling current maxima located directly on the dimer rows. At higher biases (e.g., at 2 V), the current maxima are shifted to the position in the troughs between the dimer rows, because the tunneling occurs efficiently in the pi*(2) states at k(parallel to )not equal 0 associated with the dimer-up atoms of two adjacent dimer rows, i.e., because of increased sideways tunneling. Thus, the empty-state STM images of Ge(100), albeit strongly bias-dependent, reflect the dimer arrangement rather than the backbonds and surface resonances at all experimental conditions used. The results are also discussed in comparison with the counterpart system of Si(100)

Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome

Extracellular vesicles (EVs) mediate cell-to-cell communication by delivering or displaying macromolecules to their recipient cells. While certain broad-spectrum EV effects reflect their protein cargo composition, others have been attributed to individual EV-loaded molecules such as specific miRNAs. In this work, we have investigated the contents of vesicular cargo using small RNA sequencing of cells and EVs from HEK293T, RD4, C2C12, Neuro2a and C17.2. The majority of RNA content in EVs (49-96%) corresponded to rRNA-, coding-and tRNA fragments, corroborating with our proteomic analysis of HEK293T and C2C12 EVs which showed an enrichment of ribosome and translation-related proteins. On the other hand, the overall proportion of vesicular small RNA was relatively low and variable (2-39%) and mostly comprised of miRNAs and sequences mapping to piRNA loci. Importantly, this is one of the few studies, which systematically links vesicular RNA and protein cargo of vesicles. Our data is particularly useful for future work in unravelling the biological mechanisms underlying vesicular RNA and protein sorting and serves as an important guide in developing EVs as carriers for RNA therapeutics.Peer reviewe

Atomic-Scale Modification of Oxidation Phenomena on the Ge(100) Surface by Si Alloying

Properties of Ge oxides are significantly different from those of widely used Si oxides. For example, the instability of GeOx at device junctions causes electronic defect levels that degrade the performance of Ge-containing devices (e.g., transistors and infrared detectors). Therefore, the passivating Si layers have been commonly used at Ge interfaces to reduce the effects of Ge oxide instability and mimic the successful strategy of Si oxidation. To contribute to the atomic-scale knowledge and control of oxidation of such Si-alloyed Ge interfaces (O/Si/Ge), we present a synchrotron radiation core-level study of O/Si/Ge, which is combined with scanning probe microscopy measurements. The oxidation processes and electronic properties of O/Si/Ge(100) are examined as functions of Si amount and oxidation doses. In particular, the incorporation of Si into Ge is shown to cause the strengthening of Ge−O bonds and the increase of incorporated oxygen amount in oxide/Ge junctions, supporting that the method is useful to decrease the defect-level densities.</p

Imaging tumour hypoxia with positron emission tomography.

Hypoxia, a hallmark of most solid tumours, is a negative prognostic factor due to its association with an aggressive tumour phenotype and therapeutic resistance. Given its prominent role in oncology, accurate detection of hypoxia is important, as it impacts on prognosis and could influence treatment planning. A variety of approaches have been explored over the years for detecting and monitoring changes in hypoxia in tumours, including biological markers and noninvasive imaging techniques. Positron emission tomography (PET) is the preferred method for imaging tumour hypoxia due to its high specificity and sensitivity to probe physiological processes in vivo, as well as the ability to provide information about intracellular oxygenation levels. This review provides an overview of imaging hypoxia with PET, with an emphasis on the advantages and limitations of the currently available hypoxia radiotracers.Cancer Research UK (CRUK) funded the National Cancer Research Institute (NCRI) PET Research Working party to organise a meeting to discuss imaging cancer with hypoxia tracers and Positron Emission Tomography. IF was funded by CRUK and is also supported by the Chief Scientific Office. ALH is supported by CRUK and the Breast Cancer Research Foundation. RM is funded by NIHR Cambridge Biomedical Research Centre.This is the accepted manuscript. The final version is available from Nature Publishing at http://www.nature.com/bjc/journal/vaop/ncurrent/full/bjc2014610a.html

Ribonucleotide reductase inhibitors suppress SAMHD1 ara‐CTPase activity enhancing cytarabine efficacy

The deoxycytidine analogue cytarabine (ara‐C) remains the backbone treatment of acute myeloid leukaemia (AML) as well as other haematological and lymphoid malignancies, but must be combined with other chemotherapeutics to achieve cure. Yet, the underlying mechanism dictating synergistic efficacy of combination chemotherapy remains largely unknown. The dNTPase SAMHD1, which regulates dNTP homoeostasis antagonistically to ribonucleotide reductase (RNR), limits ara‐C efficacy by hydrolysing the active triphosphate metabolite ara‐CTP. Here, we report that clinically used inhibitors of RNR, such as gemcitabine and hydroxyurea, overcome the SAMHD1‐mediated barrier to ara‐C efficacy in primary blasts and mouse models of AML, displaying SAMHD1‐dependent synergy with ara‐C. We present evidence that this is mediated by dNTP pool imbalances leading to allosteric reduction of SAMHD1 ara‐CTPase activity. Thus, SAMHD1 constitutes a novel biomarker for combination therapies of ara‐C and RNR inhibitors with immediate consequences for clinical practice to improve treatment of AML

Crystal Structures of the ATPase Domains of Four Human Hsp70 Isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B', and HSPA5/BiP/GRP78

The 70-kDa heat shock proteins (Hsp70) are chaperones with central roles in processes that involve polypeptide remodeling events. Hsp70 proteins consist of two major functional domains: an N-terminal nucleotide binding domain (NBD) with ATPase activity, and a C-terminal substrate binding domain (SBD). We present the first crystal structures of four human Hsp70 isoforms, those of the NBDs of HSPA1L, HSPA2, HSPA5 and HSPA6. As previously with Hsp70 family members, all four proteins crystallized in a closed cleft conformation, although a slight cleft opening through rotation of subdomain IIB was observed for the HSPA5-ADP complex. The structures presented here support the view that the NBDs of human Hsp70 function by conserved mechanisms and contribute little to isoform specificity, which instead is brought about by the SBDs and by accessory proteins.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1

Molecular imaging of hypoxia with radiolabelled agents

Tissue hypoxia results from an inadequate supply of oxygen (O2) that compromises biological functions. Structural and functional abnormalities of the tumour vasculature together with altered diffusion conditions inside the tumour seem to be the main causes of tumour hypoxia. Evidence from experimental and clinical studies points to a role for tumour hypoxia in tumour propagation, resistance to therapy and malignant progression. This has led to the development of assays for the detection of hypoxia in patients in order to predict outcome and identify patients with a worse prognosis and/or patients that would benefit from appropriate treatments. A variety of invasive and non-invasive approaches have been developed to measure tumour oxygenation including oxygen-sensitive electrodes and hypoxia marker techniques using various labels that can be detected by different methods such as positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), autoradiography and immunohistochemistry. This review aims to give a detailed overview of non-invasive molecular imaging modalities with radiolabelled PET and SPECT tracers that are available to measure tumour hypoxia

Comparative Structural Analysis of Lipid Binding START Domains

Steroidogenic acute regulatory (StAR) protein related lipid transfer (START) domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease.We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains.Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1