The transcription factor gene MYB was identified recently as an oncogene that is rearranged/duplicated in some human leukemias. Here we describe a new mechanism of activation of MYB in human cancer involving gene fusion. We show that the t(6;9)(q22-23;p23-24) translocation in adenoid cystic carcinomas (ACC) of the breast and head and neck consistently results in fusions encoding chimeric transcripts predominantly consisting of MYB exon 14 linked to the last coding exon(s) of NFIB. The minimal common part of MYB deleted as the result of fusion was exon 15 including the 3 -UTR, which contains several highly conserved target sites for miR-15a/16 and miR-150 microRNAs. These microRNAs recently were shown to regulate MYB expression negatively. We suggest that deletion of these target sites may disrupt repression of MYB leading to overexpression of MYB-NFIB transcripts and protein and to activation of critical MYB targets, including genes associated with apoptosis, cell cycle control, cell growth/angiogenesis, and cell adhesion. Forced overexpression of miR-15a/16 and miR-150 in primary fusion-positive ACC cells did not significantly alter the expression of MYB as compared with leukemic cells with MYB activation/duplication. Our data indicate that the MYB-NFIB fusion is a hallmark of ACC and that deregulation of the expression of MYB and its target genes is a key oncogenic event in the pathogenesis of ACC. Our findings also suggest that the gain-offunction activity resulting from the MYB-NFIB fusion is a candidate therapeutic target.chromosome translocation ͉ fusion oncogene ͉ miRNA ͉ adenoid cystic carcinoma F usion genes are potent oncogenes resulting from chromosome rearrangements, in particular translocations. Most fusion genes identified thus far have been in hematological disorders and mesenchymal neoplasms, and only a few have been found in carcinomas (1). This paucity probably results from an inability to discover these rearrangements rather than from a true lack of such genes in carcinomas. The recent discovery that the majority of prostate cancers harbor ETS gene fusions (2) is in line with this reasoning. Finding as yet unidentified fusion oncogenes in other carcinomas could provide important insights into the molecular pathogenesis of these cancers and also might facilitate the development of new targeted therapies.We previously have identified a recurrent and tumor-specific t(6;9)(q22-23;p23-24) translocation in adenoid cystic carcinoma (ACC) of the head and neck (3). The translocation has been found as the sole cytogenetic anomaly in several cases, indicating that it is a primary rearrangement in this carcinoma.ACC has been known as a histologically distinctive neoplasm for nearly 150 years. It is among the most common carcinomas of the salivary glands (4) but also may arise in other exocrine glands, such as in the breast, and in the cervix, vulva, and tracheobronchial tree (5). ACC usually is an aggressive, although slowly growing, cancer with a long-term poor prognosis. Most patients (80-90%) with ACC ...

We provide an analytical tool based on a variational Bayesian treatment of hidden Markov models to combine the information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. The method identifies the number of diffusive states and the state transition rates. Using this method we have created an objective interaction map for Hfq, a protein that mediates interactions between small regulatory RNAs and their mRNA targets.

We have fabricated and characterized tunable superconducting transmission line resonators. To change the resonance frequency, we modify the boundary condition at one end of the resonator through the tunable Josephson inductance of a superconducting quantum interference device. We demonstrate a large tuning range (several hundred megahertz), high quality factors (104), and that we can change the frequency of a few-photon field on a time scale orders of magnitude faster than the photon lifetime of the resonator. This demonstration has implications in a variety of applications.

Biochemical and genetic data show that ribosomes closely follow RNA polymerases that are transcribing protein-coding genes in bacteria. At the same time, electron and fluorescence microscopy have revealed that ribosomes are excluded from the Escherichia coli nucleoid, which seems to be inconsistent with fast translation initiation on nascent mRNA transcripts. The apparent paradox can be reconciled if translation of nascent mRNAs can start throughout the nucleoid before they relocate to the periphery. However, this mechanism requires that free ribosomal subunits are not excluded from the nucleoid. Here, we use single-particle tracking in living E. coli cells to determine the fractions of free ribosomal subunits, classify individual subunits as free or mRNA-bound, and quantify the degree of exclusion of bound and free subunits separately. We show that free subunits are not excluded from the nucleoid. This finding strongly suggests that translation of nascent mRNAs can start throughout the nucleoid, which reconciles the spatial separation of DNA and ribosomes with cotranscriptional translation. We also show that, after translation inhibition, free subunit precursors are partially excluded from the compacted nucleoid. This finding indicates that it is active translation that normally allows ribosomal subunits to assemble on nascent mRNAs throughout the nucleoid and that the effects of translation inhibitors are enhanced by the limited access of ribosomal subunits to nascent mRNAs in the compacted nucleoid.nucleoid exclusion | transcription-translation coupling | antibiotics | single-molecule tracking | single-molecule imaging I n bacteria, translation often starts soon after the ribosomebinding site emerges from the RNA exit channel of the RNA polymerase. The transcribing RNA polymerase is then closely followed by translating ribosomes in such a way that the overall transcription elongation rate is tightly controlled by the translation rate (1). This coupling between transcription and translation of nascent mRNAs is important for regulatory mechanisms that respond to the formation of gaps between the transcribing RNA polymerases and the trailing ribosomes. Such gaps may, for example, allow the formation of secondary structures that allow RNA polymerases to proceed through transcription termination sites (2). The gaps may also allow the transcription termination factor Rho to access the nascent mRNAs and terminate transcription (3).Bacterial 70S ribosomes are formed when large 50S subunits and small 30S subunits assemble on mRNAs. Electron and fluorescence microscopy have revealed that ribosomes are excluded from the Escherichia coli nucleoid (4-6), but this spatial separation of DNA and ribosomes has not yet been reconciled with cotranscriptional translation. The paradox can be resolved if translation of nascent mRNAs can start throughout the nucleoid before they relocate to the periphery (7). However, this mechanism requires that free ribosomal subunits are not excluded from the nucleoid.To determine whether free r...

Transcription factors (TFs) mediate gene regulation by site specific binding to chromosomal operators. It is commonly assumed that the level of repression is given by the equilibrium binding of a repressor to its operator alone. However, this assumption has not been possible to test in living cells. Here, we have developed a single molecule chase assay to measure how long an individual transcription factor molecule remains bound at a specific chromosomal operator site. We find that the lac repressor dimer stays bound on average 5 minutes at the native lac operator in Escherichia coli and that a stronger operator results in slower dissociation rate, but similar association rate. Our findings do not support the simple equilibrium model. The discrepancy can for example be accounted for by considering that transcription initiation drives the system out of equilibrium. Such effects need to be considered when predicting gene activity from TF binding strengths.

In this work, we measure longitudinal dressed states of a superconducting qubit, the single Cooperpair box, and an intense microwave field. The dressed states represent the hybridization of the qubit and photon degrees of freedom, and appear as avoided level crossings in the combined energy diagram. By embedding the circuit in an rf oscillator, we directly probe the dressed states. We measure their dressed gap as a function of photon number and microwave amplitude, finding good agreement with theory. In addition, we extract the relaxation and dephasing rates of these states.When matter and light interact at the quantum level, in the form of atoms and photons, it is often no longer possible to clearly distinguish the individual contribution of each to the overall behavior of the system. This mixing of the aspects of light and matter can then be described in terms of dressed states of the atoms and photons [1]. These dressed states have become an essential concept in many fields of physics. Recently, they have also been invoked to explain the behavior of electrical circuits operating in the quantum regime [2,3]. In this context, known as circuit quantum electrodynamics (QED), we directly measure a class of states, longitudinal dressed states (LDS), that have received little experimental attention in the past. We create these states by illuminating an artificial atom made from a nanofabricated superconducting circuit with microwave photons. We then observe the interaction of the dressed states and a radiofrequency (rf) oscillator. This measurement scheme allows us to directly map the dressed energy diagram and extract the relaxation and dephasing times of the states. LDS are the natural description of a strongly driven superconducting quantum bit (qubit), and may have applications in the field of quantum information processing.Significant advances have been made in the development of engineered systems that exhibit coherent quantum properties. In the new field of circuit QED, these artificial atoms have recently been used to not only reproduce results of atomic physics and quantum optics, but to explore regimes previously inaccessible to traditional experiments [4]. Here, we use circuit QED techniques to directly study LDS over a wide range of drive strengths, including the extreme driving regime where the driving field is much stronger than the polarizing field. In atomic systems, the field strengths required for this are technically difficult to achieve and often exceed the ionization threshold of the atoms. The field geometry studied is also unusual. In a typical atomic experiment, a strong, static field is used to polarize the atomic spins under study. A relatively weak ac field, aligned perpendicular to the polarizing field, is then used to drive the spins. This transverse field geometry in fact implies that the atomic and photon spins are aligned, leading to a variety of selection rules based on the conservation of angular momentum. In our experiment, the driving field is aligned parallel to the polarizing fi...

The power of nanofluidic channels to analyze DNA is described along with practical experimental hints. As an introduction, a general overview is given on conventional DNA analysis tools, as well as tools under development towards the $1000 genome. The focus of this tutorial review is the stretching of DNA in nanoscale channels for coarse-grained mapping of DNA. To understand the behavior of the DNA, basic theory is discussed. Experimental details are revealed so that the reader, with the proper equipment, should be able to perform experiments. Basic approaches to the analysis of the data are discussed. Finally, potential future directions are discussed including the application of melting mapping as a simple barcode for the DNA.

We demonstrate a confinement spectroscopy technique capable of probing small conformational changes of unanchored single DNA molecules in a manner analogous to force spectroscopy, in the regime corresponding to femtonewton forces. In contrast to force spectroscopy, various structural forms of DNA can easily be probed, as indicated by experiments on linear and circular DNA. The extension of circular DNA is found to scale according to the de Gennes exponent, unlike for linear DNA.