Two-Dimensional Crystallography of TFIIB– and IIE–RNA Polymerase II Complexes: Implications for Start Site Selection and Initiation Complex Formation

AbstractTranscription factors IIB (TFIIB) and IIE (TFIIE) bound to RNA polymerase II have been revealed by electron crystallography in projection at 15.7 Å resolution. The results lead to simple hypotheses for the roles of these factors in the initiation of transcription. TFIIB is suggested to define the distance from TATA box to transcription start site by bringing TATA DNA in contact with polymerase at that distance from the active center of the enzyme. TFIIE is suggested to participate in a key conformational switch occurring at the active center upon polymerase–DNA interaction

On a Lie Algebraic Characterization of Vector Bundles

We prove that a vector bundle $\pi : E \to M$ is characterized by the Lie algebra generated by all differential operators on $E$ which are eigenvectors of the Lie derivative in the direction of the Euler vector field. Our result is of Pursell-Shanks type but it is remarkable in the sense that it is the whole fibration that is characterized here. The proof relies on a theorem of [Lecomte P., J. Math. Pures Appl. (9) 60 (1981), 229-239] and inherits the same hypotheses. In particular, our characterization holds only for vector bundles of rank greater than 1

Broadband 300-GHz Power Amplifier MMICs in InGaAs mHEMT Technology

In this article, we report on compact solid-state power amplifier (SSPA) millimeter-wave monolithic integrated circuits (MMICs) covering the 280–330-GHz frequency range. The technology used is a 35-nm gate-length InGaAs metamorphic highelectron- mobility transistor (mHEMT) technology. Two power amplifier MMICs are reported, based on a compact unit amplifier cell, which is parallelized two times using two different Wilkinson power combiners. The Wilkinson combiners are designed using elevated coplanar waveguide and air-bridge thin-film transmission lines in order to implement low-loss 70-Ω lines in the back-endof-line of this InGaAs mHEMT technology. The five-stage SSPA MMICs achieve a measured small-signal gain around 20 dB over the 280–335-GHz frequency band. State-of-the-art output power performance is reported, achieving at least 13 dBm over the 286–310-GHz frequency band, with a peak output power of 13.7 dBm (23.4 mW) at 300 GHz. The PA MMICs are designed for a reduced chip width while maximizing the total gate width of 512 μm in the output stage, using a compact topology based on cascode and common-source devices, improving the output power per required chip width significantly

A 200 GHz Monolithic Integrated Power Amplifier in Metamorphic HEMT Technology

A millimeter-wave monolithic integrated circuit power amplifier operating in the frequency range between 186 and 212 GHz is presented. The amplifier, dedicated to high-resolution imaging radar and communication systems, is realized in a 100 nm gate length metamorphic high electron mobility transistor technology. The three-stage design with four parallel transistors in the output stage achieves a linear gain of more than 12 dB and provides a saturated output power of more than 9 dBm and 7 dBm at 192 and 200 GHz, respectively

Electron transport and optical properties of shallow GaAs/InGaAs/GaAs quantum wells with a thin central AlAs barrier

Shallow GaAs/InGaAs/GaAs quantum well structures with and without a three monolayer thick AlAs central barrier have been investigated for different well widths and Si doping levels. The transport parameters are determined by resistivity measurements in the temperature range 4-300 K and magnetotransport in magnetic fields up to 12 T. The (subband) carrier concentrations and mobilities are extracted from the Hall data and Shubnikov-de Haas oscillations. We find that the transport parameters are strongly affected by the insertion of the AlAs central barrier. Photoluminescence spectra, measured at 77 K, show an increase of the transition energies upon insertion of the barrier. The transport and optical data are analyzed with help of self-consistent calculations of the subband structure and envelope wave functions. Insertion of the AlAs central barrier changes the spatial distribution of the electron wave functions and leads to the formation of hybrid states, i.e. states which extend over the InGaAs and the delta-doped layer quantum wells.Comment: 14 pages, pdf fil

Soil water retention and hydraulic conductivity measured in a wide saturation range

Soil hydraulic properties (SHPs), particularly soil water retention capacity and hydraulic conductivity of unsaturated soils, are among the key properties that determine the hydrological functioning of terrestrial systems. Some large collections of SHPs, such as the UNSODA and HYPRES databases, have already existed for more than 2 decades. They have provided an essential basis for many studies related to the critical zone. Today, sample-based SHPs can be determined in a wider saturation range and with higher resolution by combining some recently developed laboratory methods. We provide 572 high-quality SHP data sets from undisturbed, mostly central European samples covering a wide range of soil texture, bulk density and organic carbon content. A consistent and rigorous quality filtering ensures that only trustworthy data sets are included. The data collection contains (i) SHP data, which consist of soil water retention and hydraulic conductivity data, determined by the evaporation method and supplemented by retention data obtained by the dewpoint method and saturated conductivity measurements; (ii) basic soil data, which consist of particle size distribution determined by sedimentation analysis and wet sieving, bulk density and organic carbon content; and (iii) metadata, which include the coordinates of the sampling locations. In addition, for each data set, we provide soil hydraulic parameters for the widely used van Genuchten–Mualem model and for the more advanced Peters–Durner–Iden model. The data were originally collected to develop and test SHP models and associated pedotransfer functions. However, we expect that they will be very valuable for various other purposes such as simulation studies or correlation analyses of different soil properties to study their causal relationships. The data are available at https://doi.org/10.5880/fidgeo.2023.012 (Hohenbrink et al., 2023).</p

Evidence for a remodelling of DNA-PK upon autophosphorylation from electron microscopy studies

The multi-subunit DNA-dependent protein kinase (DNA-PK), a crucial player in DNA repair by non-homologous end-joining in higher eukaryotes, consists of a catalytic subunit (DNA-PKcs) and the Ku heterodimer. Ku recruits DNA-PKcs to double-strand breaks, where DNA-PK assembles prior to DNA repair. The interaction of DNA-PK with DNA is regulated via autophosphorylation. Recent SAXS data addressed the conformational changes occurring in the purified catalytic subunit upon autophosphorylation. Here, we present the first structural analysis of the effects of autophosphorylation on the trimeric DNA-PK enzyme, performed by electron microscopy and single particle analysis. We observe a considerable degree of heterogeneity in the autophosphorylated material, which we resolved into subpopulations of intact complex, and separate DNA-PKcs and Ku, by using multivariate statistical analysis and multi-reference alignment on a partitioned particle image data set. The proportion of dimeric oligomers was reduced compared to non-phosphorylated complex, and those dimers remaining showed a substantial variation in mutual monomer orientation. Together, our data indicate a substantial remodelling of DNA-PK holo-enzyme upon autophosphorylation, which is crucial to the release of protein factors from a repaired DNA double-strand break

Broad-band high-resolution rotational spectroscopy for laboratory astrophysics

We present a new experimental set-up devoted to the study of gas phase molecules and processes using broad-band high spectral resolution rotational spectroscopy. A reactor chamber is equipped with radio receivers similar to those used by radio astronomers to search for molecular emission in space. The whole range of the Q (31.5-50 GHz) and W bands (72-116.5 GHz) is available for rotational spectroscopy observations. The receivers are equipped with 16 × 2.5 GHz fast Fourier transform spectrometers with a spectral resolution of 38.14 kHz allowing the simultaneous observation of the complete Q band and one-third of the W band. The whole W band can be observed in three settings in which the Q band is always observed. Species such as CH3CN, OCS, and SO2 are detected, together with many of their isotopologues and vibrationally excited states, in very short observing times. The system permits automatic overnight observations, and integration times as long as 2.4 × 105 s have been reached. The chamber is equipped with a radiofrequency source to produce cold plasmas, and with four ultraviolet lamps to study photochemical processes. Plasmas of CH4, N2, CH3CN, NH3, O2, and H2, among other species, have been generated and the molecular products easily identified by the rotational spectrum, and via mass spectrometry and optical spectroscopy. Finally, the rotational spectrum of the lowest energy conformer of CH3CH2NHCHO (N-ethylformamide), a molecule previously characterized in microwave rotational spectroscopy, has been measured up to 116.5 GHz, allowing the accurate determination of its rotational and distortion constants and its search in space.We thank the European Research Council for funding support under Synergy Grant ERC-2013-SyG, G.A. 610256 (NANOCOSMOS). IT, VJH, and JLD acknowledge additional partial support from the Spanish State Research Agency (AEI) through grant FIS2016-77726-C3-1-P. JAMG, LM, and GS acknowledge additional partial support from the Spanish State Research Agency (AEI) through grant MAT2017-85089-C2-1R. We thank David López Romero for his help during the process of installation, commissioning, and cleaning of the chamber. We would like to thank Kremena Makasheva for the useful comments and suggestions during the experiments with Hexamethyldisiloxane. We would also like to thank Rosa Lebrón, Jesús Quintanilla, and Cristina Soria for providing us with the sample of N-ethylformamide. Sandra I. Ramírez acknowledges support from the FONCICYT under grant number 291842. Celina Bermúdez thanks the Spanish Ministerio de Ciencia Innovación y Universidades for the Juan de la Cierva grant FJCI-2016-27983

DNA double-strand break resection occurs during non-homologous end joining in G1 but is distinct from resection during homologous recombination

Canonical non-homologous end joining (c-NHEJ) repairs DNA double-strand breaks (DSBs) in G1 cells with biphasic kinetics. We show that DSBs repaired with slow kinetics, including those localizing to heterochromatic regions or harboring additional lesions at the DSB site, undergo resection prior to repair by c-NHEJ and not alt-NHEJ. Resection-dependent c-NHEJ represents an inducible process during which Plk3 phosphorylates CtIP, mediating its interaction with Brca1 and promoting the initiation of resection. Mre11 exonuclease, EXD2, and Exo1 execute resection, and Artemis endonuclease functions to complete the process. If resection does not commence, then repair can ensue by c-NHEJ, but when executed, Artemis is essential to complete resection-dependent c-NHEJ. Additionally, Mre11 endonuclease activity is dispensable for resection in G1. Thus, resection in G1 differs from the process in G2 that leads to homologous recombination. Resection-dependent c-NHEJ significantly contributes to the formation of deletions and translocations in G1, which represent important initiating events in carcinogenesis