RNA splicing at human immunodeficiency virus type 1 3 ' splice site A2 is regulated by binding of hnRNP A/B proteins to an exonic splicing silencer element

The synthesis of human immunodeficiency virus type 1 (HIV-1) mRNAs is a complex process by which more than 30 different mRNA species are produced by alternative splicing of a single primary RNA transcript. HIV-1 splice sites are used with significantly different efficiencies, resulting in different levels of mRNA species in infected cells. Splicing of Tat mRNA, which is present at relatively low levels in infected cells, is repressed by the presence of exonic splicing silencers (ESS) within the two tat coding exons (ESS2 and ESS3). These ESS elements contain the consensus sequence PyUAG. Here we show that the efficiency of splicing at 3 ' splice site A2, which is used to generate Vpr mRNA, is also regulated by the presence of an ESS (ESSV), which has sequence homology to ESS2 and ESS3. Mutagenesis of the three PyUAG motifs within ESSV increases splicing at splice site A2, resulting in increased Vpr mRNA levels and reduced skipping of the noncoding exon flanked by A2 and D3. The increase in Vpr mRNA levels and the reduced skipping also occur when splice site D3 is mutated toward the consensus sequence. By in vitro splicing assays, we show that ESSV represses splicing when placed downstream of a heterologous splice site. A1, A1(B), A2, and B1 hnRNPs preferentially bind to ESSV RNA compared to ESSV mutant RNA. Each of these proteins, when added back to HeLa cell nuclear extracts depleted of ESSV-binding factors, is able to restore splicing repression. The results suggest that coordinate repression of HIV-1 RNA splicing is mediated by members of the hnRNP A/B protein family

Vps27-Hse1 and ESCRT-I complexes cooperate to increase efficiency of sorting ubiquitinated proteins at the endosome

Ubiquitin (Ub) attachment to cell surface proteins causes their lysosomal degradation by incorporating them into lumenal membranes of multivesicular bodies (MVBs). Two yeast endosomal protein complexes have been proposed as Ub-sorting “receptors,” the Vps27-Hse1 complex and the ESCRT-I complex. We used NMR spectroscopy and mutagenesis studies to map the Ub-binding surface for Vps27 and Vps23. Mutations in Ub that ablate only Vps27 binding or Vps23 binding blocked the ability of Ub to serve as an MVB sorting signal, supporting the idea that both the Vps27-Hse1 and ESCRT-I complexes interact with ubiquitinated cargo. Vps27 also bound Vps23 directly via two PSDP motifs present within the Vps27 COOH terminus. Loss of Vps27-Vps23 association led to less efficient sorting into the endosomal lumen. However, sorting of vacuolar proteases or the overall biogenesis of the MVB were not grossly affected. In contrast, disrupting interaction between Vps27 and Hse1 caused severe defects in carboxy peptidase Y sorting and MVB formation. These results indicate that both Ub-sorting complexes are coupled for efficient recognition of ubiquitinated cargo

Shape resonances in K -shell photodetachment of small size-selected clusters: Experiment and theory

K-shell photodetachment of size-selected B(2)(-) and B(3)(-) cluster anions has been measured and calculated. The experimental absolute photodetachment cross sections exhibit bound resonances below threshold and two shape resonances above the K-shell threshold. Similar results were obtained for all of the cationic products observed, B(+) and B(2)(+) from B(2)(-), as well as B(+), B(2)(+), and B(3)(+) from B(3)(-). The overall agreement between measured and calculated photodetachment cross sections is very good. However, the theoretical study yielded additional bound resonances not observed in the experimental data

Improved Neutron-Capture Element Abundances in Planetary Nebulae

Spectroscopy of planetary nebulae (PNe) provides the means to investigate s-process enrichments of neutron(n)-capture elements that cannot be detected in asymptotic giant branch (AGB) stars. However, accurate abundance determinations of these elements present a challenge. Corrections for unobserved ions can be large and uncertain, since in many PNe only one ion of a given n-capture element has been detected. Furthermore, the atomic data governing the ionization balance of these species are not well-determined, inhibiting the derivation of accurate ionization corrections. We present initial results of a program that addresses these challenges. Deep high resolution optical spectroscopy of ~20 PNe has been performed to detect emission lines from trans-iron species including Se, Br, Kr, Rb, and Xe. The optical spectral region provides access to multiple ions of these elements, which reduces the magnitude and importance of uncertainties in the ionization corrections. In addition, experimental and theoretical efforts are providing determinations of the photoionization cross-sections and recombination rate coefficients of Se, Kr, and Xe ions. These new atomic data will make it possible to derive robust ionization corrections for these elements. Together, our observational and atomic data results will enable n-capture element abundances to be determined with unprecedented accuracy in ionized nebulae.Comment: 6 pages, 6 figures, to appear in "The Origin of the Elements Heavier than Fe", Sep 25-27, 2008, Turin, Italy, PASA, eds. John C. Lattanzio and M. Lugar

Calculation of the positron bound state with the copper atom

A new relativistic method for calculation of positron binding to atoms is presented. The method combines a configuration interaction treatment of the valence electron and the positron with a many-body perturbation theory description of their interaction with the atomic core. We apply this method to positron binding by the copper atom and obtain the binding energy of 170 meV (+ - 10%). To check the accuracy of the method we use a similar approach to calculate the negative copper ion. The calculated electron affinity is 1.218 eV, in good agreement with the experimental value of 1.236 eV. The problem of convergence of positron-atom bound state calculations is investigated, and means to improve it are discussed. The relativistic character of the method and its satisfactory convergence make it a suitable tool for heavier atoms.Comment: 15 pages, 5 figures, RevTe

A system-on-chip microwave photonic processor solves dynamic RF interference in real time with picosecond latency

Radio-frequency interference is a growing concern as wireless technology advances, with potentially life-threatening consequences like interference between radar altimeters and 5G cellular networks. Mobile transceivers mix signals with varying ratios over time, posing challenges for conventional digital signal processing (DSP) due to its high latency. These challenges will worsen as future wireless technologies adopt higher carrier frequencies and data rates. However, conventional DSPs, already on the brink of their clock frequency limit, are expected to offer only marginal speed advancements. This paper introduces a photonic processor to address dynamic interference through blind source separation (BSS). Our system-on-chip processor employs a fully integrated photonic signal pathway in the analogue domain, enabling rapid demixing of received mixtures and recovering the signal-of-interest in under 15 picoseconds. This reduction in latency surpasses electronic counterparts by more than three orders of magnitude. To complement the photonic processor, electronic peripherals based on field-programmable gate array (FPGA) assess the effectiveness of demixing and continuously update demixing weights at a rate of up to 305 Hz. This compact setup features precise dithering weight control, impedance-controlled circuit board and optical fibre packaging, suitable for handheld and mobile scenarios. We experimentally demonstrate the processor's ability to suppress transmission errors and maintain signal-to-noise ratios in two scenarios, radar altimeters and mobile communications. This work pioneers the real-time adaptability of integrated silicon photonics, enabling online learning and weight adjustments, and showcasing practical operational applications for photonic processing

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

Citation: Ablikim, U., Bomme, C., Xiong, H., Savelyev, E., Obaid, R., Kaderiya, B., . . . Rolles, D. (2016). Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging. Scientific Reports, 6, 8. doi:10.1038/srep38202An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C2H2Br2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model

Derivation of Del180 from sediment core log data\u27 Implications for millennial-scale climate change in the Labrador Sea

Sediment core logs from six sediment cores in the Labrador Sea show millennial-scale climate variability during the last glacial by recording all Heinrich events and several major Dansgaard-Oeschger cycles. The same millennial-scale climate change is documented for surface water δ18O records of Neogloboquadrina pachyderma (left coiled); hence the surface water δ18O record can be derived from sediment core logging by means of multiple linear regression, providing a paleoclimate proxy record at very high temporal resolution (70 years). For the Labrador Sea, sediment core logs contain important information about deepwater current velocities and also reflect the variable input of ice-rafted debris from different sources as inferred from grain-size analysis, the relation of density and P wave velocity, and magnetic susceptibility. For the last glacial, faster deepwater currents, which correspond to highs in sediment physical properties, occurred during iceberg discharge and lasted from several centuries to a few millennia. Those enhanced currents might have contributed to increased production of intermediate waters during times of reduced production of North Atlantic Deep Water. Hudson Strait might have acted as a major supplier of detrital carbonate only during lowered sea level (greater ice extent). During coldest atmospheric temperatures over Greenland, deepwater currents increased during iceberg discharge in the Labrador Sea, then surface water freshened shortly thereafter, while the abrupt atmospheric temperature rise happened after a larger time lag of ≥ 1 kyr. The correlation implies a strong link and common forcing for atmosphere, sea surface, and deep water during the last glacial at millennial timescales but decoupling at orbital timescales

Improved Neutron-Capture Element Abundances in Planetary Nebulae

Spectroscopy of planetary nebulae (PNe) provides the means to investigate s-process enrichments of neutron(n)-capture elements that cannot be detected in asymptotic giant branch (AGB) stars. However, accurate abundance determinations of these elements present a challenge. Corrections for unobserved ions can be large and uncertain, since in many PNe only one ion of a given n-capture element has been detected. Furthermore, the atomic data governing the ionization balance of these species are not well-determined, inhibiting the derivation of accurate ionization corrections. We present initial results of a program that addresses these challenges. Deep high resolution optical spectroscopy of ~20 PNe has been performed to detect emission lines from trans-iron species including Se, Br, Kr, Rb, and Xe. The optical spectral region provides access to multiple ions of these elements, which reduces the magnitude and importance of uncertainties in the ionization corrections. In addition, experimental and theoretical efforts are providing determinations of the photoionization cross-sections and recombination rate coefficients of Se, Kr, and Xe ions. These new atomic data will make it possible to derive robust ionization corrections for these elements. Together, our observational and atomic data results will enable n-capture element abundances to be determined with unprecedented accuracy in ionized nebulae.Comment: 6 pages, 6 figures, to appear in "The Origin of the Elements Heavier than Fe", Sep 25-27, 2008, Turin, Italy, PASA, eds. John C. Lattanzio and M. Lugar