Protein Phosphatase-1 Activates CDK9 by Dephosphorylating Ser175

The cyclin-dependent kinase CDK9/cyclin T1 induces HIV-1 transcription by phosphorylating the carboxyterminal domain (CTD) of RNA polymerase II (RNAPII). CDK9 activity is regulated by protein phosphatase-1 (PP1) which was previously shown to dephosphorylate CDK9 Thr186. Here, we analyzed the effect of PP1 on RNAPII phosphorylation and CDK9 activity. The selective inhibition of PP1 by okadaic acid and by NIPP1 inhibited phosphorylation of RNAPII CTD in vitro and in vivo. Expression of the central domain of NIPP1 in cultured cells inhibited the enzymatic activity of CDK9 suggesting its activation by PP1. Comparison of dephosphorylation of CDK9 phosphorylated by (32P) in vivo and dephosphorylation of CDK9's Thr186 analyzed by Thr186 phospho-specific antibodies, indicated that a residue other than Thr186 might be dephosphorylated by PP1. Analysis of dephosphorylation of phosphorylated peptides derived from CDK9's T-loop suggested that PP1 dephosphorylates CDK9 Ser175. In cultured cells, CDK9 was found to be phosphorylated on Ser175 as determined by combination of Hunter 2D peptide mapping and LC-MS analysis. CDK9 S175A mutant was active and S175D – inactive, and dephosphorylation of CDK9's Ser175 upregulated HIV-1 transcription in PP1-dependent manner. Collectively, our results point to CDK9 Ser175 as novel PP1-regulatory site which dephosphorylation upregulates CDK9 activity and contribute to the activation of HIV-1 transcription

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Evidence for widespread hydrated minerals on asteroid (101955) Bennu

Early spectral data from the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) mission reveal evidence for abundant hydrated minerals on the surface of near-Earth asteroid (101955) Bennu in the form of a near-infrared absorption near 2.7 µm and thermal infrared spectral features that are most similar to those of aqueously altered CM-type carbonaceous chondrites. We observe these spectral features across the surface of Bennu, and there is no evidence of substantial rotational variability at the spatial scales of tens to hundreds of metres observed to date. In the visible and near-infrared (0.4 to 2.4 µm) Bennu’s spectrum appears featureless and with a blue (negative) slope, confirming previous ground-based observations. Bennu may represent a class of objects that could have brought volatiles and organic chemistry to Earth

The dynamic geophysical environment of (101955) Bennu based on OSIRIS-REx measurements

The top-shaped morphology characteristic of asteroid (101955) Bennu, often found among fast-spinning asteroids and binary asteroid primaries, may have contributed substantially to binary asteroid formation. Yet a detailed geophysical analysis of this morphology for a fast-spinning asteroid has not been possible prior to the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) mission. Combining the measured Bennu mass and shape obtained during the Preliminary Survey phase of the OSIRIS-REx mission, we find a notable transition in Bennu’s surface slopes within its rotational Roche lobe, defined as the region where material is energetically trapped to the surface. As the intersection of the rotational Roche lobe with Bennu’s surface has been most recently migrating towards its equator (given Bennu’s increasing spin rate), we infer that Bennu’s surface slopes have been changing across its surface within the last million years. We also find evidence for substantial density heterogeneity within this body, suggesting that its interior is a mixture of voids and boulders. The presence of such heterogeneity and Bennu’s top shape are consistent with spin-induced failure at some point in its past, although the manner of its failure cannot yet be determined. Future measurements by the OSIRIS-REx spacecraft will provide insight into and may resolve questions regarding the formation and evolution of Bennu’s top-shape morphology and its link to the formation of binary asteroids

The utility of sonographic assessment in selecting patients for percutaneous insertion of peritoneal dialysis catheter

Background: Percutaneous insertion of peritoneal dialysis (PD) catheters by nephrologists is a safe and effective alternative to open surgical techniques. These patients are usually carefully selected due to anatomical considerations and medical comorbidities, with the current literature suggesting exclusion of patients with prior abdominal surgery.Method: We conducted a retrospective cohort study of predialysis patients who attended a preprocedural clinic in a tertiary center over 6 years. Procedural complications and catheter survival were assessed. Chi-squared test and Kaplan-Meier survival analysis were undertaken. Inpatient assessments were excluded.Results: A total of 217 patients were assessed, of whom 171 (78.8%) were accepted for percutaneous PD catheter insertion by a nephrologist. The key exclusion criteria were: (1) the clinical presence of abdominal hernia (p 5.5 cm (p < 0.001) and (3) ultrasound findings of impaired visceral slide test (p < 0.001). Prior abdominal surgery was not a default exclusion criterion (p = 0.1), as 63 patients (37%) with prior abdominal surgery, average of 1.3 prior surgeries per patient, were assessed as appropriate for the percutaneous procedure. There was no difference in the procedural complication rate and catheter survival between patients with and without prior abdominal surgery.Conclusion: A comprehensive preprocedural assessment utilizing ultrasound permits an objective selection of patients for percutaneous insertion of PD catheters by nephrologists. This allowed for successful and safe percutaneous insertion of PD catheters in patients who may have otherwise been excluded, e.g., prior abdominal surgery, patients with large bilateral polycystic kidneys, and central obesity

Broadband and efficient diffraction

Surface topography dictates the deterministic functionality of diffraction by a surface. In order to maximize the efficiency with which a diffractive optical component, such as a grating or a diffractive lens, directs light into a chosen order of diffraction, it is necessary that it be "blazed". The efficiency of most diffractive optical components reported so far varies with the wavelength, and blazing is achieved only at a specific nominal energy, the blaze wavelength. The existence of spurious light in undesirable orders represents a severe limitation that prevents using diffractive components in broadband systems. Here we experimentally demonstrate that broadband blazing over almost one octave can be achieved by combining advanced optical design strategies and artificial dielectric materials that offer dispersion chromatism much stronger than those of conventional bulk materials. The possibility of maintaining an efficient funneling of the energy into a specific order over a broad spectral range may empower advanced research to achieve greater control over the propagation of light, leading to more compact, efficient and versatile optical components.Comment: accepted in Optical Advanced Material

Ionic Current Blockades from DNA and RNA Molecules in the α-Hemolysin Nanopore

We characterize the substate structure of current blockades produced when single-stranded polynucleotide molecules were electrophoretically driven into the α-hemolysin protein pore. We frequently observe substates where the ionic current is reduced by ∼50%. Most of these substates can be associated with a molecular configuration where a polymer occupies only the vestibule region of the pore, though a few appear related to a polymer occupying only the transmembrane β-barrel region of the pore. The duration of the vestibule configuration depends on polymer composition and on which end of the polymer, 3′ or 5′, subsequently threads into the narrowest constriction and initiates translocation. Below ∼140 mV a polymer is more likely to escape from the vestibule against the applied voltage gradient, while at higher voltages a polymer is more likely to follow the voltage gradient by threading through the narrowest constriction and translocating through the pore. Increasing the applied voltage also increases the duration of the vestibule configuration. A semiquantitative model of these trends suggests that escape has stronger voltage dependence than threading, and that threading is sensitive to polymer orientation while escape is not. These results emphasize the utility of α-hemolysin as a model system to study biologically relevant physical and chemical processes at the single-molecule level