Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity

After the publication of the work entitled "Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity", by Kozlowski et al., BMC Biochemistry 2011, 12:29, we found that the legends to Figures 2 to 5 contain serious mistakes that compromise the comprehension of the work. This correction article contains the correct text of the legends to Figures 2 to 5

iRGD peptide conjugation potentiates intraperitoneal tumor delivery of paclitaxel with polymersomes

Polymersomes are versatile nanoscale vesicles that can be used for cytoplasmic delivery of payloads. Recently, we demonstrated that pH-sensitive polymersomes exhibit an intrinsic selectivity towards intraperitoneal tumor lesions. A tumor homing peptide, iRGD, harbors a cryptic C-end Rule (CendR) motif that is responsible for neuropilin-1 (NRP-1) binding and for triggering extravasation and tumor penetration of the peptide. iRGD functionalization increases tumor selectivity and therapeutic efficacy of systemic drug-loaded nanoparticles in many tumor models. Here we studied whether intraperitoneally administered paclitaxel-loaded iRGD-polymersomes show improved efficacy in the treatment of peritoneal carcinomatosis. First, we demonstrated that the pH-sensitive polymersomes functionalized with RPARPAR (a prototypic CendR peptide) or iRGD internalize in the cells that express NRP-1, and that internalized polymersomes release their cargo inside the cytosol. CendR-targeted polymersomes loaded with paclitaxel were more cytotoxic on NRP-1-positive cells than on NRP-1-negative cells. In mice bearing peritoneal tumors of gastric (MKN-45P) or colon (CT26) origin, intraperitoneally administered RPARPAR and iRGD-polymersomes showed higher tumor-selective accumulation and penetration than untargeted polymersomes. Finally, iRGD-polymersomes loaded with paclitaxel showed improved efficacy in peritoneal tumor growth inhibition and in suppression of local dissemination compared to the pristine paclitaxel-polymersomes or Abraxane. Our study demonstrates that iRGD-functionalization improves efficacy of paclitaxel-polymersomes for intraperitoneal treatment of peritoneal carcinomatosis

Atomic resolution structure of serine protease proteinase K at ambient temperature

Atomic resolution structures (beyond 1.20 ?) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 ? resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites. ? 2017 The Author(s).114Ysciescopu

Hydroxyethyl cellulose matrix applied to serial crystallography

Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the determination of the structure, while requiring consumption of less than 1 mg of the sample. However, a reliable and versatile carrier matrix for a wide variety of protein samples is still elusive. Here we introduce a hydroxyethyl cellulose-matrix carrier, to determine the structure of three proteins. The de novo structure determination of proteinase K from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of the praseodymium atom was demonstrated using 3,000 diffraction images. ? 2017 The Author(s).113Ysciescopu

Neutron Star Constraints on the H Dibaryon

We study the influence of a possible H dibaryon condensate on the equation of state and the overall properties of neutron stars whose population otherwise contains nucleons and hyperons. In particular, we are interested in the question of whether neutron stars and their masses can be used to say anything about the existence and properties of the H dibaryon. We find that the equation of state is softened by the appearance of a dibaryon condensate and can result in a mass plateau for neutron stars. If the limiting neutron star mass is about that of the Hulse-Taylor pulsar a condensate of H dibaryons of vacuum mass 2.2 GeV and a moderately attractive potential in the medium could not be ruled out. On the other hand, if the medium potential were even moderately repulsive, the H, would not likely exist in neutron stars. If neutron stars of about 1.6 solar mass were known to exist, attractive medium effects for the H could be ruled out. Certain ranges of dibaryon mass and potential can be excluded by the mass of the Hulse-Taylor pulsar which we illustrate graphically.Comment: Revised by the addition of a figure showing the region of dibaryon mass and potential excluded by the Hulse-Taylor pulsar. 18 pages, 11 figures, latex (submitted to Phys. Rev. C

Effect of tensor couplings in a relativistic Hartree approach for finite nuclei

The relativistic Hartree approach describing the bound states of both nucleons and anti-nucleons in finite nuclei has been extended to include tensor couplings for the $\omega$- and $\rho$-meson. After readjusting the parameters of the model to the properties of spherical nuclei, the effect of tensor-coupling terms rises the spin-orbit force by a factor of 2, while a large effective nucleon mass $m^{*}/M_{N} \approx 0.8$ sustains. The overall nucleon spectra of shell-model states are improved evidently. The predicted anti-nucleon spectra in the vacuum are deepened about 20 -- 30 MeV.Comment: 31 pages, 4 postscript figures include

CLASSY III: The Properties of Starburst-Driven Warm Ionized Outflows

We report the results of analyses of galactic outflows in a sample of 45 low-redshift starburst galaxies in the COS Legacy Archive Spectroscopic SurveY (CLASSY), augmented by five additional similar starbursts with COS data. The outflows are traced by blueshifted absorption-lines of metals spanning a wide range of ionization potential. The high quality and broad spectral coverage of CLASSY data enable us to disentangle the absorption due to the static ISM from that due to outflows. We further use different line multiplets and doublets to determine the covering fraction, column density, and ionization state as a function of velocity for each outflow. We measure the outflow's mean velocity and velocity width, and find that both correlate in a highly significant way with the star-formation rate, galaxy mass, and circular velocity over ranges of four orders-of-magnitude for the first two properties. We also estimate outflow rates of metals, mass, momentum, and kinetic energy. We find that, at most, only about 20% of silicon created and ejected by supernovae in the starburst is carried in the warm phase we observe. The outflows' mass-loading factor increases steeply and inversely with both circular and outflow velocity (log-log slope $\sim$ -1.6), and reaches $\sim 10$ for dwarf galaxies. We find that the outflows typically carry about 10 to 100% of the momentum injected by massive stars and about 1 to 20% of the kinetic energy. We show that these results place interesting constraints on, and new insights into, models and simulations of galactic winds.Comment: 34 pages, 16 figures, 6 tables, submitted to Ap

In vivo clearance of surfactant lipids during acute pulmonary inflammation.

BACKGROUND: A decrease in pulmonary surfactant has been suggested to contribute to the lung dysfunction associated with pulmonary inflammation. A number of studies have implicated surfactant clearance as a possible mechanism for altered pool sizes. The objective of the current study was to specifically investigate the mechanisms of surfactant clearance in a rodent model of acute pulmonary inflammation. METHODS: Inflammation was induced by intrapulmonary instillation of lipopolysaccharide (LPS: 100 μg/kg). Lipid clearance was assessed at 18 and 72 hours post-LPS instillation by intratracheal administration of radiolabel surfactant-like liposomes 2 hours prior to isolation and analysis of inflammatory cells and type II cells. RESULTS: At both 18 and 72 hours after LPS instillation there was significantly less radioactivity recovered in the lavage fluid compared to respective control groups (p < 0.05). At both time points, the number of cells recovered by lavage and their associated radioactivity was greater compared to control groups (p < 0.01). There was no difference in recovery of radioactivity by isolated type II cells or other cells obtained from enzymatic digestion of lung tissue. CONCLUSION: These results show that increased clearance of surfactant lipids in our model of acute pulmonary inflammation is primarily due to the inflammatory cells recruited to the airspace and not increased uptake by alveolar type II cells

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility

Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei–DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 Å resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 Å) and Nei-R252A (2.05 Å). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a ∼50° rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme