A new system for naming ribosomal proteins

A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as 'new system' names.

Raman scattering studies on PEG functionalized hydroxyapatite nanoparticles

The pure hydroxyapatite (HAP) nanoparticles (NPs) have been synthesized by wet chemical precipitation method. Raman spectral measurements have been made for pure HAP, pure Polyethylene glycol (PEG) 6000 and PEG coated HAP in different mass ratios (sample 1, sample 2 and sample 3). The peaks observed in Raman spectrum of pure HAP and the XRD pattern have confirmed the formation of HAP NPs. Vibrational modes have been assigned for pure HAP and pure PEG 6000. The observed variation in peak position of Raman active vibrational modes of PEG in PEG coated HAP has been elucidated in this work, in terms of intermolecular interactions between PEG and HAP. Further these results suggest that the functionalization of nanoparticles may be independent of PEG mass.

4'-O-substitutions determine selectivity of aminoglycoside antibiotics

Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.

The effect of nitridation temperature on the structural, optical and electrical properties of GaN nanoparticles

Nitridation at high temperature enhances the crystalline and optical quality of GaN nanoparticles synthesized by a novel chemical co-precipitation method.

Raman spectroscopic and ab initio studies on the molecular interactions in the binary liquid mixtures of 4'-fluoroacetophenone

Raman spectral measurements were carried out for binary liquid mixtures 4'fluoroacetophenone (4F) in different volume concentration ranges at a regular intervals of 0.1 in different solvents. The asymmetric Raman peak observed at 1685 cm(-1) (carbonyl stretching mode) in pure 4F confirms the presence of self association in 4F. The optimization was performed for monomer and dimer structures of 4F as well as 4F dimer with solvents using Gaussian 03 W package. Vibrational wavenumber calculation was performed for monomer and dimer structures of 4F to explain the experimentally observed Raman spectra. The carbonyl stretching mode is the more polar group and its interaction with the solvent molecule plays a vital role in determining the physical and chemical properties of the solute. Hence the observed variation in the peak position and linewidth of carbonyl stretching mode was analysed as a result of intermolecular interactions between the solute and the solvent molecules. Also, interaction energies were calculated to support the results obtained from Raman spectra.

Bilateral silent sinus syndrome

Silent sinus syndrome is a rare clinical entity associated with progressive enophthalmos, collapse of the maxillary sinus, and hypoglobus. We report a case of bilateral silent sinus syndrome in a 29-year-old man. Representative radiographic and intraoperative images are presented. The purpose of this article is to illustrate a new presentation of the disease and to review the current diagnostic and treatment modalities.

Molecular architecture of a eukaryotic translational initiation complex

The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.

The quenching effect of silver nanoparticles on 2-amino-3-bromo-1, 4-naphthoquinone using fluorescence spectroscopy

Nanoparticles of noble metals belong to the most extensively studied colloidal systems in the field of nanoscience and nanotechnology. Silver nanoparticles of different sizes have been prepared with the chemical reduction method using sodium borohydride and characterized using optical absorption technique. Using optical absorption and fluorescence emission studies, the photo physical properties of 2-amino-3-bromo1, 4-naphthoquinone (ABNQ) on silver nanoparticle have been studied. Concentration of the silver nanoparticle has been evaluated and the particle size dependent interaction between silver nanoparticles and ABNQ has been studied. The fluorescence quantum yield of ABNQ with and without silver nanoparticles has been calculated. The Stern-Volmer quenching constants and the molar absorptivity have been evaluated.

Interaction of Schiff base ligand with tin dioxide nanoparticles: optical studies

Interaction between 1,4 Bis ((2-Methyl) thio) Phenylamino methyl benzene (BMTPMB) Schiff base with tin dioxide nanoparticles (SnO2 NPs) of various concentrations in methanol have been studied using UV-Visible and Fluorescence spectroscopic techniques. The low value of Stern-Volmer quenching constant and non-linear plot of Benesi-Hildebrand equation suggests the less affinity of SnO2 NPs towards the adsorption of BMTPMB Schiff base. The Scott equation has been employed to determine molar absorptivity of the Schiff base-NPs system.

Dynamic quenching study of 2-amino-3-bromo-1,4-naphthoquinone by titanium dioxide nano particles in solution (methanol)

The dependence of fluorescence emission of 2-amino-3-bromo-1,4-naphthoquinone on titanium dioxide (TiO2) in methanol has been investigated. The increase in TiO2 concentration causes a decrease in the fluorescence intensity of 2-amino-3-bromo-1,4-naphthoquinone. A linear Stern-Volmer plot in this study indicates the presence of dynamic quenching. The quenching and association constants have been calculated. The quenching process is due to the electron transfer from 2-amino-3-bromo-1,4-naphthoquinone to TiO2.

An investigation of solute-solvent interactions in binary liquid mixtures of 3'-methoxyacetophenone: using Raman spectroscopy and DFT calculations

Raman spectral measurements have been carried out for neat 3'-methoxy acetophenone (3'-MAP) and binary liquid mixtures of 3'-MAP in three solvents of different polarity. Also Density Functional Theory (DFT) geometry optimization and vibrational wavenumber calculation have been performed on monomer and dimer structures of 3'-MAP to analyze the experimentally observed Raman spectrum. Mulliken charge analysis has also been made on optimized geometries of 3'-MAP with solvents. The changes associated with the observed peak position, intensity and linewidth in the carbonyl stretching mode of 3'-MAP are explained as a consequence of intermolecular interactions between solute-solute and solute-solvent molecules. This analysis reports that the solute-solvent interaction is dominant in the case of binary liquid mixtures of 3'-MAP with ethanol compared to DMF and benzene.

Unusual base pairing during the decoding of a stop codon by the ribosome

During normal translation, binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires formation of two normally forbidden purine-purine base pairs¹. We have determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA^Ser bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which display an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding center to accommodate non-canonical base pairs.

Elongation factor G bound to the ribosome in an intermediate state of translocation

A key step of translation by the ribosome is translocation, which involves the movement of messenger RNA (mRNA) and transfer RNA (tRNA) with respect to the ribosome. This allows a new round of protein chain elongation by placing the next mRNA codon in the A site of the 30S subunit. Translocation proceeds through an intermediate state in which the acceptor ends of the tRNAs have moved with respect to the 50S subunit but not the 30S subunit, to form hybrid states. The guanosine triphosphatase (GTPase) elongation factor G (EF-G) catalyzes the subsequent movement of mRNA and tRNA with respect to the 30S subunit. Here, we present a crystal structure at 3 angstrom resolution of the Thermus thermophilus ribosome with a tRNA in the hybrid P/E state bound to EF-G with a GTP analog. The structure provides insights into structural changes that facilitate translocation and suggests a common GTPase mechanism for EF-G and elongation factor Tu.

Bortezomib combination therapy in multiple myeloma

Bortezomib was approved for the treatment of multiple myeloma (MM) in 2003. Since then several bortezomib-based combination therapies have emerged. Although some combinations have been preceded by preclinical investigations, most have followed the inevitable process in which active (or potentially active) drugs are combined with each other to create new treatment regimens. Regimens that have combined bortezomib with corticosteroids, alkylating agents, thalidomide, and/or lenalidomide have resulted in high response rates. Despite the higher and often deeper response rates and prolongation of progression-free survival with bortezomib-based multiagent regimens, an overall survival (OS) advantage has not been demonstrated with most combinations compared to the sequential approach of using anti-myeloma agents, particularly in patients less than 65 years of age with newly diagnosed myeloma. The unique properties of some of these regimens can be taken into account when choosing a particular regimen based on the clinical scenario. For example, the combination of bortezomib, thalidomide, and dexamethasone (VTD) has particular value in renal failure since none of the drugs need dose modification. Similarly, the combination chemotherapy regimen VDT-PACE (bortezomib, dexamethasone, thalidomide, cisplatin, doxorubicin, cyclophosphamide, and etoposide) is of particular value in patients presenting with aggressive disease such as extramedullary plasmacytomas or plasma cell leukemia. Ongoing clinical trials are testing combinations of bortezomib with several other classes of agents, including monoclonal antibodies, and inhibitors of deacetylases, heat shock proteins, phosphatidyl inositol 3-kinase/Akt/mammalian target of rapamycin pathway and farnesyl transferase.

Crystal structure of a bioactive pactamycin analog bound to the 30S ribosomal subunit

Biosynthetically and chemically derived analogs of the antibiotic pactamycin and de-6-methylsalicylyl (MSA)-pactamycin have attracted recent interest as potential antiprotozoal and antitumor drugs. Here, we report a 3.1-Å crystal structure of de-6-MSA-pactamycin bound to its target site on the Thermus thermophilus 30S ribosomal subunit. Although de-6-MSA-pactamycin lacks the MSA moiety, it shares the same binding site as pactamycin and induces a displacement of nucleic acid template bound at the E-site of the 30S. The structure highlights unique interactions between this pactamycin analog and the ribosome, which paves the way for therapeutic development of related compounds.

Search for a two-Higgs-boson doublet using a simplified model in pp collisions at sqrt[s] = 1.96 TeV

We present a search for new particles in an extension to the standard model that includes a heavy Higgs boson (H(0)), a lighter charged Higgs boson (H(±)), and an even lighter Higgs boson h(0), with decays leading to a W-boson pair and a bottom-antibottom quark pair in the final state. We use events with exactly one lepton, missing transverse momentum, and at least four jets in data corresponding to an integrated luminosity of 8.7 fb(-1) collected by the CDF II detector in proton-antiproton collisions at sqrt[s]= 1.96 TeV. We find the data to be consistent with standard model predictions and report the results in terms of a simplified Higgs-cascade-decay model, setting 95% confidence level upper limits on the product of cross section and branching fraction from 1.3 pb to 15 fb as a function of H(0) and H(±) masses for m(h)(0) = 126 GeV/c(2).

Measurements of the top-quark mass and the tt cross section in the hadronic τ+jets decay channel at sqrt[s] = 1.96 TeV

We present the first direct measurement of the top-quark mass using tt events decaying in the hadronic τ+jets decay channel. Using data corresponding to an integrated luminosity of 2.2 fb(-1) collected by the CDF II detector in pp collisions at sqrt[s] = 1.96 TeV at the Fermilab Tevatron, we measure the tt cross section, σ(tt), and the top-quark mass, M(top). We extract M(top) from a likelihood based on per-event probabilities calculated with leading-order signal and background matrix elements. We measure σ(tt) = 8.8 ± 3.3(stat) ± 2.2(syst) pb and M(top) = 172.7 ± 9.3(stat) ± 3.7(syst) GeV/c(2).