Technical note: TERMA scaling as an effective heterogeneity correction model for convolution-based external-beam photon dose calculations.

Background: In highly heterogeneous medium, such as one with lung tissue or air cavities, the dose in the low-density region or after it, as calculated by the conventional methods based on convolution with an energy-spreading kernel, is usually overestimated in comparison with measurements or more accurate predictions.

Purpose: To correct the overestimation, we propose a method of scaling the total energy released per mass (TERMA).

Methods: The scaling depends on both the density distribution and the effective beam size in the lateral direction.

Monte Carlo modeling of Halcyon and Ethos radiotherapy beam using CAD geometry: validation and IAEA-compliant phase space.

A Monte Carlo (MC) model of a Halcyon and Ethos (Varian Medical Systems, a Siemens Healthineers Company) radiotherapy beam was validated and field-independent phase space (PHSP) files were recorded above the dual-layer multileaf collimators (MLC).The treatment head geometry was modeled according to engineering drawings and the dual-layer MLC was imported from CAD (computer-aided design) files. The information for the incident electron beam was achieved from an iterative electromagnetic solver.

Russian nursing students' knowledge level and attitudes in the context of human immunodeficiency virus (HIV) - a descriptive study.

Background: The purpose of this study was to describe the knowledge of Russian nursing students regarding HIV and Acquired Immuno-Deficiency Syndrome (AIDS), and their attitudes towards caring for people/patients living with HIV or AIDS (PLWHA - People Living With HIV/AIDS) and their possible homophobic attitudes. The HIV epidemic in Russia is substantial and increasing rapidly. Hence this study provides important new information regarding this phenomenon.

Fibrinolytic and coagulative activities of Yersinia pestis.

The outer membrane protease Pla belongs to the omptin protease family spread by horizontal gene transfer into Gram-negative bacteria that infect animals or plants. Pla has adapted to support the life style of the plague bacterium Yersinia pestis. Pla has a β-barrel fold with 10 membrane-spanning β strands and five surface loops, and the barrel surface contains bound lipopolysaccharide (LPS) that is critical for the conformation and the activity of Pla.

Human single-chain urokinase is activated by the omptins PgtE of Salmonella enterica and Pla of Yersinia pestis despite mutations of active site residues.

Fibrinolysis is important in cell migration and tightly regulated by specific inhibitors and activators; of the latter, urokinase (uPA) associates with enhancement of cell migration. Active uPA is formed through cleavage of the single-chain uPA (scuPA). The Salmonella enterica strain 14028R cleaved human scuPA at the peptide bond Lys158-Ile159, the site cleaved also by the physiological activator human plasmin.

Regiospecificity and stereospecificity of human UDP-glucuronosyltransferases in the glucuronidation of estriol, 16-epiestriol, 17-epiestriol, and 13-epiestradiol.

The glucuronidation of estriol, 16-epiestriol, and 17-epiestriol by the human UDP-glucuronosyltransferases (UGTs) of subfamilies 1A, 2A, and 2B was examined. UGT1A10 is highly active in the conjugation of the 3-OH in all these estriols, whereas UGT2B7 is the most active UGT toward one of the ring D hydroxyls, the 16-OH in estriol and 16-epiestriol, but the 17-OH in 17-epiestriol. Kinetic analyses indicated that the 17-OH configuration plays a major role in the affinity of UGT2B7 for estrogens.

Glutamine synthetase and glucose-6-phosphate isomerase are adhesive moonlighting proteins of Lactobacillus crispatus released by epithelial cathelicidin LL-37.

Glutamine synthetase (GS) and glucose-6-phosphate isomerase (GPI) were identified as novel adhesive moonlighting proteins of Lactobacillus crispatus ST1. Both proteins were bound onto the bacterial surface at acidic pHs, whereas a suspension of the cells to pH 8 caused their release into the buffer, a pattern previously observed with surface-bound enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of L. crispatus.

Molecular adaptation of a plant-bacterium outer membrane protease towards plague virulence factor Pla.

Background: Omptins are a family of outer membrane proteases that have spread by horizontal gene transfer in Gram-negative bacteria that infect vertebrates or plants. Despite structural similarity, the molecular functions of omptins differ in a manner that reflects the life style of their host bacteria. To simulate the molecular adaptation of omptins, we applied site-specific mutagenesis to make Epo of the plant pathogenic Erwinia pyrifoliae exhibit virulence-associated functions of its close homolog, the plasminogen activator Pla of Yersinia pestis.

Two distinct regions in the model protein Peb1 are critical for its heterologous transport out of Escherichia coli.

Background: Escherichia coli is frequently the first-choice host organism in expression of heterologous recombinant proteins in basic research as well as in production of commercial, therapeutic polypeptides. Especially the secretion of proteins into the culture medium of E. coli is advantageous compared to intracellular production due to the ease in recovery of the recombinant protein.

The omptins of Yersinia pestis and Salmonella enterica cleave the reactive center loop of plasminogen activator inhibitor 1.

Plasminogen activator inhibitor 1 (PAI-1) is a serine protease inhibitor (serpin) and a key molecule that regulates fibrinolysis by inactivating human plasminogen activators. Here we show that two important human pathogens, the plague bacterium Yersinia pestis and the enteropathogen Salmonella enterica serovar Typhimurium, inactivate PAI-1 by cleaving the R346-M347 bait peptide bond in the reactive center loop. No cleavage of PAI-1 was detected with Yersinia pseudotuberculosis, an oral/fecal pathogen from which Y.

A molecular model of the human UDP-glucuronosyltransferase 1A1, its membrane orientation, and the interactions between different parts of the enzyme.

The vertebrate UDP-glucuronosyltransferases (UGTs) are membrane-bound enzymes of the endoplasmic reticulum that process both endogenous and exogenous substrates. The human UGTs are well known biologically, but biophysical understanding is scarce, largely because of problems in purification. The one resolved crystal structure covers the C-terminal domain of the human UGT2B7.

How many and which amino acids are responsible for the large activity differences between the highly homologous UDP-glucuronosyltransferases (UGT) 1A9 and UGT1A10?

The amino acid sequences of the human UDP-glucuronosyltransferases (UGTs) 1A9 and 1A10 are 93% identical, yet there are large differences in their activity and substrate selectivity. For example, the regioselectivity in propranolol glucuronidation, the regioselectivity in dobutamine glucuronidation, and the glucuronidation rate of alpha- and beta-estradiol differ greatly between UGT1A9 and UGT1A10. To identify the residue responsible for the activity differences, we divided the N-terminal half of the two UGTs into five comparable segments by inserting four unique restriction sites at identical positions in both genes and constructing chimeras in which segments of UGT1A9 were individually replaced by the corresponding segments from UGT1A10.

The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond.

The CuB metal center is at the core of the active site of the heme-copper oxidases, comprising a copper atom ligating three histidine residues one of which is covalently bonded to a tyrosine residue. Using quantum chemical methodology, we have studied the CuB site in several redox and ligand states proposed to be intermediates of the catalytic cycle. The importance of the His-Tyr crosslink was investigated by comparing energetics, charge, and spin distributions between systems with and without the crosslink.

A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from approximately 0.3 g of bone.

Modeling the active-site structure of the cbb3-type oxidase from Rhodobacter sphaeroides.

The active site of the heme-copper oxidases comprises a redox-active high-spin heme and a tris-histidine copper center Cu B. Two amino acids in the close vicinity of the metals, a tyrosine and a tryptophan from helix 6, have been shown to be absolutely required for the catalytic function and should be considered part of the active site. Additionally, amino acid residues from interhelical loops strongly modify the activity.

Charge parameterization of the metal centers in cytochrome c oxidase.

Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest.

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase.

In many cytochrome c oxidases glutamic acid 242 is required for proton transfer to the binuclear heme a(3)/Cu(B) site, and for proton pumping. When present, the side chain of Glu-242 is orientated "down" towards the proton-transferring D-pathway in all available crystal structures. A nonpolar cavity "above" Glu-242 is empty in these structures.

Polyglutamine variation in a flowering time protein correlates with island age in a Hawaiian plant radiation.

Background: A controversial topic in evolutionary developmental biology is whether morphological diversification in natural populations can be driven by expansions and contractions of amino acid repeats in proteins. To promote adaptation, selection on protein length variation must overcome deleterious effects of multiple correlated traits (pleiotropy). Thus far, systems that demonstrate this capacity include only ancient or artificial morphological diversifications.

A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power.

The evolution of carnivorous plants has been modeled as a selective tradeoff between photosynthetic costs and benefits in nutrient-poor habitats. Although possibly applicable for pitfall and flypaper trappers, more variables may be required for active trapping systems. Bladderwort (utricularia) suction traps react to prey stimuli with an extremely rapid release of elastic instability.

The K-pathway revisited: a computational study on cytochrome c oxidase.

Cytochrome c oxidase contains two established proton-conducting structures, the D- and K-pathways. The role of the K-pathway appears to be to conduct the first two protons to be used in water formation, which are taken up on reduction of the oxidized enzyme. Previous computational work has suggested that Lys(I)-319 is neutral over a large pH range and in various redox states.

Sequence analysis of the cbb3 oxidases and an atomic model for the Rhodobacter sphaeroides enzyme.

The cbb3-type oxidases are members of the heme-copper oxidase superfamily, distant by sequence comparisons, but sharing common functional characteristics. To understand the minimal common properties of the superfamily, and to learn about cbb3-type oxidases specifically, we have analyzed a wide set of heme-copper oxidase sequences and built a homology model of the catalytic subunit of the cbb3 oxidase from Rhodobacter sphaeroides. We conclude that with regard to the active site surroundings, the cbb3 oxidases greatly resemble the structurally known oxidases, while major differences are found in three segments: the additional N-terminal stretch of ca.

Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase.

The membrane-bound enzyme cytochrome c oxidase is responsible for cell respiration in aerobic organisms and conserves free energy from O2 reduction into an electrochemical proton gradient by coupling the redox reaction to proton-pumping across the membrane. O2 reduction produces water at the bimetallic heme a3/CuB active site next to a hydrophobic cavity deep within the membrane. Water molecules in this cavity have been suggested to play an important role in the proton-pumping mechanism.

Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation.

Much recent attention in the study of adaptation of organismal form has centered on developmental regulation. As such, the highly conserved respiratory machinery of eukaryotic cells might seem an unlikely target for selection supporting novel morphologies. We demonstrate that a dramatic molecular evolutionary rate increase in subunit I of cytochrome c oxidase (COX) from an active-trapping lineage of carnivorous plants is caused by positive Darwinian selection.

The nucleotide-binding domain of the Zn2+-transporting P-type ATPase from Escherichia coli carries a glycine motif that may be involved in binding of ATP.

In P-type ATPases, the nucleotide-binding (N) domain is located in the middle of the sequence which folds into the phosphorylation (P) domain. The N domain of ZntA, a Zn2+-translocating P-type ATPase from Escherichia coli, is approx. 13% identical with the N domain of sarcoplasmic reticulum Ca2+-ATPase.

Probing the ability of the coat and vertex protein of the membrane-containing bacteriophage PRD1 to display a meningococcal epitope.

Bacteriophage PRD1 is an icosahedral dsDNA virus with a diameter of 740 A and an outer protein shell composed of 720 copies of major coat protein P3. Spike complexes at the vertices are composed of a pentameric base (protein P31) and a spike structure (proteins P5 and P2) where the N-terminal region of the trimeric P5 is associated with the base and the C-terminal region of P5 is associated with receptor-binding protein P2. The functionality of proteins P3 and P5 was investigated using insertions and deletions.