Dynamics and Sorption Kinetics of Methanol Monomers and Clusters on Nopinone Surfaces.

Organic-organic interactions play important roles in secondary organic aerosol formation, but the interactions are complex and poorly understood. Here, we use environmental molecular beam experiments combined with molecular dynamics simulations to investigate the interactions between methanol and nopinone, as atmospheric organic proxies. In the experiments, methanol monomers and clusters are sent to collide with three types of surfaces, i.e., graphite, thin nopinone coating on graphite, and nopinone multilayer surfaces, at temperatures between 140 and 230 K. Methanol monomers are efficiently scattered from the graphite surface, whereas the scattering is substantially suppressed from nopinone surfaces. The thermal desorption from the three surfaces is similar, suggesting that all the surfaces have weak or similar influences on methanol desorption. All trapped methanol molecules completely desorb within a short experimental time scale at temperatures of 180 K and above. At lower temperatures, the desorption rate decreases, and a long experimental time scale is used to resolve the desorption, where three desorption components are identified. The fast component is beyond the experimental detection limit. The intermediate component exhibits multistep desorption character and has an activation energy of Ea = 0.18 ± 0.03 eV, in good agreement with simulation results. The slow desorption component is related to diffusion processes due to the weak temperature dependence. The molecular dynamics results show that upon collisions the methanol clusters shatter, and the shattered fragments quickly diffuse and recombine to clusters. Desorption involves a series of processes, including detaching from clusters and desorbing as monomers. At lower temperatures, methanol forms compact cluster structures while at higher temperatures, the methanol molecules form layered structures on the nopinone surface, which are visible in the simulation. Also, the simulation is used to study the liquid-liquid interaction, where the methanol clusters completely dissolve in liquid nopinone, showing ideal organic-organic mixing.

Experimental and Computational Study of Molecular Water Interactions with Condensed Nopinone Surfaces Under Atmospherically Relevant Conditions.

Water and organics are omnipresent in the atmosphere, and their interactions influence the properties and lifetime of both aerosols and clouds. Nopinone is one of the major reaction products formed from ß-pinene oxidation, a compound emitted by coniferous trees, and it has been found in both gas and particle phases in the atmosphere. Here, we investigate the interactions between water molecules and nopinone surfaces by combining environmental molecular beam (EMB) experiments and molecular dynamics (MD) simulations. The EMB method enables detailed studies of the dynamics and kinetics of water interacting with solid nopinone at 170-240 K and graphite coated with a molecularly thin nopinone layer at 200-270 K. MD simulations that mimic the experimental conditions have been performed to add insights into the molecular-level processes. Water molecules impinging on nopinone surfaces are efficiently trapped (≥97%), and only a minor fraction scatters inelastically while maintaining 35-65% of their incident kinetic energy (23.2 ± 1.0 kJ mol-1). A large fraction (60-80%) of the trapped molecules desorbs rapidly, whereas a small fraction (20-40%) remains on the surface for more than 10 ms. The MD calculations confirm both rapid water desorption and the occurrence of strongly bound surface states. A comparison of the experimental and computational results suggests that the formation of surface-bound water clusters enhances water uptake on the investigated surfaces.

Understanding water interactions with organic surfaces: environmental molecular beam and molecular dynamics studies of the water-butanol system.

The interactions between water molecules and condensed n-butanol surfaces are investigated at temperatures from 160 to 240 K using the environmental molecular beam experimental method and complementary molecular dynamics (MD) simulations. In the experiments hyperthermal water molecules are directed onto a condensed n-butanol layer and the flux from the surface is detected in different directions. A small fraction of the water molecules scatters inelastically from the surface while losing 60-90% of their initial kinetic energy in collisions, and the angular distributions of these molecules are broad for both solid and liquid surfaces. The majority of the impinging water molecules are thermalized and trapped on the surface, while subsequent desorption is governed by two different processes: one where molecules bind briefly to the surface (residence time τ < 10 µs), and another where the molecules trap for a longer time τ = 0.8-2.0 ms before desorbing. Water molecules trapped on a liquid n-butanol surface are substantially less likely to escape from the surface compared to a solid layer. The MD calculations provide detialed insight into surface melting, adsorption, absorption and desorption processes. Calculated angular distributions and kinetic energy of emitted water molecules agree well with the experimental data. In spite of its hydrophobic tail and enhanced surface organization below the melting temperature, butanol's hydrophilic functional groups are concluded to be surprisingly accessible to adsorbed water molecules; a finding that may be explained by rapid diffusion of water away from hydrophobic surface structures towards more strongly bound conformational structures.

Water-Induced Organization of Palmitic Acid at the Surface of a Model Sea Salt Particle: A Molecular Dynamics Study.

Marine aerosols represent the most important aerosol fraction in the Earth atmosphere. Field studies have revealed that fatty acids form an organic film at the surface of sea salt particles, altering the properties of the aerosol. By means of classical molecular dynamics simulation, the surface organization of palmitic acid (PA) on a salt surface, NaCl, has been investigated at two different temperatures, 235 and 300 K, and with relative humidity varying from 0 to 40%. Calculations show that water promotes the formation of well-ordered close-packed PA islands. As a result, some area of the salt may be covered by water only or by PA molecules supported by water. Depending on the relative humidity, the hydrophilic/hydrophobic character of the sea salt surface varies. This heterogeneous coating gives rise locally to very different surface properties and hence may affect the transfer of gas phase species to the salt and their reactivity.

Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics.

The 16S ribosomal RNA methyltransferase enzymes that modify nucleosides in the drug binding site to provide self-resistance in aminoglycoside-producing micro-organisms have been proposed to comprise two distinct groups of S-adenosyl-l-methionine (SAM)-dependent RNA enzymes, namely the Kgm and Kam families. Here, the nucleoside methylation sites for three Kgm family methyltransferases, Sgm from Micromonospora zionensis, GrmA from Micromonospora echinospora and Krm from Frankia sp. Ccl3, were experimentally determined as G1405 by MALDI-ToF mass spectrometry. These results significantly extend the list of securely characterized G1405 modifying enzymes and experimentally validate their grouping into a single enzyme family. Heterologous expression of the KamB methyltransferase from Streptoalloteichus tenebrarius experimentally confirmed the requirement for an additional 60 amino acids on the deduced KamB N-terminus to produce an active methyltransferase acting at A1408, as previously suggested by an in silico analysis. Finally, the modifications at G1405 and A1408, were shown to confer partially overlapping but distinct resistance profiles in Escherichia coli. Collectively, these data provide a more secure and systematic basis for classification of new aminoglycoside resistance methyltransferases from producers and pathogenic bacteria on the basis of their sequences and resistance profiles.

Reduced expression of lamin A/C results in modified cell signaling and metabolism coupled with changes in expression of structural proteins.

Nuclear lamins are intermediate filament proteins that define the shape and stability of nuclei in mammalian cells. In addition to this dominant structural role, recent studies have suggested that the lamin proteins also regulate fundamental aspects of nuclear function. In order to understand different roles played by lamin proteins, we used RNA interference to generate a series of HeLa cell lines to study loss-of-function phenotypes associated with depletion of lamin protein expression. In this study, we used genome-wide proteomic approaches to monitor global changes in protein expression in cells with <10% of normal lamin A/C expression. Of approximately 2000 protein spots analyzed by two-dimensional electrophoresis, only 38 showed significantly altered expression in lamin A/C depleted cells. Of these, 4 protein spots were up-regulated, and 34 were down-regulated. Significant changes were seen to involve the general reduction in expression of cytoskeletal proteins, consistent with altered functionality of the structural cellular networks. At the same time, alterations in expression of proteins involved in cellular metabolism correlated with altered patterns of metabolic activity. In order to link these two features, we used antibody microarrays to perform a focused analysis of expression of cell cycle regulatory proteins. This confirmed a general reduction in expression of proteins regulating cell cycle progression and alteration in signaling pathways that regulate the metabolic activity of cells. The cross-talk between signal transduction and the cytoskeleton emphasizes how structural and kinase-based networks are integrated in mammalian cells to fine-tune metabolic responses.

[Gastrointestinal tuberculosis--case report]. / Tuberkuloza gastrointestinalnog trakta--prikaz bolesnice.

Isolated tuberculosis of gastrointestinal tract is a very rare disease most commonly localized in the ileo-cecal region (over 85% of the cases). The main object of surgical therapy is intraperitoneal tuberculosis (IP-TB), which leads to complications such as bowel obstruction, perforation, fistulation and bleeding. Since gastrointestinal tuberculosis can mimic symptoms found in Crohns' disease and ileocecal cancer, definitive diagnosis can only be obtained by the finding of Mycobacterium tuberculosis in tissue and stool sample as well as by positive microbacterial cultivation. A 35 year old female patient was admitted to surgical ward with clinical and radiological signs of ileus. From personal medical history as well as previous medical documentation we learned that the patient had been treated in 1995 for lung and larynx tuberculosis at Jordanovac Hospital in Zagreb. After preoperative preparation, the patient underwent surgery during which we found numerous stenoses in the region of terminal ileum and cecum. Due to the patient's general condition, surgical treatment was performed in two acts. In the first we established an L-L ileotransverse anastomosis, and in the second we made the resection. The diagnosis was confirmed by histological findings of Mycobaterium tuberculosis in stool and tissue samples as well as in resection material during operation. The early postoperative period proceeded free from complications and after surgical treatment the patient was referred to the Klenovnik Special Hospital for Pulmonary Diseases. On follow up 18 months after the surgery, there were no signs of gastrointestinal involvement.

Changed genome heterochromatinization upon prolonged activation of the Raf/ERK signaling pathway.

The Raf/ERK (Extracellular Signal Regulated Kinase) signal transduction pathway controls numerous cellular processes, including growth, differentiation, cellular transformation and senescence. ERK activation is thought to involve complex spatial and temporal regulation, to achieve a high degree of specificity, though precisely how this is achieved remains to be confirmed. We report here that prolonged activation of a conditional form of c-Raf-1 (BXB-ER) leads to profound changes in the level and distribution of a heterochromatic histone mark. In mouse fibroblasts, the heterochromatic trimethylation of lysine 9 in histone H3 (H3K9Me3) is normally confined to pericentromeric regions. However, following ERK activation a genome-wide redistribution of H3K9Me3 correlates with loss of the histone modification from chromocentres and the appearance of numerous punctuate sites throughout the interphase nucleus. These epigenetic changes during interphase correlate with altered chromosome structure during mitosis, where robust H3K9Me3 signals appear within telomeric heterochromatin. This pattern of heterochromatinization is distinct from previously described oncogene induced senescence associated heterochromatin foci (SAHF), which are excluded from telomeres. The H3K9Me3 histone mark is known to bind the major heterochromatin protein HP1 and we show that the alterations in the distribution of this histone epistate correlate with redistribution of HP1ß throughout the nucleus. Interestingly while ERK activation is fully reversible, the observed chromatin changes induced by epigenetic modifications are not reversible once established. We describe for the first time a link from prolonged ERK activation to stable changes in genome organization through redistribution of heterochromatic domains involving the telomeres. These epigenetic changes provide a possible mechanism through which prolonged activation of Raf/ERK can lead to growth arrest or the induction of differentiation, senescence and cancer.

Lamin B1 maintains the functional plasticity of nucleoli.

The dynamic ability of genomes to interact with discrete nuclear compartments appears to be essential for chromatin function. However, the extent to which structural nuclear proteins contribute to this level of organization is largely unresolved. To test the links between structure and function, we evaluated how nuclear lamins contribute to the organization of a major functional compartment, the nucleolus. HeLa cells with compromised expression of the genes encoding lamins were analyzed using high-resolution imaging and pull-down assays. When lamin B1 expression was depleted, inhibition of RNA synthesis correlated with complex structural changes within the nucleolar active centers until, eventually, the nucleoli were dispersed completely. With normal lamin expression, the nucleoli were highly plastic, with dramatic and freely reversible structural changes correlating with the demand for ribosome biogenesis. Preservation of the nucleolar compartment throughout these structural transitions is shown to be linked to lamin B1 expression, with the lamin B1 protein interacting with the major nucleolar protein nucleophosmin/B23.

Subcellular pH and predicted pH-dependent features of proteins.

A characteristic of two-dimensional proteomics gels is a general bimodal distribution of isoelectric (pI) values. Discussion of this feature has focussed on the balance of acidic and basic ionisable residues, and potential relationships between pI distributions and organism classification or protein subcellular location. Electrostatics calculations on a set of protein structures with known subcellular location show that predicted folded state pI are similar to those calculated from sequence alone, but adjusted according to a general stabilising effect from interactions between ionisable groups. Bimodal distributions dominate both pI and the predicted pH of maximal stability. However, there are significant differences between these features. The average pH of maximal stability generally follows organelle pH. Average pI values are well removed from organelle pH in most subcellular environments, consistent with the view that proteins have evolved to carry (on average) net charge in a given subcellular location, and relevant to discussion of solubility in crowded environments. Correlation of the predicted pH of maximum stability with subcellular pH suggests an evolutionary pressure to adjust folded state interactions according to environment. Finally, our analysis of ionisable group contributions to stability suggests that Golgi proteins have the largest such term, although this dataset is small.

Identification of Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA2) target proteins by proteome analysis: activation of EBNA2 in conditionally immortalized B cells reflects early events after infection of primary B cells by EBV.

The Epstein-Barr virus (EBV) is a ubiquitous B-lymphotropic herpesvirus associated with several malignant tumors, e.g., Burkitt's lymphoma and Hodgkin's disease, and is able to efficiently immortalize primary B lymphocytes in vitro. The growth program of infected B cells is initiated and maintained by the viral transcription factor EBV nuclear antigen 2 (EBNA2), which regulates viral and cellular genes, including the proto-oncogene c-myc. In our study, patterns of protein expression in B cells with and without EBNA2 were analyzed by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. For this purpose, we used a conditional immortalization system for EBV, a B cell line (EREB2-5) that expresses an estrogen receptor-EBNA2 fusion protein. In order to discriminate downstream targets of c-Myc from c-Myc-independent EBNA2 targets, we used an EREB2-5-derived cell line, P493-6, in which c-Myc is expressed under the control of a tetracycline-regulated promoter. Of 20 identified EBNA2 target proteins, 11 were c-Myc dependent and therefore most probably associated with proliferation, and one of these proteins was a posttranslationally modified protein, i.e., hypusinylated eIF5a. Finally, to estimate the relevance of EBNA2 targets during early EBV infection, we analyzed the proteomes of primary B cells before and after infection with EBV. The protein expression pattern induced upon EBV infection was similar to that following EBNA2 activation. These findings underscore the value of EREB2-5 cells as an appropriate model system for the analysis of early events in the process of EBV-mediated B-cell immortalization.