Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Amyotrophic lateral sclerosis and structural defects in Cu,Zn superoxide dismutase

Single-site mutants in the Cu,Zn superoxide dismutase (SOD) gene (SOD1) occur in patients with the fatal neurodegenerative disorder familial amyotrophic lateral sclerosis (FALS). Complete screening of the SOD1 coding region revealed that the mutation Ala4 to Val in exon 1 was the most frequent one; mutations were identified in exons 2, 4, and 5 but not in the active site region formed by exon 3. The 2.4 A crystal structure of human SOD, along with two other SOD structures, established that all 12 observed FALS mutant sites alter conserved interactions critical to the beta-barrel fold and dimer contact, rather than catalysis. Red cells from heterozygotes had less than 50 percent normal SOD activity, consistent with a structurally defective SOD dimer. Thus, defective SOD is linked to motor neuron death and carries implications for understanding and possible treatment of FALS.

Phosphatidylinositol 3'-kinase is activated by association with IRS-1 during insulin stimulation

IRS-1 undergoes rapid tyrosine phosphorylation during insulin stimulation and forms a stable complex containing the 85 kDa subunit (p85) of the phosphatidylinositol (PtdIns) 3'-kinase, but p85 is not tyrosyl phosphorylated. IRS-1 contains nine tyrosine phosphorylation sites in YXXM (Tyr-Xxx-Xxx-Met) motifs. Formation of the IRS-1-PtdIns 3'-kinase complex in vitro is inhibited by synthetic peptides containing phosphorylated YXXM motifs, suggesting that the binding of PtdIns 3'-kinase to IRS-1 is mediated through the SH2 (src homology-2) domains of p85. Furthermore, overexpression of IRS-1 potentiates the activation of PtdIns 3-kinase in insulin-stimulated cells, and tyrosyl phosphorylated IRS-1 or peptides containing phosphorylated YXXM motifs activate PtdIns 3'-kinase in vitro. We conclude that the binding of tyrosyl phosphorylated IRS-1 to the SH2 domains of p85 is the critical step that activates PtdIns 3'-kinase during insulin stimulation.

Catalytic role of gold in gold-based catalysts: a density functional theory study on the CO oxidation on gold

Gold-based catalysts have been of intense interests in recent years, being regarded as a new generation of catalysts due to their unusually high catalytic performance. For example, CO oxidation on Au/TiO(2) has been found to occur at a temperature as low as 200 K. Despite extensive studies in the field, the microscopic mechanism of CO oxidation on Au-based catalysts remains controversial. Aiming to provide insight into the catalytic roles of Au, we have performed extensive density functional theory calculations for the elementary steps in CO oxidation on Au surfaces. O atom adsorption, CO adsorption, O(2) dissociation, and CO oxidation on a series of Au surfaces, including flat surfaces, defects and small clusters, have been investigated in detail. Many transition states involved are located, and the lowest energy pathways are determined. We find the following: (i) the most stable site for O atom on Au is the bridge site of step edge, not a kink site; (ii) O(2) dissociation on Au (O(2)-->2O(ad)) is hindered by high barriers with the lowest barrier being 0.93 eV on a step edge; (iii) CO can react with atomic O with a substantially lower barrier, 0.25 eV, on Au steps where CO can adsorb; (iv) CO can react with molecular O(2) on Au steps with a low barrier of 0.46 eV, which features an unsymmetrical four-center intermediate state (O-O-CO); and (v) O(2) can adsorb on the interface of Au/TiO(2) with a reasonable chemisorption energy. On the basis of our calculations, we suggest that (i) O(2) dissociation on Au surfaces including particles cannot occur at low temperatures; (ii) CO oxidation on Au/inactive-materials occurs on Au steps via a two-step mechanism: CO+O(2)-->CO(2)+O, and CO+O-->CO(2); and (iii) CO oxidation on Au/active-materials also follows the two-step mechanism with reactions occurring at the interface.

Quantitation of nitrotyrosine levels in lung sections of patients and animals with acute lung injury

Activated alveolar macrophages and epithelial type II cells release both nitric oxide and superoxide which react at near diffusion-limited rate (6.7 x 10(9) M-1s-1) to form peroxynitrite, a potent oxidant capable of damaging the alveolar epithelium and pulmonary surfactant. Peroxynitrite, but not nitric oxide or superoxide, readily nitrates phenolic rings including tyrosine. We quantified the presence of nitrotyrosine in the lungs of patients with the adult respiratory distress syndrome (ARDS) and in the lungs of rats exposed to hyperoxia (100% O2 for 60 h) using quantitative immunofluorescence. Fresh frozen or paraffin-embedded lung sections were incubated with a polyclonal antibody to nitrotyrosine, followed by goat anti-rabbit IgG coupled to rhodamine. Sections from patients with ARDS (n = 5), or from rats exposed to hyperoxia (n = 4), exhibited a twofold increase of specific binding over controls. This binding was blocked by the addition of an excess amount of nitrotyrosine and was absent when the nitrotyrosine antibody was replaced with nonimmune IgG. In additional experiments we demonstrated nitrotyrosine formation in rat lung sections incubated in vitro with peroxynitrite, but not nitric oxide or reactive oxygen species. These data suggest that toxic levels of peroxynitrite may be formed in the lungs of patients with acute lung injury.

Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells

Chromosomal double-strand breaks (DSBs) in mammalian cells are repaired by either homology-directed repair (HDR), using a homologous sequence as a repair template, or nonhomologous end-joining (NHEJ), which often involves sequence alterations at the DSB site. To characterize the interrelationship of these two pathways, we analyzed HDR of a DSB in cells deficient for NHEJ components. We find that the HDR frequency is enhanced in Ku70(-/-), XRCC4(-/-), and DNA-PKcs(-/-) cells, with the increase being particularly striking in Ku70(-/-) cells. Neither sister-chromatid exchange nor gene-targeting frequencies show a dependence on these NHEJ proteins. A Ku-modulated two-ended versus one-ended chromosome break model is presented to explain these results.

Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis

The 22q11.2 deletion syndrome, which includes DiGeorge and velocardiofacial syndromes (DGS/VCFS), is the most common microdeletion syndrome. The majority of deleted patients share a common 3 Mb hemizygous deletion of 22q11.2. The remaining patients include those who have smaller deletions that are nested within the 3 Mb typically deleted region (TDR) and a few with rare deletions that have no overlap with the TDR. The identification of chromosome 22-specific duplicated sequences or low copy repeats (LCRs) near the end-points of the 3 Mb TDR has led to the hypothesis that they mediate deletions of 22q11.2. The entire 3 Mb TDR has been sequenced, permitting detailed investigation of the LCRs and their involvement in the 22q11.2 deletions. Sequence analysis has identified four LCRs within the 3 Mb TDR. Although the LCRs differ in content and organization of shared modules, those modules that are common between them share 97-98% sequence identity with one another. By fluorescence in situ hybridization (FISH) analysis, the end-points of four variant 22q11.2 deletions appear to localize to the LCRs. Pulsed-field gel electrophoresis and Southern hybridization have been used to identify rearranged junction fragments from three variant deletions. Analysis of junction fragments by PCR and sequencing of the PCR products implicate the LCRs directly in the formation of 22q11.2 deletions. The evolutionary origin of the duplications on chromosome 22 has been assessed by FISH analysis of non-human primates. Multiple signals in Old World monkeys suggest that the duplication events may have occurred at least 20-25 million years ago.

Germline mutations in the ribonuclease L gene in families showing linkage with HPC1

Although prostate cancer is the most common non-cutaneous malignancy diagnosed in men in the United States, little is known about inherited factors that influence its genetic predisposition. Here we report that germline mutations in the gene encoding 2'-5'-oligoadenylate(2-5A)-dependent RNase L (RNASEL) segregate in prostate cancer families that show linkage to the HPC1 (hereditary prostate cancer 1) region at 1q24-25 (ref. 9). We identified RNASEL by a positional cloning/candidate gene method, and show that a nonsense mutation and a mutation in an initiation codon of RNASEL segregate independently in two HPC1-linked families. Inactive RNASEL alleles are present at a low frequency in the general population. RNASEL regulates cell proliferation and apoptosis through the interferon-regulated 2-5A pathway and has been suggested to be a candidate tumor suppressor gene. We found that microdissected tumors with a germline mutation showed loss of heterozygosity and loss of RNase L protein, and that RNASEL activity was reduced in lymphoblasts from heterozyogous individuals compared with family members who were homozygous with respect to the wildtype allele. Thus, germline mutations in RNASEL may be of diagnostic value, and the 2-5A pathway might provide opportunities for developing therapies for those with prostate cancer.

IRS-1 activates phosphatidylinositol 3'-kinase by associating with src homology 2 domains of p85

IRS-1 is an insulin receptor substrate that undergoes tyrosine phosphorylation and associates with the phosphatidylinositol (PtdIns) 3'-kinase immediately after insulin stimulation. Recombinant IRS-1 protein was tyrosine phosphorylated by the insulin receptor in vitro and associated with the PtdIns 3'-kinase from lysates of quiescent 3T3 fibroblasts. Bacterial fusion proteins containing the src homology 2 domains (SH2 domains) of the 85-kDa subunit (p85) of the PtdIns 3'-kinase bound quantitatively to tyrosine phosphorylated, but not unphosphorylated, IRS-1, and this association was blocked by phosphotyrosine-containing synthetic peptides. Moreover, the phosphorylated peptides and the SH2 domains each inhibited binding of PtdIns 3'-kinase to IRS-1. Phosphorylated IRS-1 activated PtdIns 3'-kinase in anti-p85 immunoprecipitates in vitro, and this activation was blocked by SH2 domain fusion proteins. These data suggest that the interaction between PtdIns 3'-kinase and IRS-1 is mediated by tyrosine phosphorylated motifs on IRS-1 and the SH2 domains of p85, and IRS-1 activates PtdIns 3'-kinase by binding to the SH2 domains of p85. Thus, IRS-1 likely serves to transmit the insulin signal by binding and regulating intracellular enzymes containing SH2 domains.

Identification of general linear relationships between activation energies and enthalpy changes for dissociation reactions at surfaces

The activation energy to reaction is a key quantity that controls catalytic activity. Having used ab inito calculations to determine an extensive and broad ranging set of activation energies and enthalpy changes for surface-catalyzed reactions, we show that linear relationships exist between dissociation activation energies and enthalpy changes. Known in the literature as empirical Brønsted-Evans-Polanyi (BEP) relationships, we identify and discuss the physical origin of their presence in heterogeneous catalysis. The key implication is that merely from knowledge of adsorption energies the barriers to catalytic elementary reaction steps can be estimated.

General rules for predicting where a catalytic reaction should occur on metal surfaces: a density functional theory study of C-H and C-O bond breaking/making on flat, stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH(4) <--> CH(3) + H and CO <--> C + O on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH(4) --> CH(3) + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH(4) <--> Ch(3) + H reaction, the dissociation barrier is reduced by approximately 0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH(3) + H on the flat surfaces and the defects. Second, for the CO <--> C + O reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH(3) + H reaction, the C + O association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.

Tyrosine phosphorylation of vav proto-oncogene product containing SH2 domain and transcription factor motifs

Activation of receptor-linked and cytoplasmic protein tyrosine kinases is crucial in the control of normal and abnormal cell growth and differentiation. Some substrates of protein tyrosine kinases such as phospholipase C gamma and ras GTPase-activating protein (GAP) contain sequences homologous to the src protein domains SH2 and SH3 (refs 3-9). The proto-oncogene vav is expressed in haematopoietic cells and its product Vav contains sequence motifs commonly found in transcription factors, such as helix-loop-helix, leucine-zipper and zinc-finger motifs and nuclear localization signals, as well as a single SH2 and two SH3 domains. Here we show that stimulation of T-cell antigen receptor on normal human peripheral blood lymphocytes or on human leukaemic T cells, and the crosslinking of IgE receptors on rat basophilic leukaemia cells, both promote the phosphorylation of tyrosine residues in Vav. Moreover, activation of the receptor for epidermal growth factor leads to marked tyrosine phosphorylation of Vav in cells transiently expressing vav, and Vav associates with the receptor through its SH2 domain. We propose that vav encodes a new class of substrates whose tyrosine phosphorylation may provide a mechanism for direct signal transduction linking receptors at the cell surface to transcriptional control.

Catalytic role of metal oxides in gold-based catalysts: a first principles study of CO oxidation on TiO2 supported Au

CO oxidation on TiO2 supported Au has been studied using density functional theory calculations. Important catalytic roles of the oxide have been identified: (i) CO oxidation occurs at the interface between Au and the oxide with a very small barrier; and (ii) O2 adsorption at the interface is the key step in the reaction. The physical origin of the oxide promotion effect has been further investigated: The oxide enhances electron transfer from the Au to the antibonding states of O2, giving rise to (i) strong ionic bonding between the adsorbed O2, Au, and the Ti cation; and (ii) a significant activation of O2 towards CO oxidation.

Macrophage and lymphocyte invasion of dorsal root ganglia after peripheral nerve lesions in the rat

The distribution of major histocompatibility complex class II (MHC II)-positive non-neuronal cells and T-lymphocytes was examined immunohistochemically in dorsal root ganglia (DRGs) up to 12 weeks following transection of one sciatic or lumbar spinal nerve in adult rats. Unlike within the brain, MHC II immunopositive (+) and T-cells are normally present within DRGs. After nerve transection, MHC II+ cell density increased (by about four times after each lesion) in DRGs projecting into lesioned nerves. Subsequently the number declined after sciatic but not spinal nerve transection. MHC II+ cells did not contain glial markers, even when these were up-regulated after the lesions. Initially, MHC II+ cells lay outside the satellite glia but, by 11 weeks, they had moved through them to lie against the somata. T-cells invaded the lesioned DRGs earlier than the MHC II+ cells. They achieved greater numbers after spinal (30 x control) than after sciatic (12 x control) nerve transection. They also increased in undamaged ganglia adjacent to the spinal nerve injury. T-cell density progressively declined after spinal but not sciatic nerve transection. Both cell types appeared to invade the DRGs initially through blood vessels and the meninges, particularly near the subarachnoid angle. At later stages, occasional neurones had dense aggregations of T-cell receptor+ and MHC II+ cells associated with them. We conclude that the magnitude and time course of changes in MHC II expression and T-cell numbers in lesioned DRGs differ from the responses within motor nuclei after axotomy. The influx of inflammatory cells may contribute to neurone survival in the short term. Their long-term presence has implications for patients. These cells have the potential to release excitatory cytokines that may generate ectopic impulse activity in sensory neurones after nerve injury and so may play a role in the generation of chronic neuropathic pain.

Identifying an O2 Supply Pathway in CO Oxidation on Au/TiO2(110): A Density Functional Theory Study on the Intrinsic Role of Water

Au catalysis has been one of the hottest topics in chemistry in the last 10 years or so. How O2 is supplied and what role water plays in CO oxidation are the two challenging issues in the field at the moment. In this study, using density functional theory we show that these two issues are in fact related to each other. The following observations are revealed: (i) water that can dissociate readily into OH groups can facilitate O2 adsorption on TiO2; (ii) the effect of OH group on the O2 adsorption is surprisingly long-ranged; and (iii) O2 can also diffuse along the channel of Ti (5c) atoms on TiO2(110), and this may well be the rate-limiting step for the CO oxidation. We provide direct evidence that O2 is supplied by O2 adsorption on TiO2 in the presence of OH and can diffuse to the interface of Au/TiO2 to participate in CO oxidation. Furthermore, the physical origin of the water effects on Au catalysis has been identified by electronic structure analyses: There is a charge transfer from TiO2 in the presence of OH to O2, and the O2 adsorption energy depends linearly on the O2 charge. These results are of importance to understand water effects in general in heterogeneous catalysis.

Catalytic water formation on platinum: a first-principles study

The study of catalytic behavior begins with one seemingly simple process, namely the hydrogenation of O to H2O on platinum. Despite the apparent simplicity its mechanism has been much debated. We have used density functional theory with gradient corrections to examine microscopic reaction pathways for several elementary steps implicated in this fundamental catalytic process. We find that H2O formation from chemisorbed O and H atoms is a highly activated process. The largest barrier along this route, with a value of approximately 1 eV, is the addition of the first H to O to produce OH. Once formed, however, OH groups are easily hydrogenated to H2O with a barrier of approximately 0.2 eV. Disproportionation reactions with 1:1 and 2:1 stoichiometries of H2O and O have been examined as alternative routes for OH formation. Both stoichiometries of reaction produce OH groups with barriers that are much lower than that associated with the O + H reaction. H2O, therefore, acts as an autocatalyst in the overall H2O formation process. Disproportionation with a 2:1 stoichiometry is thermodynamically and kinetically favored over disproportionation with a 1:1 stoichiometry. This highlights an additional (promotional) role of the second H2O molecule in this process. In support of our previous suggestion that the key intermediate in the low-temperature H2O formation reaction is a mixed OH and H2O overlayer we find that there is a very large barrier for the dissociation of the second H2O molecule in the 2:1 disproportionation process. We suggest that the proposed intermediate is then hydrogenated to H2O through a very facile proton-transfer mechanism.

Ablation of uroplakin III gene results in small urothelial plaques, urothelial leakage, and vesicoureteral reflux

Urothelium synthesizes a group of integral membrane proteins called uroplakins, which form two-dimensional crystals (urothelial plaques) covering >90% of the apical urothelial surface. We show that the ablation of the mouse uroplakin III (UPIII) gene leads to overexpression, defective glycosylation, and abnormal targeting of uroplakin Ib, the presumed partner of UPIII. The UPIII-depleted urothelium features small plaques, becomes leaky, and has enlarged ureteral orifices resulting in the back flow of urine, hydronephrosis, and altered renal function indicators. Thus, UPIII is an integral subunit of the urothelial plaque and contributes to the permeability barrier function of the urothelium, and UPIII deficiency can lead to global anomalies in the urinary tract. The ablation of a single urothelial-specific gene can therefore cause primary vesicoureteral reflux (VUR), a hereditary disease affecting approximately 1% of pregnancies and representing a leading cause of renal failure in infants. The fact that VUR caused by UPIII deletion seems distinct from that caused by the deletion of angiotensin receptor II gene suggests the existence of VUR subtypes. Mutations in multiple gene, including some that are urothelial specific, may therefore cause different subtypes of primary reflux. Studies of VUR in animal models caused by well-defined genetic defects should lead to improved molecular classification, prenatal diagnosis, and therapy of this important hereditary problem.

Understanding complete oxidation of methane on spinel oxides at a molecular level

It is crucial to develop a catalyst made of earth-abundant elements highly active for a complete oxidation of methane at a relatively low temperature. NiCo2O4 consisting of earth-abundant elements which can completely oxidize methane in the temperature range of 350-550 °C. Being a cost-effective catalyst, NiCo2O4 exhibits activity higher than precious-metal-based catalysts. Here we report that the higher catalytic activity at the relatively low temperature results from the integration of nickel cations, cobalt cations and surface lattice oxygen atoms/oxygen vacancies at the atomic scale. In situ studies of complete oxidation of methane on NiCo2O4 and theoretical simulations show that methane dissociates to methyl on nickel cations and then couple with surface lattice oxygen atoms to form -CH3O with a following dehydrogenation to -CH2O; a following oxidative dehydrogenation forms CHO; CHO is transformed to product molecules through two different sub-pathways including dehydrogenation of OCHO and CO oxidation.

A role for PML and the nuclear body in genomic stability

The PML gene of acute promyelocytic leukemia (APL) encodes a cell-growth and tumor suppressor. PML localizes to discrete nuclear bodies (NBs) that are disrupted in APL cells. The Bloom syndrome gene BLM encodes a RecQ DNA helicase, whose absence from the cell results in genomic instability epitomized by high levels of sister-chromatid exchange (SCE) and cancer predisposition. We show here that BLM co-localizes with PML to the NB. In cells from persons with Bloom syndrome the localization of PML is unperturbed, whereas in APL cells carrying the PML-RARalpha oncoprotein, both PML and BLM are delocalized from the NB into microspeckled nuclear regions. Treatment with retinoic acid (RA) induces the relocalization of both proteins to the NB. In primary PML-/- cells, BLM fails to accumulate in the NB. Strikingly, in PML-/- cells the frequency of SCEs is increased relative to PML+/+ cells. These data demonstrate that BLM is a constituent of the NB and that PML is required for its accumulation in these nuclear domains and for the normal function of BLM. Thus, our findings suggest a role for BLM in APL pathogenesis and implicate the PML NB in the maintenance of genomic stability.

DFT and In Situ EXAFS Investigation of Gold/Ceria−Zirconia Low-Temperature Water Gas Shift Catalysts: Identification of the Nature of the Active Form of Gold

A combined experimental and theoretical investigation of the nature of the active form of gold in oxide-supported gold catalysts for the water gas shift reaction has been performed. In situ extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) experiments have shown that in the fresh catalysts the gold is in the form of highly dispersed gold ions. However, under water gas shift reaction conditions, even at temperatures as low as 100 degrees C, the evidence from EXAFS and XANES is only consistent with rapid, and essentially complete, reduction of the gold to form metallic clusters containing about 50 atoms. The presence of Au-Ce distances in the EXAFS spectra, and the fact that about 15% of the gold atoms can be reoxidized after exposure to air at 150 degrees C, is indicative of a close interaction between a fraction (ca. 15%) of the gold atoms and the oxide support. Density functional theory (DFT) calculations are entirely consistent with this model and suggest that an important aspect of the active and stable form of gold under water gas shift reaction conditions is the location of a partially oxidized gold (Audelta+) species at a cerium cation vacancy in the surface of the oxide support. It is found that even with a low loading gold catalysts (0.2%) the fraction of ionic gold under water gas shift conditions is below the limit of detection by XANES (<5%). It is concluded that under water gas shift reaction conditions the active form of gold comprises small metallic gold clusters in intimate contact with the oxide support.