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PubMed1997

Oxidation Reactions of Dithiocarbamate Complexes of Ruthenium(II).

The reaction of Ru(Et(2)dtc)(2)(DMSO)(2) (Et(2)dtc = N,N-diethyldithiocarbamate; DMSO = dimethyl sulfoxide) with t-BuNC gave trans-Ru(Et(2)dtc)(2)(CN-t-Bu)(2), 1. Complex 1 crystallizes in the monoclinic space group P2(1)/n with a = 9.753(2) Å, b = 11.583(2) Å, c = 12.974(2) Å, and beta = 91.8(2) degrees for Z = 2. The crystal structure of 1 shows the trans disposition of the two isocyanides; the mean Ru-S and Ru-C distances are 2.409 and 1.977(2) Å, respectively. Treatment of [Ru(diene)Cl(2)](n)() with Na(Et(2)dtc) afforded Ru(Et(2)dtc)(2)(diene) (diene = bicyclo[2.2.1]hepta-2,5-diene (NBD), 2, 1,5-cyclooctadiene (COD), 3). Complex 2 crystallizes in the triclinic space group P&onemacr; with a = 7.316(1) Å, b = 10.346(1) Å, c = 15.123(2) Å, alpha = 103.69(2) degrees, beta = 93.54(2) degrees, and gamma = 100.61(2) degrees for Z = 2. The mean Ru-S and Ru-C distances in 2 are 2.416 and 2.137 Å, respectively. The reaction of cis-Ru(Et(2)dtc)(2)(CO)(2) with iodine gave the 2:1 molecular iodine complex cis-Ru(Et(2)dtc)(2)(CO)(2).(1)/(2)I(2) 4, which crystallizes in the monoclinic space group P2(1)/c with a = 7.347(2), b = 22.227(2) Å, c = 12.891(2) Å, and beta =95.98 (2) degrees for Z = 4. The mean Ru-S and Ru-C and the I-I distances in complex 4 are 2.427, 1.903, and 2.745(1) Å, respectively. Treatment of Ru(Et(2)dtc)(2)(DMSO)(2) with I(2) gave the linear Ru(II)-Ru(III)-Ru(III) trimer [Ru(3)(Et(2)dtc)(6)(DMSO)(2)](I(3))(2), 5, which crystallizes in the triclinic space group P&onemacr; with a = 14.125(3) Å, b = 20.829(6) Å, c = 13.658(3) Å, alpha = 97.57(2) degrees, beta = 110.01(2) degrees, and gamma = 71.25(2) degrees for Z = 2. The structure of complex 6 can be viewed as consisting of a {Ru(2)(III)(Et(2)dtc)(4)}(2+) core and a {Ru(II)(Et(2)dtc)(2)(DMSO)(2)} moiety, which are linked together via the two dithiocarbamate sulfurs of the latter. While the two Ru(III) centers are connected by a Ru-Ru single bond (Ru-Ru = 2.826(2) Å), there is no direct interaction between the Ru(III) and Ru(II) centers. Oxidation of Ru(Et(2)dtc)(2)L(2) (L = PPh(3), t-BuNC) by I(2) gave the respective [Ru(Et(2)dtc)(2)L(2)](+) cations. The reaction of cis-Ru(Et(2)dtc)(2)(PPh(3))(2) with excess tosyl azide gave the diamagnetic Ru(IV) tetrazene complex Ru(Et(2)dtc)(2)(Ts(2)N(4)), 7. Complex 7 crystallizes in the triclinic space group P&onemacr; with a = 10.380(1) Å, b = 11.322(1) Å, c = 15.310(1) Å, alpha = 106.84(2) degrees, beta = 106.87(2) degrees, and gamma = 92.63(2) degrees for Z = 2. The Ru-S and Ru-N(alpha) distances in 7 are 2.385 and 1.98 Å, respectively. The formal potentials of the Ru dithiocarbamate complexes were determined by cyclic voltammetry.

Journal Article↗
PubMed2003

An improved method for Lewis acid catalyzed phosphoryl transfer with Ti(t-BuO)4.

Several inorganic esters have been evaluated as phosphoryl transfer catalysts. Of these, Ti(t-BuO)(4) was found to be the most effective catalyst giving excellent yields of the desired phosphate esters. The loading of the catalyst could be reduced to a little as 5 mol % for a majority of substrates with no loss in the yield of product. This methodology is significantly more versatile than using TiCl(4) and is suitable for the phosphorylation of more complex carbohydrates and molecules of biological interest.

Journal Article↗
PubMed2005

Smicl is a novel Smad interacting protein and cleavage and polyadenylation specificity factor associated protein.

Ligand-bound receptors of the Transforming Growth Factor-beta (TGF-beta) family promote the formation of complexes between Smad proteins that subsequently accumulate in the nucleus and interact there with other transcriptional regulators, leading to modulation of target gene expression. We identified a novel nuclear protein, Smicl, which binds to Smad proteins. Smicl and Smads cooperate and enhance TGF-beta mediated activation of a Smad-responsive reporter gene. A domain with five CCCH-type zinc fingers in Smicl is structurally and functionally, at least in vitro, similar to a domain in CPSF-30, the 30 kDa subunit of Cleavage and Polyadenylation Specificity Factor (CPSF). Like CPSF-30, Smicl can associate with some other CPSF subunits characterized previously. Its effect on the induction of a reporter gene for TGF-beta requires the cleavage/polyadenylation signal downstream of the coding sequence of that gene. Thus, Smicl is a novel protein that displays CPSF-30-like activities, interacts in the nucleus with activated Smads, and potentiates in TGF-beta stimulated cells Smad-dependent transcriptional responses, possibly in conjunction with the activity of CPSF complexes.

Activin Receptors, Type I↗
PubMed2022

A graph-based approach for the visualisation and analysis of bacterial pangenomes.

BACKGROUND: The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. RESULTS: Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences. CONCLUSIONS: We anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenome datasets, thereby enhancing interpretation of these complex data.

Bacteria↗
PubMed2006

Structural basis of hepatocyte growth factor/scatter factor and MET signalling.

The polypeptide growth factor, hepatocyte growth factor/scatter factor (HGF/SF), shares the multidomain structure and proteolytic mechanism of activation of plasminogen and other complex serine proteinases. HGF/SF, however, has no enzymatic activity. Instead, it controls the growth, morphogenesis, or migration of epithelial, endothelial, and muscle progenitor cells through the receptor tyrosine kinase MET. Using small-angle x-ray scattering and cryo-electron microscopy, we show that conversion of pro(single-chain)HGF/SF into the active two-chain form is associated with a major structural transition from a compact, closed conformation to an elongated, open one. We also report the structure of a complex between two-chain HGF/SF and the MET ectodomain (MET928) with 1:1 stoichiometry in which the N-terminal and first kringle domain of HGF/SF contact the face of the seven-blade beta-propeller domain of MET harboring the loops connecting the beta-strands b-c and d-a, whereas the C-terminal serine proteinase homology domain binds the opposite "b" face. Finally, we describe a complex with 2:2 stoichiometry between two-chain HGF/SF and a truncated form of the MET ectodomain (MET567), which is assembled around the dimerization interface seen in the crystal structure of the NK1 fragment of HGF/SF and displays the features of a functional, signaling unit. The study shows how the proteolytic mechanism of activation of the complex proteinases has been adapted to cell signaling in vertebrate organisms, offers a description of monomeric and dimeric ligand-receptor complexes, and provides a foundation to the structural basis of HGF/SF-MET signaling.

Animals↗
PubMed1994

MSF, a novel cytoplasmic chaperone which functions in precursor targeting to mitochondria.

Mitochondrial import stimulation factor (MSF) unfolds wheat germ lysate synthesized aggregated mitochondrial precursor proteins and stimulates their mitochondrial import in an ATP dependent manner. Here we analysed the function of MSF mainly by utilizing chemically pure adrenodoxin precursor (pAd). MSF bound to the unfolded pAd and prevented it from losing import competence and also restored the import competence of the aggregated pAd dependent on ATP hydrolysis. The import incompetent aggregated mitochondrial precursors induced the ATPase activity of MSF and the activity was strongly inhibited by isolated mitochondrial outer membrane (OM) but not by trypsin treated outer membrane (tOM). The precursor induced ATPase activity of N-ethylmaleimide (NEM)-treated MSF was not inhibited by OM. In this context, the MSF-precursor complex specifically bound to OM and binding was abolished both by the treatment of OM with trypsin and by the treatment of MSF with NEM. These results show that MSF is a novel cytoplasmic chaperone protein with a mitochondrial precursor-targeting function.

Adenosine Triphosphatases↗
PubMed2003

Thyroid hormones interact with glucocorticoids to affect somatotroph abundance in chicken embryonic pituitary cells in vitro.

Our laboratory has reported that somatotroph differentiation occurs between d 14 and d 16 of chicken embryonic development and that corticosterone (CORT) can induce somatotroph differentiation at an earlier age in vitro and in vivo. The objective of the present study was to test for thyroid hormone-CORT interactions on somatotroph differentiation in vitro. Pituitary cells from d 11 chicken embryos were treated with CORT and thyroid hormones, and GH-producing somatotrophs were detected by reverse hemolytic plaque assays and immunocytochemistry. We found that thyroid hormones can act synergistically with CORT to further augment the abundance of somatotrophs in vitro but have little to no effect on their own. Both T(4) and T(3) could act synergistically with CORT to increase somatotroph abundance, but the effects of T(3) were biphasic, inhibiting CORT actions at higher concentrations. The monodeiodination inhibitor iopanoic acid inhibited the synergistic effect of T(4) on CORT induction of GH cells in vitro but not the synergistic effect of CORT and T(3) or the effect of CORT alone. Furthermore, T(3) treatment overcame the iopanoic acid-induced reduction in the T(4)-CORT effect. Our findings indicate that thyroid hormones act synergistically with CORT to further augment the abundance of somatotrophs in vitro and that conversion of T(4) to T(3) within the pituitary is involved in T(4) modulation of somatotroph abundance. Somatotroph differentiation during normal development may be regulated by complex interactions of hormones produced by the embryonic thyroid and adrenal glands.

Animals↗
PubMed2005

Recruitment of the p97 ATPase and ubiquitin ligases to the site of retrotranslocation at the endoplasmic reticulum membrane.

Misfolded proteins are eliminated from the endoplasmic reticulum (ER) by retrotranslocation into the cytosol, a pathway hijacked by certain viruses to destroy MHC class I heavy chains. The translocation of polypeptides across the ER membrane requires their polyubiquitination and subsequent extraction from the membrane by the p97 ATPase [also called valosin-containing protein (VCP) or, in yeast, Cdc48]. In higher eukaryotes, p97 is bound to the ER membrane by a membrane protein complex containing Derlin-1 and VCP-interacting membrane protein (VIMP). How the ubiquitination machinery is recruited to the p97/Derlin/VIMP complex is unclear. Here, we report that p97 interacts directly with several ubiquitin ligases and facilitates their recruitment to Derlin-1. During retrotranslocation, a substrate first interacts with Derlin-1 before p97 and other factors join the complex. These data, together with the fact that Derlin-1 is a multispanning membrane protein forming homo-oligomers, support the idea that Derlin-1 is part of a retrotranslocation channel that is associated with both the polyubiquitination and p97-ATPase machineries.

Adenosine Triphosphatases↗
PubMed2003

Inhibition of C5a-induced inflammation with preserved C5b-9-mediated bactericidal activity in a human whole blood model of meningococcal sepsis.

The complement system plays an important role in the initial defense against Neisseria meningitidis. In contrast, uncontrolled activation in meningococcal sepsis contributes to the development of tissue damage and shock. In a novel human whole blood model of meningococcal sepsis, we studied the effect of complement inhibition on inflammation and bacterial killing. Monoclonal antibodies (mAbs) blocking lectin and alternative pathways inhibited complement activation by N meningitidis and oxidative burst induced in granulocytes and monocytes. Oxidative burst was critically dependent on CD11b/CD18 (CR3) expression but not on Fc gamma-receptors. Specific inhibition of C5a using mAb 137-26 binding the C5a moiety of C5 before cleavage prohibited CR3 up-regulation, phagocytosis, and oxidative burst but had no effect on C5b-9 (TCC) formation, lysis, and bacterial killing. An mAb-blocking cleavage of C5, preventing C5a and TCC formation, showed the same effect on CR3, phagocytosis, and oxidative burst as the anti-C5a mAb but additionally inhibited TCC formation, lysis, and bacterial killing, consistent with a C5b-9-dependent killing mechanism. In conclusion, the anti-C5a mAb 137-26 inhibits the potentially harmful effects of N meningitidis-induced C5a formation while preserving complement-mediated bacterial killing. We suggest that this may be an attractive approach for the treatment of meningococcal sepsis.

Antibodies, Monoclonal↗
PubMed2006

An evaluation of the metaphylactic effect of ceftiofur crystalline free Acid in feedlot calves.

The relative effect of metaphylactic ceftiofur crystalline free acid (CCFA) versus metaphylactic tilmicosin was evaluated in beef calves under commercial feedlot conditions in Nebraska. At feedlot arrival, 11,605 animals at ultrahigh risk of developing bovine respiratory disease (BRD) were allocated to one of three experimental groups: CCFA-3 (6.6 mg/kg SC), CCFA-7 (6.6 mg/kg), or TILM-3 (tilmicosin, 10 mg/kg SC). Animals were eligible for subsequent BRD treatment 3 (CCFA-3 and TILM-3 groups) or 7 (CCFA-7 group) days later. Compared with the TILM-3 group, overall chronicity, overall mortality, BRD mortality, and metabolic mortality rates were significantly (P < .05) lower in the CCFA-3 and CCFA-7 groups; average daily gain was significantly (P < .05) higher in the CCFA-3 group; the proportion of quality grade No Roll carcasses was significantly (P < .05) lower in the CCFA-3 and CCFA-7 groups; and there were per-animal advantages of 22.05 dollars and 18.98 dollars in the CCFA-3 and CCFA-7 groups, respectively. In beef calves at ultrahigh risk of developing BRD, it is more cost effective to administer metaphylactic CCFA than tilmicosin at feedlot arrival.

Animals↗
PubMed2025

Runaway evolution of telomeres in ascomycetous yeasts was accompanied by the replacement of ancestral telomeric proteins.

Telomeres are crucial parts of eukaryotic chromosomes, contributing to DNA replication, chromosome segregation, and genome stability. While in most phylogenetic lineages, telomere-maintenance systems are conserved, ascomycetous yeasts exhibit a high degree of variability in telomeric repeats and the associated proteins. The determinants that enabled this divergent evolutionary process, however, have been unclear. Here, we show that DNA-binding properties of yeast telomere-binding proteins (TBPs) support the scenario where the gradual divergence of telomeric repeats led to their replacement. We analyzed the DNA-protein interactions between Tay1p from Yarrowia lipolytica, Rap1p from Saccharomyces cerevisiae, and Taz1p from Schizosaccharomyces pombe and a set of telomeric repeats from several yeast species and delineated how the ancestral (Tay1p-like) TBPs were replaced by Rap1p (in budding yeasts) or Taz1p (in fission yeasts). We also postulate two different driving forces for these replacements: (i) Tay1p-to-Rap1p transition appears to be driven by differences in sequence preferences of Tay1p and Rap1p, while (ii) Taz1p became the principal TBP in fission yeast presumably due to its DNA-binding flexibility. Together, our results suggest that in telomeric DNA-protein complexes, the replacement of protein component triggered by the initial variation in DNA sequence space opens the door to further divergence in a runaway-style evolution.

Telomere-Binding Proteins↗
PubMed2003

A modular cross-linking approach for exploring protein interactions.

A method is described for the elucidation of protein-protein interactions using novel cross-linking reagents and mass spectrometry. The method incorporates (1) a modular solid-phase synthetic strategy for generating the cross-linking reagents, (2) enrichment and digestion of cross-linked proteins using microconcentrators, (3) mass spectrometric analysis of cross-linked peptides, and (4) comprehensive computational analysis of the cross-linking data. This integrated approach has been applied to the study of cross-linking between the components of the heterodimeric protein complex negative cofactor 2.

Acrylic Resins↗
PubMed2004

Candidate defense genes as predictors of quantitative blast resistance in rice.

Although quantitative trait loci (QTL) underpin many desirable agronomic traits, their incorporation into crop plants through marker-assisted selection is limited by the low predictive value of markers on phenotypic performance. Here we used candidate defense response (DR) genes to dissect quantitative resistance in rice using recombinant inbred (RI) and advanced backcross (BC) populations derived from a blast-resistant cultivar, Sanhuangzhan 2 (SHZ-2). Based on DNA profiles of DR genes, RI lines were clustered into two groups corresponding to level of resistance. Five DR genes, encoding putative oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein, accounted for 30.0, 23.0, 15.8, 6.7, and 5.5% of diseased leaf area (DLA) variation, respectively. Together, they accounted for 60.3% of the DLA variation and co-localized with resistance QTL identified by interval mapping. Average phenotypic contributions of oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein in BC lines were 26.1, 19.0, 18.0, 11.5, and 10.6%, respectively, across environments. Advanced BC lines with four to five effective DR genes showed enhanced resistance under high disease pressure in field tests. Our results demonstrate that the use of natural variation in a few candidate genes can solve a long-standing problem in rice production and has the potential to address other problems involving complex traits.

DNA, Plant↗
PubMed2002

Nonlinear methods of biosignal analysis in assessing terbutaline-induced heart rate and blood pressure changes.

The aim of this study was to characterize how different nonlinear methods characterize heart rate and blood pressure dynamics in healthy subjects at rest. The randomized, placebo-controlled crossover study with intravenous terbutaline was designed to induce four different stationary states of cardiovascular regulation system. The R-R interval, systolic arterial blood pressure, and heart rate time series were analyzed with a set of methods including approximate entropy, sample entropy, Lempel-Ziv entropy, symbol dynamic entropy, cross-entropy, correlation dimension, fractal dimensions, and stationarity test. Results indicate that R-R interval and systolic arterial pressure subsystems are mutually connected but have different dynamic properties. In the drug-free state the subsystems share many common features. When the strength of the baroreflex feedback loop is modified with terbutaline, R-R interval and systolic blood pressure lose mutual synchrony and drift toward their inherent state of operation. In this state the R-R interval system is rather complex and irregular, but the blood pressure system is much simpler than in the drug-free state.

Adult↗
PubMed2005

Structure and evolution of the mouse pregnancy-specific glycoprotein (Psg) gene locus.

BACKGROUND: The pregnancy-specific glycoprotein (Psg) genes encode proteins of unknown function, and are members of the carcinoembryonic antigen (Cea) gene family, which is a member of the immunoglobulin gene (Ig) superfamily. In rodents and primates, but not in artiodactyls (even-toed ungulates / hoofed mammals), there have been independent expansions of the Psg gene family, with all members expressed exclusively in placental trophoblast cells. For the mouse Psg genes, we sought to determine the genomic organisation of the locus, the expression profiles of the various family members, and the evolution of exon structure, to attempt to reconstruct the evolutionary history of this locus, and to determine whether expansion of the gene family has been driven by selection for increased gene dosage, or diversification of function. RESULTS: We collated the mouse Psg gene sequences currently in the public genome and expressed-sequence tag (EST) databases and used systematic BLAST searches to generate complete sequences for all known mouse Psg genes. We identified a novel family member, Psg31, which is similar to Psg30 but, uniquely amongst mouse Psg genes, has a duplicated N1 domain. We also identified a novel splice variant of Psg16 (bCEA). We show that Psg24 and Psg30 / Psg31 have independently undergone expansion of N-domain number. By mapping BAC, YAC and cosmid clones we described two clusters of Psg genes, which we linked and oriented using fluorescent in situ hybridisation (FISH). Comparison of our Psg locus map with the public mouse genome database indicates good agreement in overall structure and further elucidates gene order. Expression levels of Psg genes in placentas of different developmental stages revealed dramatic differences in the developmental expression profile of individual family members. CONCLUSION: We have combined existing information, and provide new information concerning the evolution of mouse Psg exon organization, the mouse Psg genomic locus structure, and the expression patterns of individual Psg genes. This information will facilitate functional studies of this complex gene family.

Alternative Splicing↗
PubMed2006

Entropy and barrier-controlled fluctuations determine conformational viscoelasticity of single biomolecules.

Biological macromolecules have complex and nontrivial energy landscapes, endowing them with a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is important to molecular biology and emerging fields such as nanotechnology. Here we analyze single molecule fluctuations in an atomic force microscope, using a generic model of biopolymer viscoelasticity that includes local "internal" conformational dissipation. Comparing two biopolymers, dextran and cellulose (polysaccharides with and without local bistable transitions), demonstrates that signatures of simple conformational change are minima in both the elastic and internal friction constants around a characteristic force. A novel analysis of dynamics on a bistable energy landscape provides a simple explanation: an elasticity driven by the entropy, and friction by a barrier-controlled hopping time of populations between states, which is surprisingly distinct to the well-known relaxation time. This nonequilibrium microscopic analysis thus provides a means of quantifying new dynamical features of the energy landscape of the glucopyranose ring, revealing an unexpected underlying roughness and information on the shape of the barrier of the chair-boat transition in dextran. The results presented herein provide a basis toward probing the viscoelasticity of macromolecular conformational transitions on more complex energy landscapes, such as during protein folding.

Biopolymers↗
PubMed2006

Potential roles for ubiquitin and the proteasome during ribosome biogenesis.

We have investigated the possible involvement of the ubiquitin-proteasome system (UPS) in ribosome biogenesis. We find by immunofluorescence that ubiquitin is present within nucleoli and also demonstrate by immunoprecipitation that complexes associated with pre-rRNA processing factors are ubiquitinated. Using short proteasome inhibition treatments, we show by fluorescence microscopy that nucleolar morphology is disrupted for some but not all factors involved in ribosome biogenesis. Interference with proteasome degradation also induces the accumulation of 90S preribosomes, alters the dynamic properties of a number of processing factors, slows the release of mature rRNA from the nucleolus, and leads to the depletion of 18S and 28S rRNAs. Together, these results suggest that the UPS is probably involved at many steps during ribosome biogenesis, including the maturation of the 90S preribosome.

Cell Line↗