Functions and intramolecular interactions of ribosomal RNA in decoding of termination codons

Two regions in the 3$\prime$ domain of 16S rRNA (the RNA of the small ribosomal subunit) have been implicated in decoding of termination codons. Using segment-directed PCR random mutagenesis, I isolated 33 translational suppressor mutations in the 3$\prime$ domain of 16S rRNA. Characterization of the mutations by both genetic and biochemical methods indicated that some of the mutations are defective in UGA-specific peptide chain termination and that others may be defective in peptide chain termination at all termination codons. The studies of the mutations at an internal loop in the non-conserved region of helix 44 also indicated that this structure, in a non-conserved region of 16S rRNA, is involved in both peptide chain termination and assembly of 16S rRNA.^ With a suppressible trpA UAG nonsense mutation, a spontaneously arising translational suppressor mutation was isolated in the rrnB operon cloned into a pBR322-derived plasmid. The mutation caused suppression of UAG at two codon positions in trpA but did not suppress UAA or UGA mutations at the same trpA positions. The specificity of the rRNA suppressor mutation suggests that it may cause a defect in UAG-specific peptide chain termination. The mutation is a single nucleotide deletion (G2484$\Delta$) in helix 89 of 23S rRNA (the large RNA of the large ribosomal subunit). The result indicates a functional interaction between two regions of 23S rRNA. Furthermore, it provides suggestive in vivo evidence for the involvement of the peptidyl-transferase center of 23S rRNA in peptide chain termination. The $\Delta$2484 and A1093/$\Delta$2484 (double) mutations were also observed to alter the decoding specificity of the suppressor tRNA lysT(U70), which has a mutation in its acceptor stem. That result suggests that there is an interaction between the stem-loop region of helix 89 of 23S rRNA and the acceptor stem of tRNA during decoding and that the interaction is important for the decoding specificity of tRNA.^ Using gene manipulation procedures, I have constructed a new expression vector to express and purify the cellular protein factors required for a recently developed, realistic in vitro termination assay. The gene for each protein was cloned into the newly constructed vector in such a way that expression yielded a protein with an N-terminal affinity tag, for specific, rapid purification. The amino terminus was engineered so that, after purification, the unwanted N-terminal tag can be completely removed from the protein by thrombin cleavage, yielding a natural amino acid sequence for each protein. I have cloned the genes for EF-G and all three release factors into this new expression vector and the genes for all the other protein factors into a pCAL-n expression vector. These constructs will allow our laboratory group to quickly and inexpensively purify all the protein factors needed for the new in vitro termination assay. (Abstract shortened by UMI.) ^

Cloning of a protease gene family of Fasciola hepatica by the polymerase chain reaction

Degenerate oligonucleotide primers derived from conserved cysteine protease sequences were used in the reverse transcription polymerase chain reaction to amplify seven different cysteine protease cDNA clones, Fcp1-7, from RNA isolated from adult Fasciola hepatica. Five of the amplified F. hepatica sequences showed homology to the cathepsin L type and two were more related to the cathepsin B type. Southern blot analysis suggests that some members of this protease gene family are present in multiple copies. Northern blot analysis revealed differences in the levels of steady state mRNA expression for some of these proteases. The 5' and the 3' regions of Fcp1 were amplified using the rapid amplification of cDNA ends PCR protocol (RACE-PCR) and an additional clone was obtained by screening a lambda gt10 cDNA library using Fcp1 as a probe. The Fcp1 cDNA fragment was also subcloned in the expression vector pGEX and expressed as a glutathione-S-transferase (GST) fusion protein in Escherichia coli. Antibodies, raised in rabbits against the GST:Fcp1 fusion protein, were used in western blot analysis to examine expression in different life-cycle stages of F. hepatica. In extracts from adult and immature parasites, the immune serum recognised predominantly two proteins of 30 kDa and 38 kDa. In other parasite stages, proteins of different molecular weight were recognised by the anti-GST:Fcp1 antiserum, indicating stage-specific gene expression or processing of Fcp1. In gelatine substrate gel analysis, strong proteolytic activity could be detected at 30 kDa, but not at 38 kDa, suggesting that the 30 kDa protein represents the mature enzyme and the 38 kDa protein the proenzyme.

Ovarian cancer angiogenesis, biology and therapy

The progressive growth of epithelial ovarian cancer tumor is regulated by proangiogenic molecules and growth factors released by tumor cells and the microenvironment. Previous studies showed that the expression of interleukin-8 (IL-8) directly correlates with the progression of human ovarian carcinomas implanted into the peritoneal cavity of nude mice. We examined the expression level of IL-8 in archival specimens of primary human ovarian carcinoma from patients undergoing curative surgery by in situ mRNA hybridization technique. The expression of IL-8 was significantly higher in patients with stage III disease than in patients with stage I disease. To investigate the role of IL-8 in the progressive growth of ovarian cancer, we isolated high- and low-IL-8 producing clones from parental Hey-A8 human ovarian cancer cells, and compared their proliferative activity and tumorigenicity in nude mice. The effect of exogenous IL-8 and IL-8 neutralizing antibody on ovarian cancer cell proliferation was investigated. Finally, we studied the modulation of IL-8 expression in ovarian cancer cells by sense and antisense IL-8 expression vector transfection and its effect on proliferation and tumorigenicity. We concluded that IL-8 has a direct growth potentiating activity in human ovarian cancer cells. ^ The expression level of IL-8 directly correlates with disease progression of human ovarian cancer, but the mechanism of induction is unknown. Since hypoxia and acidic pH are common features in solid tumors, we determined whether hypoxic and acidic conditions could regulate the expression of IL-8. Culturing the human ovarian cancer cells in hypoxic or acidic medium led to a significant increase in IL-8 mRNA and protein. Hypoxic- and acidosis-mediated transient increase in IL-8 expression involved both transcriptional activation of the IL-8 gene and enhanced stability of the IL-8 mRNA. Furthermore, we showed that IL-8 transcription activation by hypoxia or acidosis required the cooperation of NF-κB and AP-1 binding sites. ^ Finally, we studied novel therapies against human ovarian cancer. First, we determined whether inhibition of the catalytic tyrosine kinase activity of the receptors for vascular endothelial growth factor/vascular permeability factor (VEGF/VPF) inhibits the formation of malignant ascites and the progressive growth of human ovarian carcinoma cells implanted into the peritoneal cavity of nude mice. Our results suggest that blockade of the VEGF/VPF receptor may be an efficient strategy to inhibit formation of malignant ascites and growth of VEGF/VPF-dependent human ovarian carcinomas. Secondly, we determined whether local sustained production of murine interferon-β could inhibit the growth of human ovarian cancer cells in the peritoneal cavity of nude mice. Our results showed that local production of IFN-β could inhibit the in vivo growth of human ovarian cancer cells by upregulating the expression of the inducible nitric oxide synthase (NOS) in host macrophages. ^

Functional differences of beta-tubulin isotypes: A study of microtubule assembly and antimitotic drug resistance

Mammalian cells express 7 β-tubulin isotypes in a tissue specific manner. This has long fueled the speculation that different isotypes carry out different functions. To provide direct evidence for their functional significance, class III, IVa, and VI β-tubulin cDNAs were cloned into a tetracycline regulated expression vector and stably transfected Chinese hamster ovary cell lines expressing different levels of ectopic β-tubulin were compared for effects on microtubule organization, microtubule assembly and sensitivity to antimitotic drugs. It was found that all three isotypes coassembled with endogenous β-tubulin. βVI expression caused distinct microtubule rearrangements including microtubule dissociation from the centrosome and accumulation at the cell periphery; whereas expression of βIII and βVIa caused no observable changes in the interphase microtubule network. Overexpression of all 3 isotypes caused spindle malformation and mitotic defects. Both βIII and βIVa disrupted microtubule assembly in proportion to their abundance and thereby conferred supersensitivity to microtubule depolymerizing drugs. In contrast, βVI stabilized microtubules at low stoichiometry and thus conferred resistance to many microtubule destabilizing drugs but not vinblastine. The 3 isotypes caused differing responses to microtubule stabilizing drugs. Expression of βIII conferred paclitaxel resistance while βVI did not. Low expression of βIVa caused supersensitivity to paclitaxel, whereas higher expression resulted in the loss of supersensitivity. The results suggest that βIVa may possess an enhanced ability to bind paclitaxel that increases sensitivity to the drug and acts substoichiometrically. At high levels of βVIa expression, however, microtubule disruptive effects counteract the assembly promoting pressure exerted by increased paclitaxel binding, and drug supersensitivity is lost. From this study, I concluded that β-tubulin isotypes behave differently from each other in terms of microtubule organization, microtubule assembly and dynamics, and antimitotic drug sensitivity. The isotype composition of cell can impart subtle to dramatic effects on the properties of microtubules leading to potential functional consequences and opening the opportunity to exploit differences in microtubule isotype composition for therapeutic gain. ^

Protease-activated receptor-1 signaling plays a major role in melanoma growth and metastasis

Overexpression of the thrombin receptor (Protease-Activated-Receptor-1), PAR-1, in cell lines and tissue specimens correlates with the metastatic potential of human melanoma. Utilizing lentiviral shRNA to stably silence PAR-1 in metastatic melanoma cell lines results in decreased tumor growth and lung metastasis in vivo. Since the use of viral technology is not ideal for clinical therapies, neutral liposomes (DOPC) were utilized as a delivery vehicle for PAR-1 siRNA. Our data suggest that PAR-1 siRNA-DOPC treatment by systemic delivery significantly decreases tumor growth and lung metastasis in nude mice. Concomitant decreases in angiogenic and invasive factors (IL-8, VEGF, MMP-2) were observed in PAR-1 siRNA-DOPC-treated mice. Utilizing a cDNA microarray platform, several novel PAR-1 downstream target genes were identified, including Connexin 43 (Cx-43) and Maspin. Cx-43, known to be involved in tumor cell diapedesis and attachment to endothelial cells, is decreased after PAR-1 silencing. Furthermore, the Cx-43 promoter activity was significantly inhibited in PAR-1-silenced cells suggesting transcriptional regulation of Cx-43 by PAR-1. ChIP analysis revealed a reduction in SP-1 and AP-1 binding to the Cx-43 promoter. Moreover, melanoma cell attachment to HUVEC was significantly decreased in PAR-1-silenced cells as well as in Cx-43 shRNA transduced cells. As both SP-1 and AP-1 transcription factors act as positive regulators of Cx-43, our data provide a novel mechanism for the regulation of Cx-43 expression by PAR-1. Maspin, a serine protease inhibitor with tumor-suppressor function, was found to be upregulated after PAR-1 silencing. Our results indicate that PAR-1 transcriptionally regulates Maspin, as the promoter activity was significantly increased after PAR-1 silencing. ChIP analysis revealed that silencing PAR-1 increased binding of Ets and c-Jun to the Maspin promoter. As Maspin was recently found to be a tumor-suppressor in melanoma by reducing the invasive capacity of melanoma cells, invasion assays revealed a decrease in invasion after PAR-1 silencing and in cells transduced with a Maspin expression vector. We propose that PAR-1 is key to the progression and metastasis of melanoma in part by regulating the expression of Cx-43 and Maspin. Taken together, we propose that PAR-1 is an attractive target for the treatment of melanoma.^

Aberrant regulation of the Src -FAK signaling pathway in the human colon adenocarcinoma cell line HT-29

c-Src, a protein tyrosine kinase (PTK) the specific activity of which is increased $>$20-fold in $\sim$80% of colon tumors and colon tumor cell lines, plays a role in both growth regulation and tumorigenicity of colon tumor cells. To examine the effect of increased c-Src specific activity on colon tumor cells, coumarin-derived tyrosine analog PTK inhibitors were assessed in a standard colon tumor cell line, HT-29. Of the nine compounds tested for inhibiting c-Src activity in a standard immune complex kinase assay from c-Src precipitated from HT-29 cells, the 7,8-dihydroxy-containing compounds daphnetin and fraxetin were most effective, with IC$\sb{50}$s of 0.6 $\pm$ 0.2 mM and 0.6 $\pm$ 0.3 mM, respectively. Treatment of HT-29 cells with daphnetin resulted in inhibition of cell growth in a dose-dependent manner. In contrast, scopoletin, a relatively poor Src inhibitor in vitro, did not inhibit HT-29 cell growth in the concentration range tested. In daphnetin treated cells, a dose-dependent decrease of c-Src activity paralleling cell growth inhibition was also observed; the IC$\sb{50}$ was 0.3 $\pm$ 0.1 mM for c-Src autophosphorylation. In contrast, the IC$\sb{50}$ for c-Src protein level was $>$ 0.6 mM, indicating that the effects of daphnetin were primarily an enzymatic activity of c-Src, rather than protein level in HT-29 cells. These results are the first to demonstrate that c-Src specific activity regulates colon tumor cell growth.^ To elucidate the signaling pathways activated by c-Src in colon tumor cells, the Src family substrate FAK, which has been shown to play a role in both extracellular matrix-dependent cell growth and survival, was examined. Coprecipitation assays showed Src-FAK association in detergent insoluble fractions of both attached and detached HT-29 cells, indicating that Src-FAK association in HT-29 cells is stable and, unlike untransformed cells, not dependent on cell-substratum contact. FAK also coprecipitated with Grb2, an adaptor protein also playing a role in cell proliferation and survival, in both attached and detached HT-29 cells, suggesting that a Src-FAK-Grb2-mediated signaling pathway(s) in HT-29 cells is/are constitutively activated.^ FAK was also analyzed in c-src antisense HT-29 clones AS15 and AS33 in which c-Src is specifically reduced by transfection of an antisense expression vector. FAK protein level is unexpectedly decreased in both AS15 and AS33 cells by 5-fold and 1.5-fold compared to HT-29, respectively, corresponding with the decreased expression of c-Src observed in these cells. FAK protein level was not decreased compared to parental in the c-src "sense" clone S8. Northern blot analyses showed decreased FAK mRNA levels compared to parental in AS15 and AS33, correlating with decreased FAK protein level, indicating that FAK activity in the antisense cells is regulated, at least in part, by altering FAK expression, and that this regulation is Src dependent. Because FAK has been implicated in anoikis, the ability of c-src antisense cells to survive in the absence of cell-substratum contact was examined. Decreased cell survival is seen in both AS15 and AS33, correlating with the decreases in c-Src and FAK levels and tumorigenicity in these cells. These results suggest that at least one mechanism by which activation of c-Src contributes to tumorigenic phenotype of colon tumor cells is by aberrantly promoting a survival signal through unregulated Src-FAK-Grb2 complexes. (Abstract shortened by UMI.) ^

Plasmid -encoded virulence determinants of Borrelia burgdorferi

Borrelia burgdorferi, a spirochete and the causative agent of Lyme disease, infects both mammals and ticks. Its genome, sequenced in 1997, consists of one linear chromosome and over 20 linear and circular plasmids. Continuous passage of organisms in culture causes them to lose certain plasmids and also results in loss of infectivity in mammals. In this work, 19 B. burgdorferi clonal isolates were examined for infectivity in mice and for plasmid content utilizing polymerase chain reaction (PCR). Two plasmids, a 28 kilobase (kb) linear plasmid (Ip28-1) and a 25 kb linear plasmid (Ip25) were found to be required for full infectivity. Previous studies had demonstrated that Ip28-1 contains the vls locus, which is involved in antigenic variation and immune evasion. Gene BBE22 on Ip25 is predicted to encode the nicotinamidase PncA, an enzyme that converts nicotinamide to nicotinic acid as part of a pathway for NAD synthesis. To examine the potential role of BBE22 in infectivity, a shuttle vector containing BBE22 (pBBE22) was constructed and used to transform B. burgdorferi clone 5A13, which contains all plasmids except lp25. Transformation with pBBE22 restored infectivity of clone 5A13 in mice, whereas 5A13 transformed with the shuttle vector alone was not infectious. To determine whether BBE22 acts as a nicotinamidase in vivo, a Salmonella typhimurium pncA− nadB− transposon mutant was transformed with pBBE22 or with pQE30:BBE22, which contained BBE22 in an E. coli expression vector. Both constructs complemented the Salmonella mutant, permitting growth in minimal media plus nicotinamide. Salmonella cells over-expressing BBE22 also exhibited nicotinamidase activity, as determined by ammonia production in the presence of nicotinamide. Site-directed mutagenesis of BBE22 at the predicted active site (resulting in a Cys120Ala substitution) abrogated the ability to restore infectivity to B. burgdorferi 5A13 and to complement the pncA mutation in S. typhimurium. These studies indicate that BBE22 is a nicotinamidase required for NAD synthesis and survival of B. burgdorferi in mammals. This is also the first demonstration of ‘molecular Koch's postulates’ in B. burgdorferi, i.e. that a specific gene is essential for infectivity of the Lyme disease spirochete. ^

Roles of p38 mitogen-activated protein kinase pathway in the regulation of SOX9 activity and chondrogenesis

Sox9 is a master transcription factor in chondrocyte differentiation. Several lines of evidence suggest that the p38 mitogen-activated protein kinase (MAPK) pathway is involved in chondrocyte differentiation. In the present study, we examined the roles of p38 in the regulation of SOX9 activity and chondrogenesis. ^ COS7 cells were transfected with a SOX9 expression vector and 4x48-p89, a luciferase construction harboring four tandem copies of a SOX9-dependent 48-bp enhancer in Col2a1. Coexpression of MKK6EE, a constitutively active mutant of MKK6, a MAPKK that specifically activates p38, further increased the activity of the SOX9-dependent 48-bp enhancer about 5-fold, and SOX9 protein levels were not increased under these conditions. This increase in enhancer activity was not observed in a mutant enhancer construct harboring mutations that abolish SOX9 binding. These data strongly suggested that activation of the p38 pathway results in increased activity of SOX9. In addition, the increase of the activity of the SOX9-dependent 48-bp enhancer by MKK6EE was also observed in primary chondrocytes, and this increase was abolished by coexpression of a p38 phosphatase, MKP5, and p38 specific inhibitors. Furthermore, treatment of primary chondrocytes with p38 inhibitors decreased the expression of Col2a1, a downstream target of Sox9, without affecting Sox9 RNA levels, further supporting the hypothesis that p38 plays a role in regulating Sox9 activity in chondrocytes. ^ To further study the role of the p38 MAPK pathway in chondrogenesis, we generated transgenic mice that express MKK6EE in chondrocytes under the control of the Col2a1 promoter/intron regulatory sequences. These mice showed a dwarf phenotype characterized by reduced chondrocyte proliferation and a delay in the formation of primary and secondary ossification centers. Histological analysis using in situ hybridization showed reduced expression of Indian hedgehog, PTH/PTHrP receptor, cyclin D1 and increased expression of p21. In addition, consistent with the notion that Sox9 activity was increased in these mice, transgenic mice that express MKK6EE in chondrocytes showed phenotypes similar to those of mice that overexpress SOX9 in chondrocytes. Therefore, our study provides in vivo evidence for the role of p38 in chondrocyte differentiation and suggests that Sox9 is a downstream target of the p38 MAPK pathway. ^

Proceedings of the Eighteenth Annual Biochemical Engineering Symposium

The eighteenth annual biochemical engineering symposium was held during April 22–23, 1988 at the YMCA of the Rockies conference center in Estes Park, Colorado, under the sponsorship of the University of Colorado. Previous symposia in this series have been hosted by Kansas State University (1st, 3rd, 5th, 9th, 12th, 16th), University of Nebraska-Lincoln (2nd, 4th), Iowa State University (6th, 7th, l0th, 13th, 17th), University of Missouri–Columbia (8th, 14th), and Colorado State University (11th, 15th). Next year's symposium is scheduled to be held at the University of Missouri-Columbia. The symposia are devoted to talks by students about their ongoing research. Because final publication usually takes place elsewhere, the papers included in the proceedings are brief, and often cover work in progress. ContentsApplications of mass spectrometers in biochemical engineeringJohn P. McDonald, Ayush Gupta, and Lourdes Taladriz, Kansas State University Enzymatic hydrolysis of corn gluten proteinsJulie Hardwick; Iowa State University Improved Acetone-Butanol Fermentation AnalysisZ. Buday; Colorado State University On-Line State Identification for Batch FermentationD. A. Gee and W. F. Ramirez; University of Colorado Role of Spargers in Air-Lift ReactorsPeter U. Sohn and Rakesh K. Bajpai; University of Missouri–Columbia The Interaction of Microcarriers and Turbulence within an Airlift FermenterG. Travis Jones; Kansas State University Oxygen Diffusion in the Inter-Fiber Gel/Cell Matrix of NMR-Compatible Hollow Fiber Bio-ReactorsS. L. Hanson, B. E. Dale, and R. J. Gillies; Colorado State University Characterization of Ca-alginate Gel Beads FormationHorngtwu Su, Rakesh K. Bajpai, and George W. Preckshot; University of Missouri–Columbia Metabolic Effects of Chloramphenicol Resistance in the Recombinant Host/Vector System: E. coli RRl [pBR329]William E. Bentley, Dana C. Andersen, Dhinakar S. Kompala, and Robert H. Davis; University of Colorado Genetic Engineering of Beta-Galactosidase to Aid in Fermentation Product Recovery by Polyelectrolyte PrecipitationD. E. Parker, C. E. Glatz, J. Zhao, C. F. Ford, S. M. Gendel, and M. A. Rougvie; Iowa State University Biodegradation of Organic Compounds in SoilLourdes Taladriz, L. E. Erickson, and L. T. Fan; Kansas State University Effect of Dilution, pH and Nutrient Composition on the Biodegradation of Metalworking FluidsAyush Gupta, L. E. Erickson, and L. T. Fan; Kansas State University Dissolved Hydrogen Correlation with Redox Potential in Acetone-Butanol FermentationXiangdong Zhou; Colorado State University Modeling of Ensiling Fermentation of Sweet SorghumA. K. Hilaly; Colorado State University

Caracterización de un robot para aplicaciones de mecanizado con requerimientos de tolerancias

El presente Trabajo fin Fin de Máster, versa sobre una caracterización preliminar del comportamiento de un robot de tipo industrial, configurado por 4 eslabones y 4 grados de libertad, y sometido a fuerzas de mecanizado en su extremo. El entorno de trabajo planteado es el de plantas de fabricación de piezas de aleaciones de aluminio para automoción. Este tipo de componentes parte de un primer proceso de fundición que saca la pieza en bruto. Para series medias y altas, en función de las propiedades mecánicas y plásticas requeridas y los costes de producción, la inyección a alta presión (HPDC) y la fundición a baja presión (LPC) son las dos tecnologías más usadas en esta primera fase. Para inyección a alta presión, las aleaciones de aluminio más empleadas son, en designación simbólica según norma EN 1706 (entre paréntesis su designación numérica); EN AC AlSi9Cu3(Fe) (EN AC 46000) , EN AC AlSi9Cu3(Fe)(Zn) (EN AC 46500), y EN AC AlSi12Cu1(Fe) (EN AC 47100). Para baja presión, EN AC AlSi7Mg0,3 (EN AC 42100). En los 3 primeros casos, los límites de Silicio permitidos pueden superan el 10%. En el cuarto caso, es inferior al 10% por lo que, a los efectos de ser sometidas a mecanizados, las piezas fabricadas en aleaciones con Si superior al 10%, se puede considerar que son equivalentes, diferenciándolas de la cuarta. Las tolerancias geométricas y dimensionales conseguibles directamente de fundición, recogidas en normas como ISO 8062 o DIN 1688-1, establecen límites para este proceso. Fuera de esos límites, las garantías en conseguir producciones con los objetivos de ppms aceptados en la actualidad por el mercado, obligan a ir a fases posteriores de mecanizado. Aquellas geometrías que, funcionalmente, necesitan disponer de unas tolerancias geométricas y/o dimensionales definidas acorde a ISO 1101, y no capaces por este proceso inicial de moldeado a presión, deben ser procesadas en una fase posterior en células de mecanizado. En este caso, las tolerancias alcanzables para procesos de arranque de viruta se recogen en normas como ISO 2768. Las células de mecanizado se componen, por lo general, de varios centros de control numérico interrelacionados y comunicados entre sí por robots que manipulan las piezas en proceso de uno a otro. Dichos robots, disponen en su extremo de una pinza utillada para poder coger y soltar las piezas en los útiles de mecanizado, las mesas de intercambio para cambiar la pieza de posición o en utillajes de equipos de medición y prueba, o en cintas de entrada o salida. La repetibilidad es alta, de centésimas incluso, definida según norma ISO 9283. El problema es que, estos rangos de repetibilidad sólo se garantizan si no se hacen esfuerzos o éstos son despreciables (caso de mover piezas). Aunque las inercias de mover piezas a altas velocidades hacen que la trayectoria intermedia tenga poca precisión, al inicio y al final (al coger y dejar pieza, p.e.) se hacen a velocidades relativamente bajas que hacen que el efecto de las fuerzas de inercia sean menores y que permiten garantizar la repetibilidad anteriormente indicada. No ocurre así si se quitara la garra y se intercambia con un cabezal motorizado con una herramienta como broca, mandrino, plato de cuchillas, fresas frontales o tangenciales… Las fuerzas ejercidas de mecanizado generarían unos pares en las uniones tan grandes y tan variables que el control del robot no sería capaz de responder (o no está preparado, en un principio) y generaría una desviación en la trayectoria, realizada a baja velocidad, que desencadenaría en un error de posición (ver norma ISO 5458) no asumible para la funcionalidad deseada. Se podría llegar al caso de que la tolerancia alcanzada por un pretendido proceso más exacto diera una dimensión peor que la que daría el proceso de fundición, en principio con mayor variabilidad dimensional en proceso (y por ende con mayor intervalo de tolerancia garantizable). De hecho, en los CNCs, la precisión es muy elevada, (pudiéndose despreciar en la mayoría de los casos) y no es la responsable de, por ejemplo la tolerancia de posición al taladrar un agujero. Factores como, temperatura de la sala y de la pieza, calidad constructiva de los utillajes y rigidez en el amarre, error en el giro de mesas y de colocación de pieza, si lleva agujeros previos o no, si la herramienta está bien equilibrada y el cono es el adecuado para el tipo de mecanizado… influyen más. Es interesante que, un elemento no específico tan común en una planta industrial, en el entorno anteriormente descrito, como es un robot, el cual no sería necesario añadir por disponer de él ya (y por lo tanto la inversión sería muy pequeña), puede mejorar la cadena de valor disminuyendo el costo de fabricación. Y si se pudiera conjugar que ese robot destinado a tareas de manipulación, en los muchos tiempos de espera que va a disfrutar mientras el CNC arranca viruta, pudiese coger un cabezal y apoyar ese mecanizado; sería doblemente interesante. Por lo tanto, se antoja sugestivo poder conocer su comportamiento e intentar explicar qué sería necesario para llevar esto a cabo, motivo de este trabajo. La arquitectura de robot seleccionada es de tipo SCARA. La búsqueda de un robot cómodo de modelar y de analizar cinemática y dinámicamente, sin limitaciones relevantes en la multifuncionalidad de trabajos solicitados, ha llevado a esta elección, frente a otras arquitecturas como por ejemplo los robots antropomórficos de 6 grados de libertad, muy populares a nivel industrial. Este robot dispone de 3 uniones, de las cuales 2 son de tipo par de revolución (1 grado de libertad cada una) y la tercera es de tipo corredera o par cilíndrico (2 grados de libertad). La primera unión, de tipo par de revolución, sirve para unir el suelo (considerado como eslabón número 1) con el eslabón número 2. La segunda unión, también de ese tipo, une el eslabón número 2 con el eslabón número 3. Estos 2 brazos, pueden describir un movimiento horizontal, en el plano X-Y. El tercer eslabón, está unido al eslabón número 4 por la unión de tipo corredera. El movimiento que puede describir es paralelo al eje Z. El robot es de 4 grados de libertad (4 motores). En relación a los posibles trabajos que puede realizar este tipo de robot, su versatilidad abarca tanto operaciones típicas de manipulación como operaciones de arranque de viruta. Uno de los mecanizados más usuales es el taladrado, por lo cual se elige éste para su modelización y análisis. Dentro del taladrado se elegirá para acotar las fuerzas, taladrado en macizo con broca de diámetro 9 mm. El robot se ha considerado por el momento que tenga comportamiento de sólido rígido, por ser el mayor efecto esperado el de los pares en las uniones. Para modelar el robot se utiliza el método de los sistemas multicuerpos. Dentro de este método existen diversos tipos de formulaciones (p.e. Denavit-Hartenberg). D-H genera una cantidad muy grande de ecuaciones e incógnitas. Esas incógnitas son de difícil comprensión y, para cada posición, hay que detenerse a pensar qué significado tienen. Se ha optado por la formulación de coordenadas naturales. Este sistema utiliza puntos y vectores unitarios para definir la posición de los distintos cuerpos, y permite compartir, cuando es posible y se quiere, para definir los pares cinemáticos y reducir al mismo tiempo el número de variables. Las incógnitas son intuitivas, las ecuaciones de restricción muy sencillas y se reduce considerablemente el número de ecuaciones e incógnitas. Sin embargo, las coordenadas naturales “puras” tienen 2 problemas. El primero, que 2 elementos con un ángulo de 0 o 180 grados, dan lugar a puntos singulares que pueden crear problemas en las ecuaciones de restricción y por lo tanto han de evitarse. El segundo, que tampoco inciden directamente sobre la definición o el origen de los movimientos. Por lo tanto, es muy conveniente complementar esta formulación con ángulos y distancias (coordenadas relativas). Esto da lugar a las coordenadas naturales mixtas, que es la formulación final elegida para este TFM. Las coordenadas naturales mixtas no tienen el problema de los puntos singulares. Y la ventaja más importante reside en su utilidad a la hora de aplicar fuerzas motrices, momentos o evaluar errores. Al incidir sobre la incógnita origen (ángulos o distancias) controla los motores de manera directa. El algoritmo, la simulación y la obtención de resultados se ha programado mediante Matlab. Para realizar el modelo en coordenadas naturales mixtas, es preciso modelar en 2 pasos el robot a estudio. El primer modelo se basa en coordenadas naturales. Para su validación, se plantea una trayectoria definida y se analiza cinemáticamente si el robot satisface el movimiento solicitado, manteniendo su integridad como sistema multicuerpo. Se cuantifican los puntos (en este caso inicial y final) que configuran el robot. Al tratarse de sólidos rígidos, cada eslabón queda definido por sus respectivos puntos inicial y final (que son los más interesantes para la cinemática y la dinámica) y por un vector unitario no colineal a esos 2 puntos. Los vectores unitarios se colocan en los lugares en los que se tenga un eje de rotación o cuando se desee obtener información de un ángulo. No son necesarios vectores unitarios para medir distancias. Tampoco tienen por qué coincidir los grados de libertad con el número de vectores unitarios. Las longitudes de cada eslabón quedan definidas como constantes geométricas. Se establecen las restricciones que definen la naturaleza del robot y las relaciones entre los diferentes elementos y su entorno. La trayectoria se genera por una nube de puntos continua, definidos en coordenadas independientes. Cada conjunto de coordenadas independientes define, en un instante concreto, una posición y postura de robot determinada. Para conocerla, es necesario saber qué coordenadas dependientes hay en ese instante, y se obtienen resolviendo por el método de Newton-Rhapson las ecuaciones de restricción en función de las coordenadas independientes. El motivo de hacerlo así es porque las coordenadas dependientes deben satisfacer las restricciones, cosa que no ocurre con las coordenadas independientes. Cuando la validez del modelo se ha probado (primera validación), se pasa al modelo 2. El modelo número 2, incorpora a las coordenadas naturales del modelo número 1, las coordenadas relativas en forma de ángulos en los pares de revolución (3 ángulos; ϕ1, ϕ 2 y ϕ3) y distancias en los pares prismáticos (1 distancia; s). Estas coordenadas relativas pasan a ser las nuevas coordenadas independientes (sustituyendo a las coordenadas independientes cartesianas del modelo primero, que eran coordenadas naturales). Es necesario revisar si el sistema de vectores unitarios del modelo 1 es suficiente o no. Para este caso concreto, se han necesitado añadir 1 vector unitario adicional con objeto de que los ángulos queden perfectamente determinados con las correspondientes ecuaciones de producto escalar y/o vectorial. Las restricciones habrán de ser incrementadas en, al menos, 4 ecuaciones; una por cada nueva incógnita. La validación del modelo número 2, tiene 2 fases. La primera, al igual que se hizo en el modelo número 1, a través del análisis cinemático del comportamiento con una trayectoria definida. Podrían obtenerse del modelo 2 en este análisis, velocidades y aceleraciones, pero no son necesarios. Tan sólo interesan los movimientos o desplazamientos finitos. Comprobada la coherencia de movimientos (segunda validación), se pasa a analizar cinemáticamente el comportamiento con trayectorias interpoladas. El análisis cinemático con trayectorias interpoladas, trabaja con un número mínimo de 3 puntos máster. En este caso se han elegido 3; punto inicial, punto intermedio y punto final. El número de interpolaciones con el que se actúa es de 50 interpolaciones en cada tramo (cada 2 puntos máster hay un tramo), resultando un total de 100 interpolaciones. El método de interpolación utilizado es el de splines cúbicas con condición de aceleración inicial y final constantes, que genera las coordenadas independientes de los puntos interpolados de cada tramo. Las coordenadas dependientes se obtienen resolviendo las ecuaciones de restricción no lineales con el método de Newton-Rhapson. El método de las splines cúbicas es muy continuo, por lo que si se desea modelar una trayectoria en el que haya al menos 2 movimientos claramente diferenciados, es preciso hacerlo en 2 tramos y unirlos posteriormente. Sería el caso en el que alguno de los motores se desee expresamente que esté parado durante el primer movimiento y otro distinto lo esté durante el segundo movimiento (y así sucesivamente). Obtenido el movimiento, se calculan, también mediante fórmulas de diferenciación numérica, las velocidades y aceleraciones independientes. El proceso es análogo al anteriormente explicado, recordando la condición impuesta de que la aceleración en el instante t= 0 y en instante t= final, se ha tomado como 0. Las velocidades y aceleraciones dependientes se calculan resolviendo las correspondientes derivadas de las ecuaciones de restricción. Se comprueba, de nuevo, en una tercera validación del modelo, la coherencia del movimiento interpolado. La dinámica inversa calcula, para un movimiento definido -conocidas la posición, velocidad y la aceleración en cada instante de tiempo-, y conocidas las fuerzas externas que actúan (por ejemplo el peso); qué fuerzas hay que aplicar en los motores (donde hay control) para que se obtenga el citado movimiento. En la dinámica inversa, cada instante del tiempo es independiente de los demás y tiene una posición, una velocidad y una aceleración y unas fuerzas conocidas. En este caso concreto, se desean aplicar, de momento, sólo las fuerzas debidas al peso, aunque se podrían haber incorporado fuerzas de otra naturaleza si se hubiese deseado. Las posiciones, velocidades y aceleraciones, proceden del cálculo cinemático. El efecto inercial de las fuerzas tenidas en cuenta (el peso) es calculado. Como resultado final del análisis dinámico inverso, se obtienen los pares que han de ejercer los cuatro motores para replicar el movimiento prescrito con las fuerzas que estaban actuando. La cuarta validación del modelo consiste en confirmar que el movimiento obtenido por aplicar los pares obtenidos en la dinámica inversa, coinciden con el obtenido en el análisis cinemático (movimiento teórico). Para ello, es necesario acudir a la dinámica directa. La dinámica directa se encarga de calcular el movimiento del robot, resultante de aplicar unos pares en motores y unas fuerzas en el robot. Por lo tanto, el movimiento real resultante, al no haber cambiado ninguna condición de las obtenidas en la dinámica inversa (pares de motor y fuerzas inerciales debidas al peso de los eslabones) ha de ser el mismo al movimiento teórico. Siendo así, se considera que el robot está listo para trabajar. Si se introduce una fuerza exterior de mecanizado no contemplada en la dinámica inversa y se asigna en los motores los mismos pares resultantes de la resolución del problema dinámico inverso, el movimiento real obtenido no es igual al movimiento teórico. El control de lazo cerrado se basa en ir comparando el movimiento real con el deseado e introducir las correcciones necesarias para minimizar o anular las diferencias. Se aplican ganancias en forma de correcciones en posición y/o velocidad para eliminar esas diferencias. Se evalúa el error de posición como la diferencia, en cada punto, entre el movimiento teórico deseado en el análisis cinemático y el movimiento real obtenido para cada fuerza de mecanizado y una ganancia concreta. Finalmente, se mapea el error de posición obtenido para cada fuerza de mecanizado y las diferentes ganancias previstas, graficando la mejor precisión que puede dar el robot para cada operación que se le requiere, y en qué condiciones. -------------- This Master´s Thesis deals with a preliminary characterization of the behaviour for an industrial robot, configured with 4 elements and 4 degrees of freedoms, and subjected to machining forces at its end. Proposed working conditions are those typical from manufacturing plants with aluminium alloys for automotive industry. This type of components comes from a first casting process that produces rough parts. For medium and high volumes, high pressure die casting (HPDC) and low pressure die casting (LPC) are the most used technologies in this first phase. For high pressure die casting processes, most used aluminium alloys are, in simbolic designation according EN 1706 standard (between brackets, its numerical designation); EN AC AlSi9Cu3(Fe) (EN AC 46000) , EN AC AlSi9Cu3(Fe)(Zn) (EN AC 46500), y EN AC AlSi12Cu1(Fe) (EN AC 47100). For low pressure, EN AC AlSi7Mg0,3 (EN AC 42100). For the 3 first alloys, Si allowed limits can exceed 10% content. Fourth alloy has admisible limits under 10% Si. That means, from the point of view of machining, that components made of alloys with Si content above 10% can be considered as equivalent, and the fourth one must be studied separately. Geometrical and dimensional tolerances directly achievables from casting, gathered in standards such as ISO 8062 or DIN 1688-1, establish a limit for this process. Out from those limits, guarantees to achieve batches with objetive ppms currently accepted by market, force to go to subsequent machining process. Those geometries that functionally require a geometrical and/or dimensional tolerance defined according ISO 1101, not capable with initial moulding process, must be obtained afterwards in a machining phase with machining cells. In this case, tolerances achievables with cutting processes are gathered in standards such as ISO 2768. In general terms, machining cells contain several CNCs that they are interrelated and connected by robots that handle parts in process among them. Those robots have at their end a gripper in order to take/remove parts in machining fixtures, in interchange tables to modify position of part, in measurement and control tooling devices, or in entrance/exit conveyors. Repeatibility for robot is tight, even few hundredths of mm, defined according ISO 9283. Problem is like this; those repeatibilty ranks are only guaranteed when there are no stresses or they are not significant (f.e. due to only movement of parts). Although inertias due to moving parts at a high speed make that intermediate paths have little accuracy, at the beginning and at the end of trajectories (f.e, when picking part or leaving it) movement is made with very slow speeds that make lower the effect of inertias forces and allow to achieve repeatibility before mentioned. It does not happens the same if gripper is removed and it is exchanged by an spindle with a machining tool such as a drilling tool, a pcd boring tool, a face or a tangential milling cutter… Forces due to machining would create such big and variable torques in joints that control from the robot would not be able to react (or it is not prepared in principle) and would produce a deviation in working trajectory, made at a low speed, that would trigger a position error (see ISO 5458 standard) not assumable for requested function. Then it could be possible that tolerance achieved by a more exact expected process would turn out into a worst dimension than the one that could be achieved with casting process, in principle with a larger dimensional variability in process (and hence with a larger tolerance range reachable). As a matter of fact, accuracy is very tight in CNC, (its influence can be ignored in most cases) and it is not the responsible of, for example position tolerance when drilling a hole. Factors as, room and part temperature, manufacturing quality of machining fixtures, stiffness at clamping system, rotating error in 4th axis and part positioning error, if there are previous holes, if machining tool is properly balanced, if shank is suitable for that machining type… have more influence. It is interesting to know that, a non specific element as common, at a manufacturing plant in the enviroment above described, as a robot (not needed to be added, therefore with an additional minimum investment), can improve value chain decreasing manufacturing costs. And when it would be possible to combine that the robot dedicated to handling works could support CNCs´ works in its many waiting time while CNCs cut, and could take an spindle and help to cut; it would be double interesting. So according to all this, it would be interesting to be able to know its behaviour and try to explain what would be necessary to make this possible, reason of this work. Selected robot architecture is SCARA type. The search for a robot easy to be modeled and kinematically and dinamically analyzed, without significant limits in the multifunctionality of requested operations, has lead to this choice. Due to that, other very popular architectures in the industry, f.e. 6 DOFs anthropomorphic robots, have been discarded. This robot has 3 joints, 2 of them are revolute joints (1 DOF each one) and the third one is a cylindrical joint (2 DOFs). The first joint, a revolute one, is used to join floor (body 1) with body 2. The second one, a revolute joint too, joins body 2 with body 3. These 2 bodies can move horizontally in X-Y plane. Body 3 is linked to body 4 with a cylindrical joint. Movement that can be made is paralell to Z axis. The robt has 4 degrees of freedom (4 motors). Regarding potential works that this type of robot can make, its versatility covers either typical handling operations or cutting operations. One of the most common machinings is to drill. That is the reason why it has been chosen for the model and analysis. Within drilling, in order to enclose spectrum force, a typical solid drilling with 9 mm diameter. The robot is considered, at the moment, to have a behaviour as rigid body, as biggest expected influence is the one due to torques at joints. In order to modelize robot, it is used multibodies system method. There are under this heading different sorts of formulations (f.e. Denavit-Hartenberg). D-H creates a great amount of equations and unknown quantities. Those unknown quatities are of a difficult understanding and, for each position, one must stop to think about which meaning they have. The choice made is therefore one of formulation in natural coordinates. This system uses points and unit vectors to define position of each different elements, and allow to share, when it is possible and wished, to define kinematic torques and reduce number of variables at the same time. Unknown quantities are intuitive, constrain equations are easy and number of equations and variables are strongly reduced. However, “pure” natural coordinates suffer 2 problems. The first one is that 2 elements with an angle of 0° or 180°, give rise to singular positions that can create problems in constrain equations and therefore they must be avoided. The second problem is that they do not work directly over the definition or the origin of movements. Given that, it is highly recommended to complement this formulation with angles and distances (relative coordinates). This leads to mixed natural coordinates, and they are the final formulation chosen for this MTh. Mixed natural coordinates have not the problem of singular positions. And the most important advantage lies in their usefulness when applying driving forces, torques or evaluating errors. As they influence directly over origin variable (angles or distances), they control motors directly. The algorithm, simulation and obtaining of results has been programmed with Matlab. To design the model in mixed natural coordinates, it is necessary to model the robot to be studied in 2 steps. The first model is based in natural coordinates. To validate it, it is raised a defined trajectory and it is kinematically analyzed if robot fulfils requested movement, keeping its integrity as multibody system. The points (in this case starting and ending points) that configure the robot are quantified. As the elements are considered as rigid bodies, each of them is defined by its respectively starting and ending point (those points are the most interesting ones from the point of view of kinematics and dynamics) and by a non-colinear unit vector to those points. Unit vectors are placed where there is a rotating axis or when it is needed information of an angle. Unit vectors are not needed to measure distances. Neither DOFs must coincide with the number of unit vectors. Lengths of each arm are defined as geometrical constants. The constrains that define the nature of the robot and relationships among different elements and its enviroment are set. Path is generated by a cloud of continuous points, defined in independent coordinates. Each group of independent coordinates define, in an specific instant, a defined position and posture for the robot. In order to know it, it is needed to know which dependent coordinates there are in that instant, and they are obtained solving the constraint equations with Newton-Rhapson method according to independent coordinates. The reason to make it like this is because dependent coordinates must meet constraints, and this is not the case with independent coordinates. When suitability of model is checked (first approval), it is given next step to model 2. Model 2 adds to natural coordinates from model 1, the relative coordinates in the shape of angles in revoluting torques (3 angles; ϕ1, ϕ 2 and ϕ3) and distances in prismatic torques (1 distance; s). These relative coordinates become the new independent coordinates (replacing to cartesian independent coordinates from model 1, that they were natural coordinates). It is needed to review if unit vector system from model 1 is enough or not . For this specific case, it was necessary to add 1 additional unit vector to define perfectly angles with their related equations of dot and/or cross product. Constrains must be increased in, at least, 4 equations; one per each new variable. The approval of model 2 has two phases. The first one, same as made with model 1, through kinematic analysis of behaviour with a defined path. During this analysis, it could be obtained from model 2, velocities and accelerations, but they are not needed. They are only interesting movements and finite displacements. Once that the consistence of movements has been checked (second approval), it comes when the behaviour with interpolated trajectories must be kinematically analyzed. Kinematic analysis with interpolated trajectories work with a minimum number of 3 master points. In this case, 3 points have been chosen; starting point, middle point and ending point. The number of interpolations has been of 50 ones in each strecht (each 2 master points there is an strecht), turning into a total of 100 interpolations. The interpolation method used is the cubic splines one with condition of constant acceleration both at the starting and at the ending point. This method creates the independent coordinates of interpolated points of each strecht. The dependent coordinates are achieved solving the non-linear constrain equations with Newton-Rhapson method. The method of cubic splines is very continuous, therefore when it is needed to design a trajectory in which there are at least 2 movements clearly differents, it is required to make it in 2 steps and join them later. That would be the case when any of the motors would keep stopped during the first movement, and another different motor would remain stopped during the second movement (and so on). Once that movement is obtained, they are calculated, also with numerical differenciation formulas, the independent velocities and accelerations. This process is analogous to the one before explained, reminding condition that acceleration when t=0 and t=end are 0. Dependent velocities and accelerations are calculated solving related derivatives of constrain equations. In a third approval of the model it is checked, again, consistence of interpolated movement. Inverse dynamics calculates, for a defined movement –knowing position, velocity and acceleration in each instant of time-, and knowing external forces that act (f.e. weights); which forces must be applied in motors (where there is control) in order to obtain requested movement. In inverse dynamics, each instant of time is independent of the others and it has a position, a velocity, an acceleration and known forces. In this specific case, it is intended to apply, at the moment, only forces due to the weight, though forces of another nature could have been added if it would have been preferred. The positions, velocities and accelerations, come from kinematic calculation. The inertial effect of forces taken into account (weight) is calculated. As final result of the inverse dynamic analysis, the are obtained torques that the 4 motors must apply to repeat requested movement with the forces that were acting. The fourth approval of the model consists on confirming that the achieved movement due to the use of the torques obtained in the inverse dynamics, are in accordance with movements from kinematic analysis (theoretical movement). For this, it is necessary to work with direct dynamics. Direct dynamic is in charge of calculating the movements of robot that results from applying torques at motors and forces at the robot. Therefore, the resultant real movement, as there was no change in any condition of the ones obtained at the inverse dynamics (motor torques and inertial forces due to weight of elements) must be the same than theoretical movement. When these results are achieved, it is considered that robot is ready to work. When a machining external force is introduced and it was not taken into account before during the inverse dynamics, and torques at motors considered are the ones of the inverse dynamics, the real movement obtained is not the same than the theoretical movement. Closed loop control is based on comparing real movement with expected movement and introducing required corrrections to minimize or cancel differences. They are applied gains in the way of corrections for position and/or tolerance to remove those differences. Position error is evaluated as the difference, in each point, between theoretical movemment (calculated in the kinematic analysis) and the real movement achieved for each machining force and for an specific gain. Finally, the position error obtained for each machining force and gains are mapped, giving a chart with the best accuracy that the robot can give for each operation that has been requested and which conditions must be provided.

Territorial cohesion impacts of high-speed rail under different zoning systems

Large-scale transport infrastructure projects such as high-speed rail (HSR) produce significant effects on the spatial distribution of accessibility. These effects, commonly known as territorial cohesion effects, are receiving increasing attention in the research literature. However, there is little empirical research into the sensitivity of these cohesion results to methodological issues such as the definition of the limits of the study area or the zoning system. In a previous paper (Ortega et al., 2012), we investigated the influence of scale issues, comparing the cohesion results obtained at four different planning levels. This paper makes an additional contribution to our research with the investigation of the influence of zoning issues. We analyze the extent to which changes in the size of the units of analysis influence the measurement of spatial inequalities. The methodology is tested by application to the Galician (north-western) HSR corridor, with a length of nearly 670 km, included in the Spanish PEIT (Strategic Transport and Infrastructure Plan) 2005-2020. We calculated the accessibility indicators for the Galician HSR corridor and assessed their corresponding territorial distribution. We used five alternative zoning systems depending on the method of data representation used (vector or raster), and the level of detail (cartographic accuracy or cell size). Our results suggest that the choice between a vector-based and raster-based system has important implications. The vector system produces a higher mean accessibility value and a more polarized accessibility distribution than raster systems. The increased pixel size of raster-based systems tends to give rise to higher mean accessibility values and a more balanced accessibility distribution. Our findings strongly encourage spatial analysts to acknowledge that the results of their analyses may vary widely according to the definition of the units of analysis.

Extended phone log-likelihood ratio features and acoustic-based I-vectors for language recognition

This paper presents new techniques with relevant improvements added to the primary system presented by our group to the Albayzin 2012 LRE competition, where the use of any additional corpora for training or optimizing the models was forbidden. In this work, we present the incorporation of an additional phonotactic subsystem based on the use of phone log-likelihood ratio features (PLLR) extracted from different phonotactic recognizers that contributes to improve the accuracy of the system in a 21.4% in terms of Cavg (we also present results for the official metric during the evaluation, Fact). We will present how using these features at the phone state level provides significant improvements, when used together with dimensionality reduction techniques, especially PCA. We have also experimented with applying alternative SDC-like configurations on these PLLR features with additional improvements. Also, we will describe some modifications to the MFCC-based acoustic i-vector system which have also contributed to additional improvements. The final fused system outperformed the baseline in 27.4% in Cavg.

GADD45 induction of a G2/M cell cycle checkpoint

G1/S and G2/M cell cycle checkpoints maintain genomic stability in eukaryotes in response to genotoxic stress. We report here both genetic and functional evidence of a Gadd45-mediated G2/M checkpoint in human and murine cells. Increased expression of Gadd45 via microinjection of an expression vector into primary human fibroblasts arrests the cells at the G2/M boundary with a phenotype of MPM2 immunopositivity, 4n DNA content and, in 15% of the cells, centrosome separation. The Gadd45-mediated G2/M arrest depends on wild-type p53, because no arrest was observed either in p53-null Li–Fraumeni fibroblasts or in normal fibroblasts coexpressed with p53 mutants. Increased expression of cyclin B1 and Cdc25C inhibited the Gadd45-mediated G2/M arrest in human fibroblasts, indicating that the mechanism of Gadd45-mediated G2/M checkpoint is at least in part through modulation of the activity of the G2-specific kinase, cyclin B1/p34cdc2. Genetic and physiological evidence of a Gadd45-mediated G2/M checkpoint was obtained by using GADD45-deficient human or murine cells. Human cells with endogenous Gadd45 expression reduced by antisense GADD45 expression have an impaired G2/M checkpoint after exposure to either ultraviolet radiation or methyl methanesulfonate but are still able to undergo G2 arrest after ionizing radiation. Lymphocytes from gadd45-knockout mice (gadd45 −/−) also retained a G2/M checkpoint initiated by ionizing radiation and failed to arrest at G2/M after exposure to ultraviolet radiation. Therefore, the mammalian genome is protected by a multiplicity of G2/M checkpoints in response to specific types of DNA damage.

Efficient loading of HLA-DR with a T helper epitope by genetic exchange of CLIP

The HLA class II-associated invariant chain (Ii)-derived peptide (CLIP) occupies the peptide binding groove during assembly in the endoplasmic reticulum, travels with HLA class II to endosomal compartments, and is subsequently released to allow binding of antigenic peptides. We investigated whether the exchange of CLIP with a known T helper epitope at the DNA level would lead to efficient loading of this helper epitope onto HLA class II. For this purpose, a versatile Ii-encoding expression vector was created in which CLIP can be replaced with a helper epitope of choice. Upon supertransfection of HLA-DR1-transfected 293 cells with an Ii vector encoding a known T helper epitope (HA307–319), predominantly length variants of this epitope were detected in association with the HLA-DR1 molecules of these cells. Moreover, this transfectant was efficiently recognized by a peptide-specific T helper clone (HA1.7). The results suggest that this type of Ii vector can be used to create potent class II+ cellular vaccines in which defined T cell epitopes are continuously synthesized.

Three members of a novel small gene-family from Arabidopsis thaliana able to complement functionally an Escherichia coli mutant defective in PAPS reductase activity encode proteins with a thioredoxin-like domain and “APS reductase” activity

Three different cDNAs, Prh-19, Prh-26, and Prh-43 [3′-phosphoadenosine-5′-phosphosulfate (PAPS) reductase homolog], have been isolated by complementation of an Escherichia coli cysH mutant, defective in PAPS reductase activity, to prototrophy with an Arabidopsis thaliana cDNA library in the expression vector λYES. Sequence analysis of the cDNAs revealed continuous open reading frames encoding polypeptides of 465, 458, and 453 amino acids, with calculated molecular masses of 51.3, 50.5, and 50.4 kDa, respectively, that have strong homology with fungal, yeast, and bacterial PAPS reductases. However, unlike microbial PAPS reductases, each PRH protein has an N-terminal extension, characteristic of a plastid transit peptide, and a C-terminal extension that has amino acid and deduced three-dimensional homology to thioredoxin proteins. Adenosine 5′-phosphosulfate (APS) was shown to be a much more efficient substrate than PAPS when the activity of the PRH proteins was tested by their ability to convert 35S-labeled substrate to acid-volatile 35S-sulfite. We speculate that the thioredoxin-like domain is involved in catalytic function, and that the PRH proteins may function as novel “APS reductase” enzymes. Southern hybridization analysis showed the presence of a small multigene family in the Arabidopsis genome. RNA blot hybridization with gene-specific probes revealed for each gene the presence of a transcript of ≈1.85 kb in leaves, stems, and roots that increased on sulfate starvation. To our knowledge, this is the first report of the cloning and characterization of plant genes that encode proteins with APS reductase activity and supports the suggestion that APS can be utilized directly, without activation to PAPS, as an intermediary substrate in reductive sulfate assimilation.