Diversity Arrays: a solid state technology for sequence information independent genotyping

Here we present the successful application of the microarray technology platform to the analysis of DNA polymorphisms. Using the rice genome as a model, we demonstrate the potential of a high-throughput genome analysis method called Diversity Array Technology, DArT‘. In the format presented here the technology is assaying for the presence (or amount) of a specific DNA fragment in a representation derived from the total genomic DNA of an organism or a population of organisms. Two different approaches are presented: the first involves contrasting two representations on a single array while the second involves contrasting a representation with a reference DNA fragment common to all elements of the array. The Diversity Panels created using this method allow genetic fingerprinting of any organism or group of organisms belonging to the gene pool from which the panel was developed. Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures.

A genetic model provides evidence that the receptor for atrial natriuretic peptide (guanylyl cyclase-A) inhibits cardiac ventricular myocyte hypertrophy

Guanylyl cyclase-A (NPR-A; GC-A) is the major and possibly the only receptor for atrial natriuretic peptide (ANP) or B-type natriuretic peptide. Although mice deficient in GC-A display an elevated blood pressure, the resultant cardiac hypertrophy is much greater than in other mouse models of hypertension. Here we overproduce GC-A in the cardiac myocytes of wild-type or GC-A null animals. Introduction of the GC-A transgene did not alter blood pressure or heart rate as a function of genotype. Cardiac myocyte size was larger (approximately 20%) in GC-A null than in wild-type animals. However, introduction of the GC-A transgene reduced cardiac myocyte size in both wild-type and null mice. Coincident with the reduction in myocyte size, both ANP mRNA and ANP content were significantly reduced by overexpression of GC-A, and this reduction was independent of genotype. This genetic model, therefore, separates a regulation of cardiac myocyte size by blood pressure from local regulation by a GC-mediated pathway.

Enhancement of translation by the epsilon element is independent of the sequence of the 460 region of 16S rRNA

The epsilon enhancer element is a pyrimidine-rich sequence that increases expression of T7 gene 10 and a number of Escherichia coli mRNAs during initiation of translation and inhibits expression of the recF mRNA during elongation. Based on its complementarity to the 460 region of 16S rRNA, it has been proposed that epsilon exerts its enhancer activity by base pairing to this complementary rRNA sequence. We have tested this model of enhancer action by constructing mutations in the 460 region of 16S rRNA and examining expression of epsilon-containing CAT reporter genes and recF–lacZ fusions in strains expressing the mutant rRNAs. Replacement of the 460 E.coli stem–loop with that of Salmonella enterica serovar Typhimurium or a stem–loop containing a reversal of all 8 bp in the helical region produced fully functional rRNAs with no apparent effect on cell growth or expression of any epsilon-containing mRNA. Our experiments confirm the reported effects of the epsilon elements on gene expression but show that these effects are independent of the sequence of the 460 region of 16S rRNA, indicating that epsilon–rRNA base pairing does not occur.

Ligand-independent oligomerization of cell-surface erythropoietin receptor is mediated by the transmembrane domain

Binding of erythropoietin (Epo) to the Epo receptor (EpoR) is crucial for production of mature red cells. Although it is well established that the Epo-bound EpoR is a dimer, it is not clear whether, in the absence of ligand, the intact EpoR is a monomer or oligomer. Using antibody-mediated immunofluorescence copatching (oligomerizing) of epitope-tagged receptors at the surface of live cells, we show herein that a major fraction of the full-length murine EpoR exists as preformed dimers/oligomers in BOSC cells, which are human embryo kidney 293T-derived cells. This observed oligomerization is specific because, under the same conditions, epitope-tagged EpoR did not oligomerize with several other tagged receptors (thrombopoietin receptor, transforming growth factor β receptor type II, or prolactin receptor). Strikingly, the EpoR transmembrane (TM) domain but not the extracellular or intracellular domains enabled the prolactin receptor to copatch with EpoR. Preformed EpoR oligomers are not constitutively active and Epo binding was required to induce signaling. In contrast to tyrosine kinase receptors (e.g., insulin receptor), which cannot signal when their TM domain is replaced by the strongly dimerizing TM domain of glycophorin A, the EpoR could tolerate the replacement of its TM domain with that of glycophorin A and retained signaling. We propose a model in which TM domain-induced dimerization maintains unliganded EpoR in an inactive state that can readily be switched to an active state by physiologic levels of Epo.

A Model for Signal Transduction during Gamete Release in the Fucoid Alga Pelvetia compressa1

Fucoid algae release gametes into seawater following an inductive light period (potentiation), and gamete expulsion from potentiated receptacles of Pelvetia compressa began about 2 min after a light-to-dark transition. Agitation of the medium reversed potentiation, with an exponential time course completed in about 3 h. Light regulated two signaling pathways during potentiation and gamete expulsion: a photosynthetic pathway and a photosynthesis-independent pathway in which red light was active but blue light was not. Uptake of K+ appears to have an important role in potentiation, because a 50% inhibition of potentiation occurred in the presence of the tetraethylammonium ion, a K+-channel blocker. A central role of anion channels in the maintenance of potentiation is suggested by the premature release of gametes in the light when receptacles were incubated with inhibitors of slow-type anion channels. An inhibitor of tyrosine kinases, tyrphostin A63, also inhibited potentiation. A model for gamete release from P. compressa is presented that proposes that illumination results in the accumulation of ions (e.g. K+) throughout the cells of the receptacle during potentiation, which then move into the extracellular matrix during gamete expulsion to generate osmomechanical force, resulting in gamete release.

Interleukin 7 independent development of human B cells.

Mammalian hematopoietic stem cell (HSC) commitment and differentiation into lymphoid lineage cells proceed through a series of developmentally restricted progenitor compartments. A complete understanding of this process, and how it differs from HSC commitment and differentiation into cells of the myeloid/erythroid lineages, requires the development of model systems that support HSC commitment to the lymphoid lineages. We now describe a human bone marrow stromal cell culture that preferentially supports commitment and differentiation of human HSC to CD19+ B-lineage cells. Fluorescence activated cell sorterpurified CD34++/lineage-cells were isolated from fetal bone marrow and cultured on human fetal bone marrow stromal cells in serum-free conditions containing no exogenous cytokines. Over a period of 3 weeks, CD34++/lineage- cells underwent commitment, differentiation, and expansion into the B lineage. Progressive changes included: loss of CD34, acquisition of and graded increases in the level of cell surface CD19, and appearance of immature B cells expressing mu/kappa or mu/lambda cell surface Ig receptors. The tempo and phenotype of B-cell development was not influenced by the addition of IL-7 (10 ng/ml), or by the addition of goat anti-IL-7 neutralizing antibody. These results indicate a profound difference between mouse and human in the requirement for IL-7 in normal B-cell development, and provide an experimental system to identify and characterize human bone marrow stromal cell-derived molecules crucial for human B lymphopoiesis.

Trials of the beta model for complex inheritance.

Theoretical advantages of nonparametric logarithm of odds to map polygenic diseases are supported by tests of the beta model that depends on a single logistic parameter and is the only model under which paternal and maternal transmissions to sibs of specified phenotypes are independent. Although it does not precisely describe recurrence risks in monozygous twins, the beta model has greater power to detect family resemblance or linkage than the more general delta model which describes the probability of 0, 1, or 2 alleles identical by descent (ibd) with two parameters. Available data on ibd in sibs are consistent with the beta model, but not with the equally parsimonious but less powerful gamma model that assumes a fixed probability of 1/2 for 1 allele ibd. Additivity of loci on the liability scale is not disproven. A simple equivalence extends the beta model to multipoint analysis.

Cellular stress inhibits transposition of the yeast retrovirus-like element Ty3 by a ubiquitin-dependent block of virus-like particle formation.

Many stress proteins and their cognates function as molecular chaperones or as components of proteolytic systems. Viral infection can stimulate synthesis of stress proteins and particular associations of viral and stress proteins have been documented. However, demonstrations of functions for stress proteins in viral life cycles are few. We have initiated an investigation of the roles of stress proteins in eukaryotic viral life cycles using as a model the Ty3 retrovirus-like element of Saccharomyces cerevisiae. During stress, Ty3 transposition is inhibited; Ty3 DNA is not synthesized and, although precursor proteins are detected, mature Ty3 proteins and virus-like particles (VLPs) do not accumulate. The same phenotype is observed in the constitutively stressed ssa1 ssa2 mutant, which lacks two cytoplasmic members of the hsp70 family of chaperones. Ty3 VLPs preformed under nonstress conditions are degraded more rapidly if cells are shifted from 30 degrees C to 37 degrees C. These results suggest that Ty3 VLPs are destroyed by cellular stress proteins. Elevated expression of the yeast UBP3 gene, which encodes a protease that removes ubiquitin from proteins, allows mature Ty3 proteins and VLPs to accumulate in the ssa1 ssa2 mutant, suggesting that, at least under stress conditions, ubiquitination plays a role in regulating Ty3 transposition.

The intrinsic ability of ribosomes to bind to endoplasmic reticulum membranes is regulated by signal recognition particle and nascent-polypeptide-associated complex.

Signal peptides direct the cotranslational targeting of nascent polypeptides to the endoplasmic reticulum (ER). It is currently believed that the signal recognition particle (SRP) mediates this targeting by first binding to signal peptides and then by directing the ribosome/nascent chain/SRP complex to the SRP receptor at the ER. We show that ribosomes can mediate targeting by directly binding to translocation sites. When purified away from cytosolic factors, including SRP and nascent-polypeptide-associated complex (NAC), in vitro assembled translation intermediates representing ribosome/nascent-chain complexes efficiently bound to microsomal membranes, and their nascent polypeptides could subsequently be efficiently translocated. Because removal of cytosolic factors from the ribosome/nascent-chain complexes also resulted in mistargeting of signalless nascent polypeptides, we previously investigated whether readdition of cytosolic factors, such as NAC and SRP, could restore fidelity to targeting. Without SRP, NAC prevented all nascent-chain-containing ribosomes from binding to the ER membrane. Furthermore, SRP prevented NAC from blocking ribosome-membrane association only when the nascent polypeptide contained a signal. Thus, NAC is a global ribosome-binding prevention factor regulated in activity by signal-peptide-directed SRP binding. A model presents ribosomes as the targeting vectors for delivering nascent polypeptides to translocation sites. In conjunction with signal peptides, SRP and NAC contribute to this specificity of ribosomal function by regulating exposure of a ribosomal membrane attachment site that binds to receptors in the ER membrane.

Membrane-associated CD19-LYN complex is an endogenous p53-independent and Bc1-2-independent regulator of apoptosis in human B-lineage lymphoma cells.

CD19 receptor is expressed at high levels on human B-lineage lymphoid cells and is physically associated with the Src protooncogene family protein-tyrosine kinase Lyn. Recent studies indicate that the membrane-associated CD19-Lyn receptor-enzyme complex plays a pivotal role for survival and clonogenicity of immature B-cell precursors from acute lymphoblastic leukemia patients, but its significance for mature B-lineage lymphoid cells (e.g., B-lineage lymphoma cells) is unknown. CD19-associated Lyn kinase can be selectively targeted and inhibited with B43-Gen, a CD19 receptor-specific immunoconjugate containing the naturally occurring protein-tyrosine kinase inhibitor genistein (Gen). We now present experimental evidence that targeting the membrane-associated CD19-Lyn complex in vitro with B43-Gen triggers rapid apoptotic cell death in highly radiation-resistant p53-Bax- Ramos-BT B-lineage lymphoma cells expressing high levels of Bcl-2 protein without affecting the Bcl-2 expression level. The therapeutic potential of this membrane-directed apoptosis induction strategy was examined in a scid mouse xenograft model of radiation-resistant high-grade human B-lineage lymphoma. Remarkably, in vivo treatment of scid mice challenged with an invariably fatal number of Ramos-BT cells with B43-Gen at a dose level < 1/10 the maximum tolerated dose resulted in 70% long-term event-free survival. Taken together, these results provide unprecedented evidence that the membrane-associated anti-apoptotic CD19-Lyn complex may be at least as important as Bcl-2/Bax ratio for survival of lymphoma cells.

Peptide inhibitors of peptidyltransferase alter the conformation of domains IV and V of large subunit rRNA: a model for nascent peptide control of translation.

Peptides of 5 and 8 residues encoded by the leaders of attenuation regulated chloramphenicol-resistance genes inhibit the peptidyltransferase of microorganisms from the three kingdoms. Therefore, the ribosomal target for the peptides is likely to be a conserved structure and/or sequence. The inhibitor peptides "footprint" to nucleotides of domain V in large subunit rRNA when peptide-ribosome complexes are probed with dimethyl sulfate. Accordingly, rRNA was examined as a candidate for the site of peptide binding. Inhibitor peptides MVKTD and MSTSKNAD were mixed with rRNA phenol-extracted from Escherichia coli ribosomes. The conformation of the RNA was then probed by limited digestion with nucleases that cleave at single-stranded (T1 endonuclease) and double-stranded (V1 endonuclease) sites. Both peptides selectively altered the susceptibility of domains IV and V of 23S rRNA to digestion by T1 endonuclease. Peptide effects on cleavage by V1 nuclease were observed only in domain V. The T1 nuclease susceptibility of domain V of in vitro-transcribed 23S rRNA was also altered by the peptides, demonstrating that peptide binding to the rRNA is independent of ribosomal protein. We propose the peptides MVKTD and MSTSKNAD perturb peptidyltransferase center catalytic activities by altering the conformation of domains IV and V of 23S rRNA. These findings provide a general mechanism through which nascent peptides may cis-regulate the catalytic activities of translating ribosomes.

Tissue factor promotes melanoma metastasis by a pathway independent of blood coagulation.

Several studies have established a link between blood coagulation and cancer, and more specifically between tissue factor (TF), a transmembrane protein involved in initiating blood coagulation, and tumor metastasis. In the study reported here, a murine model of human melanoma metastasis was used for two experiments. (i) The first experiment was designed to test the effect of varying the level of TF expression in human melanoma cells on their metastatic potential. Two matched sets of cloned human melanoma lines, one expressing a high level and the other a low level of the normal human TF molecule, were generated by retroviral-mediated transfections of a nonmetastatic parental line. The metastatic potential of the two sets of transfected lines was compared by injecting the tumor cells into the tail vein of severe combined immunodeficiency (SCID) mice and later examining the lungs and other tissues for tumor development. Metastatic tumors were detected in 86% of the mice injected with the high-TF lines and in 5% of the mice injected with the low-TF lines, indicating that a high TF level promotes metastasis of human melanoma in the SCID mouse model. This TF effect on metastasis occurs with i.v.-injected melanoma cells but does not occur with primary tumors formed from s.c.-injected melanoma cells, suggesting that TF acts at a late stage of metastasis, after tumor cells have escaped from the primary site and entered the blood. (ii) The second experiment was designed to analyze the mechanism by which TF promotes melanoma metastasis. The procedure involved testing the effect on metastasis of mutations in either the extracellular or cytoplasmic domains of the transmembrane TF molecule. The extracellular mutations introduced two amino acid substitutions that inhibited initiation by TF of the blood-coagulation cascade; the cytoplasmic mutation deleted most of the cytoplasmic domain without impairing the coagulation function of TF. Several human melanoma lines expressing high levels of either of the two mutant TF molecules were generated by retroviral-mediated transfection of the corresponding TF cDNA into the nonmetastatic parental melanoma line, and the metastatic potential of each transfected line was tested in the SCID mouse model. Metastases occurred in most mice injected with the melanoma lines expressing the extracellular TF mutant but were not detected in most mice injected with the melanoma lines expressing the cytoplasmic TF mutant. Results with the extracellular TF mutant indicate that the metastatic effect of TF in the SCID mouse model does not involve products of the coagulation cascade. Results with the cytoplasmic TF mutant indicate that the cytoplasmic domain of TF is important for the metastatic effect, suggesting that the TF could transduce a melanoma cell signal that promotes metastasis.

Genetic and redox determinants of nitric oxide cytotoxicity in a Salmonella typhimurium model.

Paradoxically, nitric oxide (NO) has been found to exhibit cytotoxic, antiproliferative, or cytoprotective activity under different conditions. We have utilized Salmonella mutants deficient in antioxidant defenses or peptide transport to gain insights into NO actions. Comparison of three NO donor compounds reveals distinct and independent cellular responses associated with specific redox forms of NO. The peroxynitrite (OONO-) generator 3-morpholinosydnonimine hydrochloride mediates oxygen-dependent Salmonella killing, whereas S-nitrosoglutathione (GSNO) causes oxygen-independent cytostasis, and the NO. donor diethylenetriamine-nitric oxide adduct has no antibacterial activity. GSNO has the greatest activity for stationary cells, a characteristic relevant to latent or intracellular pathogens. Moreover, the cytostatic activity of GSNO may best correlate with antiproliferative or antimicrobial effects of NO, which are unassociated with overt cell injury. dpp mutants defective in active dipeptide transport are resistant to GSNO, implicating heterolytic NO+ transfer rather than homolytic NO. release in the mechanism of cytostasis. This transport system may provide a specific pathway for GSNO-mediated signaling in biological systems. The redox state and associated carrier molecules are critical determinants of NO activity.

Polpa de guavira (Campomanesia cambessedeana Berg) desidratada em spray dryer: efeitos das condições de processo e composição da alimentação nas propriedades físico químicas e atividade antioxidante

O objetivo desse trabalho foi obter polpa de guavira desidratada por atomização, utilizando maltodextrina ou goma arábica como agentes carreadores. Inicialmente, avaliou-se a influência das condições de processo, temperatura do ar de secagem (130, 155 e 180) °C e vazão volumétrica da mistura (20 e 40) mL/min, o tipo e concentração de agente carreador (10 e 20) % nas características físicas, físico-químicas e atividade antioxidante do produto obtido. As propriedades analisadas foram umidade, atividade de água, higroscopicidade, solubilidade, cor, distribuição e tamanho médio de partículas, morfologia, compostos fenólicos totais e atividade antioxidante. A temperatura do ar de secagem e a vazão volumétrica de alimentação influenciaram significativamente todas as propriedades da guavira em pó. A umidade e atividade de água apresentaram os menores valores na temperatura intermediária, independentemente do tipo e concentração do carreador usado. A solubilidade das amostras adicionadas de maltodextrina foram superiores às amostras com goma arábica. O aumento da concentração de agente carreador, em geral, proporcionou um aumento no parâmetro L* e diminuição dos parâmetros a* e b*, tornando as amostras mais claras e reduzindo as tonalidades vermelha e amarela. A guavira em pó apresentou coloração próxima do amarelo e marrom, com grande variação nos parâmetros de cor C* e H* em função das diferentes condições de secagem. A distribuição do tamanho de partículas não teve um padrão definido e o tamanho médio das amostras com maltodextrina foram maiores do que as com goma arábica para a temperatura do ar a 130 °C. No entanto, para as outras temperaturas (155 e 180) °C não houve um comportamento específico do tamanho das partículas em função da vazão de alimentação, tipo e ou concentração de agente carreador. A análise de microscopia eletrônica de varredura permitiu observar que as partículas obtidas tanto com maltodextrina como goma arábica apresentaram formato esférico, superfície rugosa e com adesão de partículas menores nas de maior tamanho, sendo que a superfície das partículas com goma arábica também apresentaram concavidades. A atividade antioxidante foi superior quando utilizada a temperatura de secagem intermediária. A partir das condições selecionadas na primeira etapa (temperatura do ar de 155 °C, vazão volumétrica da mistura de 40 mL/min e 10% de maltodextrina ou goma arábica) a polpa de guavira em pó foi caracterizada quanto a temperatura de transição vítrea, as isotermas de adsorção e a estabilidade à estocagem do ácido ascórbico, compostos fenólicos totais e da atividade antioxidante da polpa de guavira em pó produzida por spray drying ao longo de 120 dias. As temperaturas de transição vítrea foram de (25,2 ± 2,7 °C e 31,4 ± 0,4) °C para os pós produzidos com goma arábica e maltodextrina, respectivamente. O modelo de BET apresentou ajuste muito bom (R2>0,99) para descrever o comportamento de sorção de água das amostras nas temperaturas de (20, 30 e 40) °C. A polpa de guavira em pó produzida com goma arábica apresentou maior adsorção de água do que as amostras obtidas com maltodextrina. No estudo da estabilidade, as amostras foram acondicionadas em embalagem de polietileno laminado e armazenadas a 25 °C e umidade relativa de 75%. A embalagem de polietileno laminado foi eficiente na manutenção do teor de ácido ascórbico e atividade antioxidante da guavira em pó por um período de 120 dias, independente do carreador adicionado. O teor de compostos fenólicos para a guavira em pó com goma arábica apresentou uma redução nos primeiros 22 dias, contudo a amostra com maltodextrina manteve-se estável durante 120 dias de armazenamento.

Síntese e caracterização de nanomateriais superparamagnéticos do tipo core-shell para aplicação em catálise e biomedicina

As diversas aplicações tecnológicas de nanopartículas magnéticas (NPM) vêm intensificando o interesse por materiais com propriedades magnéticas diferenciadas, como magnetização de saturação (MS) intensificada e comportamento superparamagnético. Embora MNP metálicas de Fe, Co e bimetálicas de FeCo e FePt possuam altos valores de MS, sua baixa estabilidade química dificulta aplicações em escala nanométrica. Neste trabalho foram sintetizadas NPM de Fe, Co, FeCo e FePt com alta estabilidade química e rigoroso controle morfológico. NPM de óxido metálicos (Fe e Co) também foram obtidas. Dois métodos de síntese foram empregados. Usando método baseado em sistemas nanoheterogêneos (sistemas micelares ou de microemulsão inversa), foram sintetizadas NPM de Fe3O4 e Co metálico. Foram empregados surfactantes cátion-substituídos: dodecil sulfato de ferro(III) (FeDS) e dodecil sulfato de cobalto(II) (CoDS). Para a síntese das NPM, foram estudados e determinados a concentração micelar crítica do FeDS em 1-octanol (cmc = 0,90 mmol L-1) e o diagrama de fases pseudoternário para o sistema n-heptano/CoDS/n-butanol/H2O. NPM esferoidais de magnetita com3,4 nm de diâmetro e comportamento quase-paramagnético foram obtidas usando sistemas micelares de FeDS em 1-octanol. Já as NPM de Co obtidas via microemulsão inversa, apesar da larga distribuição de tamanho e baixa MS, são quimicamente estáveis e superparamagnéticas. O segundo método é baseado na decomposição térmica de complexos metálicos, pelo qual foram preparadas NPM esféricas de FePt e de óxidos metálicos (Fe3O4, FeXO1-X, (Co,Fe)XO1-X e CoFe2O4) com morfologia controlada e estabilidade química. O método não mostrou a mesma efetividade na síntese de NPM de FeAg e FeCo: a liga FeAg não foi obtida enquanto que NPM de FeCo com estabilidade química foram obtidas sem controle morfológico. NPM de Fe e FeCo foram preparadas a partir da redução térmica de NPM de Fe3O4 e CoFe2O4, as quais foram previamente recobertas com sílica. A sílica previne a sinterização inter-partículas, além de proporcionar caráter hidrofílico e biocompatibilidade ao material. As amostras reduzidas apresentaram aumento dos valores de MS (entre 21,3 e 163,9%), o qual é diretamente proporcional às dimensões das NPM. O recobrimento com sílica foi realizado via hidrólise de tetraetilortosilicato (TEOS) em sistema de microemulsão inversa. A espessura da camada de sílica foi controlada variando-se o tempo de reação e as concentrações de TEOS e de NPM, sendo então proposto um mecanismo do processo de recobrimento. Algumas amostras receberam um recobrimento adicional de TiO2 na fase anatase, para o qual foi empregado etilenoglicol como solvente e ligante para formação de glicolato de Ti como precursor. A espessura da camada de TiO2 (2-12 nm) é controlada variando as quantidades relativas entre NPM e o precursor de Ti. Ensaios de hipertermia magnética foram realizados para as amostras recobertas com sílica. Ensaios de hipertermia magnéticas mostram grande aumento da taxa de aquecimento das amostras após a redução térmica, mesmo para dispersões diluídas de NPM (0,6 a 4,5 mg mL-1). Taxas de aquecimento entre 0,3 e 3,0oC min-1 e SAR entre 37,2 e 96,3 W g-1. foram obtidos. A atividade fotocatalítica das amostras recobertas foram próximas à da fase anatase pura, com a vantagem de possuir um núcleo magnético que permite a recuperação do catalisador pela simples aplicação de campos magnéticos externos. Os resultados preliminares dos ensaios de hipertermia magnética e fotocatálise indicam um forte potencial dos materiais aqui relatados para aplicações em biomedicina e em fotocatálise.