Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 37
Filtrar
1.
Methods ; 54(4): 407-12, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21722733

RESUMO

Previous high throughput data analysis from several different approaches to affinity purification of protein complexes have revealed catalogues of contaminating proteins that persistently co-purify. Some of these contaminating proteins appear to be specific to one particular affinity matrix used or even to the artificial affinity tags introduced into endogenous proteins for the purpose of purification. A recent approach to minimising non-specific protein interactions in high throughput screens utilises pre-equilibration of affinity surfaces with thiocyanate anions to reduce non-specific binding of proteins. This approach not only reduces the effect of contaminating proteins but also promotes the enrichment of the specific binding partners. Here, we have taken this method and adapted it in an attempt to reduce the abundance of common contaminants in affinity purification experiments. We found the effect varied depending on the bait used, most likely due to its endogenous abundance.


Assuntos
Cromatografia de Afinidade/métodos , Proteínas de Drosophila/isolamento & purificação , Animais , Proteínas de Drosophila/química , Drosophila melanogaster , Espectrometria de Massas/métodos , Tiocianatos/química
2.
Insect Mol Biol ; 20(3): 303-10, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21199019

RESUMO

The Arctic springtail, Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola), is one of the few organisms known to survive the extreme stresses of its environment by using cryoprotective dehydration. We have undertaken a proteomics study comparing M. arctica, acclimated at -2°C, the temperature known to induce the production of the anhydroprotectant trehalose in this species, and -6°C, the temperature at which trehalose expression plateaus, against control animals acclimated at +5°C. Using difference gel electrophoresis, and liquid chromatography tandem mass spectrometry, we identified three categories of differentially expressed proteins with specific functions, up-regulated in both the -2°C and -6°C animals, that were involved in metabolism, membrane transport and protein folding. Proteins involved in cytoskeleton organisation were only up-regulated in the -6°C animals.


Assuntos
Aclimatação/genética , Temperatura Baixa , Insetos/metabolismo , Trealose/biossíntese , Água/metabolismo , Animais , Regiões Árticas , Proteínas de Insetos/genética , Proteínas de Insetos/metabolismo , Insetos/genética , Proteômica , Trealose/genética
3.
Mol Psychiatry ; 13(12): 1118-28, 2008 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-17938634

RESUMO

Although some insights into the etiology of schizophrenia have been gained, an understanding of the illness at the molecular level remains elusive. Recent advances in proteomic profiling offer great promise for the discovery of markers underlying pathophysiology of diseases. In the present study, we employed two high-throughput proteomic techniques together with traditional methods to investigate cerebrospinal fluid (CSF), brain and peripheral tissues (liver, red blood cells and serum) of schizophrenia patients in an attempt to identify peripheral/surrogate disease markers. The cohorts used to investigate each tissue were largely independent, although some CSF and serum samples were collected from the same patient. To address the major confounding factor of antipsychotic drug treatment, we also included a large cohort of first-onset drug-naive patients. Apolipoprotein A1 (apoA1) showed a significant decrease in expression in schizophrenia patients compared to controls in all five tissues examined. Specifically, using SELDI-TOF mass spectrometry, apoA1 was found decreased in CSF from schizophrenia patients (-35%, P=0.00001) and, using 2D-DIGE, apoA1 was also found downregulated in liver (-30%, P=0.02) and RBCs (-60%, P=0.003). Furthermore, we found a significant reduction of apoA1 in sera of first-onset drug-naive schizophrenia patients using enzyme-linked immunosorbent assay (-18%, P=0.00008) and in two investigations of post-mortem brain tissue using western blot analysis (-35%, P=0.05; -51%, P=0.05). These results show that apoA1 is consistently downregulated in the central nervous system as well as peripheral tissues of schizophrenia patients and may be linked to the underlying disease mechanism.


Assuntos
Apolipoproteína A-I/metabolismo , Encéfalo/metabolismo , Regulação para Baixo/fisiologia , Proteoma/metabolismo , Esquizofrenia , Adulto , Eletroforese em Gel Bidimensional , Ensaio de Imunoadsorção Enzimática , Feminino , Humanos , Masculino , Espectrometria de Massas , Análise Serial de Proteínas/métodos , Proteômica/métodos , Esquizofrenia/sangue , Esquizofrenia/líquido cefalorraquidiano , Esquizofrenia/patologia , Adulto Jovem
4.
PLoS One ; 11(1): e0147698, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26808156

RESUMO

The macrolide antibiotic, azithromycin (AZM), has been reported to improve the clinical outcome of cystic fibrosis patients, many of whom are chronically-infected with Pseudomonas aeruginosa. However, the highest clinically-achievable concentrations of this drug are well-below the minimum inhibitory concentration for P. aeruginosa, raising the question of why AZM exhibits therapeutic activity. One possibility that has been raised by earlier studies is that AZM inhibits quorum sensing (QS) by P. aeruginosa. To explicitly test this hypothesis the changes brought about by AZM treatment need to be compared with those associated with specific QS mutants grown alongside in the same growth medium, but this has not been done. In this work, we used quantitative 2D-difference gel electrophoresis and 1H-NMR spectroscopy footprint analysis to examine whether a range of clinically-relevant AZM concentrations elicited proteomic and metabolomic changes in wild-type cultures that were similar to those seen in cultures of defined QS mutants. Consistent with earlier reports, over half of the AZM-induced spot changes on the 2D gels were found to affect QS-regulated proteins. However, AZM modulated very few protein spots overall (compared with QS) and collectively, these modulated proteins comprised only a small fraction (12-13%) of the global QS regulon. We conclude that AZM perturbs a sub-regulon of the QS system but does not block QS per se. Reinforcing this notion, we further show that AZM is capable of attenuating virulence factor production in another Gram-negative species that secretes copious quantities of exoenzymes (Serratia marcescens), even in the absence of a functional QS system.


Assuntos
Antibacterianos/farmacologia , Azitromicina/farmacologia , Proteínas de Bactérias/metabolismo , Proteoma , Pseudomonas aeruginosa/efeitos dos fármacos , Percepção de Quorum/efeitos dos fármacos , Eletroforese em Gel Bidimensional , Fluorescência , Genes Bacterianos , Metabolômica , Espectroscopia de Prótons por Ressonância Magnética , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Pseudomonas aeruginosa/fisiologia , Percepção de Quorum/genética
5.
J Neuroendocrinol ; 28(1)2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26606900

RESUMO

The choroid plexus (CP) epithelium is a unique structure in the brain that forms an interface between the peripheral blood and the cerebrospinal fluid (CSF), which is mostly produced by the CP itself. Because the CP transcriptome is regulated by the sex hormone background, the present study compared gene/protein expression profiles in the CP and CSF from male and female rats aiming to better understand sex-related differences in CP functions and brain physiology. We used data previously obtained by cDNA microarrays to compare the CP transcriptome between male and female rats, and complemented these data with the proteomic analysis of the CSF of castrated and sham-operated males and females. Microarray analysis showed that 17 128 and 17 002 genes are expressed in the male and female CP, which allowed the functional annotation of 141 and 134 pathways, respectively. Among the most expressed genes, canonical pathways associated with mitochondrial dysfunctions and oxidative phosphorylation were the most prominent, whereas the most relevant molecular and cellular functions annotated were protein synthesis, cellular growth and proliferation, cell death and survival, molecular transport, and protein trafficking. No significant differences were found between males and females regarding these pathways. Seminal functions of the CP differentially regulated between sexes were circadian rhythm signalling, as well as several canonical pathways related to stem cell differentiation, metabolism and the barrier function of the CP. The proteomic analysis identified five down-regulated proteins in the CSF samples from male rats compared to females and seven proteins exhibiting marked variation in the CSF of gonadectomised males compared to sham animals, whereas no differences were found between sham and ovariectomised females. These data clearly show sex-related differences in CP gene expression and CSF protein composition that may impact upon neurological diseases.


Assuntos
Encéfalo/metabolismo , Líquido Cefalorraquidiano/metabolismo , Plexo Corióideo/metabolismo , Caracteres Sexuais , Animais , Transporte Biológico/genética , Ritmo Circadiano/genética , Feminino , Masculino , Fosforilação Oxidativa , Proteômica , Ratos , Ratos Wistar , Transcriptoma
6.
Biochim Biophys Acta ; 1080(3): 191-7, 1991 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-1954226

RESUMO

The amino acid sequence is reported for CNBr and tryptic peptide fragments of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum. Together with the N-terminal sequence, these make up about 75% of the total sequence. The sequence shows extensive similarity with that of the NADP(+)-dependent glutamate dehydrogenase of Escherichia coli (52% identical residues out of the 332 compared) allowing confident placing of the peptide fragments within the overall sequence. This demonstrated sequence similarity with the E. coli enzyme, despite different coenzyme specificity, is much greater than the similarity (31% identities) between the GDH's of C. symbiosum and Peptostreptococcus asaccharolyticus, both NAD(+)-linked. The evolutionary implications are discussed. In the 'fingerprint' region of the nucleotide binding fold the sequence Gly X Gly X X Ala is found, rather than Gly X Gly X X Gly. The sequence found here has previously been associated with NADP+ specificity and its finding in a strictly NAD(+)-dependent enzyme requires closer examination of the function of this structural motif.


Assuntos
Clostridium/enzimologia , Glutamato Desidrogenase/química , Sequência de Aminoácidos , Evolução Biológica , Brometo de Cianogênio , Glutamato Desidrogenase/isolamento & purificação , Dados de Sequência Molecular , NAD/fisiologia , Homologia de Sequência do Ácido Nucleico , Tripsina
7.
Endocrinology ; 132(2): 640-5, 1993 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-8425483

RESUMO

Previously, we demonstrated that nondiabetic insulin-resistant monkeys had reduced covalent insulin activation of muscle glycogen synthase (GS) compared to normal monkeys and that covalent insulin activation of adipose tissue GS was absent in these monkeys. Covalent insulin activation of muscle and adipose tissue GS in monkeys with impaired glucose tolerance and noninsulin-dependent diabetes (NIDDM) was also absent. As in humans, monkeys with NIDDM have a lower urinary excretion rate of chiroinositol (CI), a component of a putative mediator of insulin action, compared to normal monkeys. To determine whether the urinary excretion rate of CI was related to insulin resistance, which develops naturally in many obese rhesus monkeys, we examined the relationships between 24-h urinary CI excretion rate and 1) whole body insulin-mediated glucose disposal rates (M) and insulin-mediated changes in 2) the skeletal muscle GS activity ratio (sm delta GSAR), 3) the skeletal muscle glycogen phosphorylase activity ratio, and 4) the adipose tissue GS activity ratio (at delta GSAR) in 27 monkeys ranging from normal (n = 12) to insulin resistant (n = 8) to overtly diabetic (n = 7). The urinary CI excretion rate was significantly correlated with M (r = 0.47; P < 0.02), sm delta GSAR (r = 0.38; P < 0.05), skeletal muscle glycogen phosphorylase activity ratio (r = -0.49; P < 0.01), and at delta GSAR (r = 0.46; P < 0.02). The urinary CI excretion rate was also correlated with glucose tolerance (r = 0.39; P < 0.05). There was a wide range of urinary CI excretion rates (0.42-5.17 mumol/day) in monkeys with normal fasting plasma glucose concentrations. However, of the 7 diabetic monkeys, 6 had a urinary CI excretion rate below 2.0 mumol/day, and in the subgroup of 16 monkeys with a urinary CI excretion rate less than 2.0 mumol/day, the associations of urinary CI with M rate (r = 0.65; P < 0.005), glucose tolerance (r = 0.63; P < 0.01), and sm delta GSAR (r = 0.73; P < 0.001) increased in strength and significance. We propose that the urinary CI excretion rate may be 1) a biochemical indicator of both in vivo and in vitro insulin resistance and 2) a noninvasive diagnostic tool with potential for the identification of those individuals at risk for NIDDM and other related diseases with insulin resistance.


Assuntos
Diabetes Mellitus Tipo 2/veterinária , Inositol/deficiência , Inositol/urina , Resistência à Insulina/fisiologia , Doenças dos Macacos , Análise de Variância , Animais , Diabetes Mellitus Tipo 2/fisiopatologia , Diabetes Mellitus Tipo 2/urina , Feminino , Teste de Tolerância a Glucose , Hiperinsulinismo/fisiopatologia , Hiperinsulinismo/urina , Hiperinsulinismo/veterinária , Isomerismo , Macaca mulatta , Masculino
8.
J Clin Endocrinol Metab ; 81(3): 1051-7, 1996 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-8772575

RESUMO

A novel low mol wt inositol phosphoglycan antagonist of insulin action of oxidative glucose metabolism in isolated rat adipocytes was partially purified from normal human plasma and shown to be increased in type II diabetic plasma. It was characterized chemically as a myo-inositol phosphoglycan containing a cyclic 1,2-phosphate. This antagonist, termed fraction V3, is now shown to inhibit the action of an inositol glycan insulin pH 2.0 mediator that stimulates pyruvate dehydrogenase phosphatase in a similar manner to insulin. In addition, fraction V3 inhibits stimulation of the pyruvate dehydrogenase (PDH) phosphatase by Mg2+, the enzyme's required metal, and by spermine, a polyamine. Fraction V3 does not inhibit active PDH itself. The inhibitory effect is dose dependent and apparently noncompetitive or nonsurmountable for the insulin inositol glycan pH 2.0 mediator, thus comparing kinetically with its insulin antagonistic action on intact adipocytes. Its inhibitory action on PDH phosphatase is dose dependent and competitive for Mg2+ stimulation of the phosphatase. Additionally, fraction V3 is shown to inhibit stimulation by Mg2+ of cloned recombinant PDH phosphatase catalytic subunit. Inhibition by fraction V3 of Mg(2+)-stimulated PDH phosphatase and its cloned catalytic subunit helps explain its mechanism of action to inhibit insulin-stimulated oxidative glucose metabolism in adipocytes and its potential clinical significance in insulin resistance.


Assuntos
Fenômenos Fisiológicos Sanguíneos , Fosfatos de Inositol/sangue , Fosfatos de Inositol/farmacologia , Antagonistas da Insulina/farmacologia , Resistência à Insulina , Polissacarídeos/sangue , Polissacarídeos/farmacologia , Piruvato Desidrogenase (Lipoamida)-Fosfatase/metabolismo , Animais , Bovinos , Humanos , Magnésio/farmacologia , Miocárdio/enzimologia , Espermina/farmacologia
9.
FEBS Lett ; 262(2): 327-9, 1990 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-2335214

RESUMO

The multicatalytic proteinase complex is a high molecular weight nonlysosomal proteinase which is composed of many different types of subunit. As part of a study of the possible relationships between subunits, polypeptides derived from the multicatalytic proteinase from rat liver have been subjected to N-terminal amino acid sequence analysis. Although several of the subunits are blocked at their N-termini, sequences have been obtained for 7 of the polypeptides. Each of the 7 sequences is unique but they show considerable sequence similarity, suggesting that the proteins are encoded by members of the same gene family.


Assuntos
Cisteína Endopeptidases/genética , Fígado/enzimologia , Complexos Multienzimáticos/genética , Família Multigênica , Sequência de Aminoácidos , Animais , Dados de Sequência Molecular , Complexo de Endopeptidases do Proteassoma , Conformação Proteica , Ratos
10.
J Biomol Tech ; 10(4): 187-93, 1999 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19499025

RESUMO

The Nucleic Acids Research Group of the Association of Biomolecular Resource Facilities (ABRF) last surveyed DNA synthesis core facilities in April 1995. Because of the introduction of new technologies and dramatic changes in the market, we sought to update survey information and to determine how academic facilities responded to the challenge presented by commercial counterparts. The online survey was opened in January 1999 by notifying members and subscribers to the ABRF electronic discussion group. The survey consisted of five parts: general facility information, oligonucleotide production profile, oligonucleotide charges, synthesis protocols, and trends in DNA synthesis (including individual comments). All submitted data were anonymously coded. Respondents from DNA synthesis facilities were primarily from the academic category and were established between 1984 and 1991. Typically, a facility provides additional services such as DNA sequencing and has upgraded to electronic ordering. There is stability in staffing profiles for these facilities in that the total number of employees is relatively unchanged, the tenure for staff averages 5.9 years, and experience is extensive. On average, academic facilities annually produce approximately 1/16 the number of oligonucleotides produced by the average commercial facilities, but all facilities report an increase in demand. Charges for standard oligonucleotides from academic facilities are relatively higher than from commercial companies; however, the opposite is true for modified phosphoramidites. Subsidized facilities charge less than nonsubsidized facilities. Synthesis protocols and reagents are standard across the categories. Most facilities offer typical modifications such as biotinylation. Despite the competition by large commercial facilities that have reduced costs dramatically, academic facilities remain a stable entity. Academic facilities enhance the quality of service by focusing on nonstandard oligonucleotides and valuable services such as personal consultations, electronic ordering, and diversifying into other services.

11.
Environ Mol Mutagen ; 28(4): 430-3, 1996.
Artigo em Inglês | MEDLINE | ID: mdl-8991074

RESUMO

Tamoxifen, an important drug in breast cancer treatment, causes liver cancer in rats. The standard range of in vitro tests have failed to show that it causes DNA damage, but 32P-postlabelling and DNA-binding studies have shown that tamoxifen forms DNA adducts in rat liver. In 1995 a transgenic rat (Big Blue; Stratagene, La Jolla, CA) became available which harbours the bacterial lacI gene, thereby allowing the in vivo study of tamoxifen mutagenesis. Recently, we [Styles JA et al. (1996): Toxicologist 30; 161] showed that tamoxifen caused on increase in the mutation frequency at the lacI gene in these transgenic rats. In this study, we report on our preliminary analysis of the mutational spectra of 33 control and 38 tamoxifen-induced mutant lacI genes. Plasmid DNA containing the lacI gene was isolated from the mutant phages and its DNA sequence determined. In the control animal group, 81% of the mutant lacI genes were point mutations, whilst in the tamoxifen-treated group, 62% of the mutant lacI genes were point mutations. Of the tamoxifen-induced mutants, 43% were GC-->TA transversions and 70% of point mutations. In the control group, GC-->TA transversions were 19% of all mutations and 24% of point mutations. Thus, compared with control animals, tamoxifen treatment had significantly increased the proportion of GC-->TA transversions.


Assuntos
Animais Geneticamente Modificados/genética , Proteínas de Bactérias/genética , Proteínas de Escherichia coli , Fígado/efeitos dos fármacos , Mutação , Proteínas Repressoras/genética , Tamoxifeno/toxicidade , Animais , Antineoplásicos Hormonais/toxicidade , Proteínas de Bactérias/efeitos dos fármacos , Repressores Lac , Masculino , Polimorfismo Conformacional de Fita Simples , Ratos , Ratos Endogâmicos F344 , Proteínas Repressoras/efeitos dos fármacos
12.
J Chromatogr A ; 781(1-2): 99-105, 1997 Sep 26.
Artigo em Inglês | MEDLINE | ID: mdl-9368381

RESUMO

Mass spectrometry (MS) detection using electrospray ionization (ESI) has been explored for the separation by capillary electrophoresis (CE) of a number of sample mixtures containing low-molecular-mass species. Optimal sheath liquid composition has been determined using a peptide mixture in which femtomolar quantities of analyte were easily observed. Effects of CE buffer choice were studied in detail. Also, a separation of basic drugs in cough syrup has been successfully detected by ESI-MS. Using negative ionization, a mixture of alkyl sulfonates and a mixture of food dyes were analyzed. All components were easily resolved and identified by molecular weight.


Assuntos
Alcanossulfonatos/análise , Antitussígenos/análise , Corantes/análise , Eletroforese Capilar/métodos , Espectrometria de Massas/métodos , Peptídeos/análise , Antitussígenos/química , Soluções Tampão , Concentração de Íons de Hidrogênio , Peso Molecular , Peptídeos/química
13.
J Inorg Biochem ; 35(1): 9-22, 1989 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-2709002

RESUMO

Ferritin molecules contain 24 subunits forming a shell around an inorganic iron-core. Release of iron(III) from ferritin and its isolated iron-cores by a series of hydroxypyridinone chelators with high affinities for iron(III) has been compared. The results collectively suggest that the chelators act by penetrating the protein shell and interacting directly with the iron-core in ferritin. Iron(III) is probably removed bound to a single ligand, but once outside the protein shell, the trihydroxypyridinone iron(III) complex predominates. The order of effectiveness of a group of pyridinones found for iron removal from ferritin molecules in solution differs from that obtained with hepatocytes in culture or with whole animals, where membrane solubility and other factors may modulate the response.


Assuntos
Ferritinas/metabolismo , Ferro/metabolismo , Piridonas/farmacologia , Animais , Quelantes/farmacologia , Desferroxamina , Cavalos , Concentração de Íons de Hidrogênio , Técnicas In Vitro , Ratos , Especificidade da Espécie
14.
Int J Food Microbiol ; 96(1): 35-48, 2004 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-15358504

RESUMO

To date, the survival of Escherichia coli O157:H7 and other verocytotoxin-producing E. coli (VTEC) in chocolate and other confectionery products has not been fully established, unlike Salmonella, which have been responsible for occasional outbreaks of infection linked to contaminated chocolate and related products, although none of these outbreaks have been related to products produced in the United Kingdom. The United Kingdom Biscuit, Cake, Chocolate and Confectionery Alliance commissioned this study to obtain information on the decline and potential survival of E. coli, particularly verocytotoxin-producing strains, in reduced aw confectionery products chocolate, biscuit cream and mallow. These products were artificially contaminated with high (4 log10 cfu/g) and low (2 log10 cfu/g) levels of E. coli O157:H7, O111:H- and O26:H11 and their survival, as affected by storage temperature (10, 22 and 38 degrees C), was monitored over 12 months. Preliminary studies to establish the best inoculation and recovery procedures indicated that differences between counts on selective and non-selective media used were not sufficiently different to influence the outcome of this study. Irrespective of sample type, rapid decline was observed in products stored at 38 degrees C and increased survival occurred in products stored at 10 degrees C. In chocolate (average aw 0.40), these bacteria were detected for up to 43 days in samples stored at 38 degrees C. At 22 degrees C they survived for up to 90 days and in product stored at 10 degrees C they could still be detected after 366 days storage. In biscuit cream (average aw 0.75) they survived for 2 days at 38 degrees C, 42 days at 22 degrees C and 58 days at 10 degrees C. Whilst mallow (aw ca. 0.73) was not stored at 38 degrees C, these bacteria could still be detected in samples stored for up to 113 and 273 days at 22 and 10 degrees C, respectively. The observed prolonged survival of these bacteria under conditions of reduced aw and lowered storage temperature in this study is supported by previous studies with Salmonella and E. coli O157:H7 in other foods. In the same way that Salmonella bacteria can survive for long periods, in excess of 12 months, in chocolate, this study provides evidence that E. coli, including pathogenic strains, can also survive for similar periods of time. Assuming the routes of transmission are similar, controls currently used by the confectionery industry to prevent contamination by Salmonella should also be effective against E. coli, including VT-producing strains, providing that all raw materials have been suitably processed, stored and handled before and during manufacture.


Assuntos
Cacau/microbiologia , Escherichia coli O157/crescimento & desenvolvimento , Escherichia coli/crescimento & desenvolvimento , Manipulação de Alimentos/métodos , Microbiologia de Alimentos , Contagem de Colônia Microbiana , Contaminação de Alimentos/análise , Contaminação de Alimentos/prevenção & controle , Temperatura , Fatores de Tempo
15.
Cell Death Differ ; 21(1): 161-71, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24141718

RESUMO

Post-transcriptional control of gene expression is mediated by the interaction of RNA-binding proteins with their cognate mRNAs that specifically regulate their stability, localization and translation. mRNA-binding proteins are multifunctional and it has been proposed therefore that a combinatorial RNA-binding protein code exists that allows specific protein sub-complexes to control cytoplasmic gene expression under a range of pathophysiological conditions. We show that polypyrimidine tract-binding protein (PTB) is central to one such complex that forms in apoptotic cells. Thus, during apoptosis initiated by TNF-related apoptosis inducing ligand there is a change in the repertoire of RNA-binding proteins with which PTB interacts. We show that altering the cellular levels of PTB and its binding partners, either singly or in combination, is sufficient to directly change the rates of apoptosis with increased expression of PTB, YBX1, PSF and NONO/p54(nrb) accelerating this process. Mechanistically, we show that these proteins post-transcriptionally regulate gene expression, and therefore apoptotic rates, by interacting with and stimulating the activity of RNA elements (internal ribosome entry segments) found in mRNAs that are translated during apoptosis. Taken together, our data show that PTB function is controlled by a set of co-recruited proteins and importantly provide further evidence that it is possible to dictate cell fate by modulating cytoplasmic gene expression pathways alone.


Assuntos
Apoptose/efeitos dos fármacos , Proteína de Ligação a Regiões Ricas em Polipirimidinas/metabolismo , Ligante Indutor de Apoptose Relacionado a TNF/farmacologia , Núcleo Celular/metabolismo , Ciclina T/genética , Ciclina T/metabolismo , Proteínas de Ligação a DNA , Células HeLa , Histona-Lisina N-Metiltransferase/genética , Histona-Lisina N-Metiltransferase/metabolismo , Humanos , Células MCF-7 , Proteínas Associadas à Matriz Nuclear/antagonistas & inibidores , Proteínas Associadas à Matriz Nuclear/genética , Proteínas Associadas à Matriz Nuclear/metabolismo , Fatores de Transcrição de Octâmero/antagonistas & inibidores , Fatores de Transcrição de Octâmero/genética , Fatores de Transcrição de Octâmero/metabolismo , Fator de Processamento Associado a PTB , Proteína de Ligação a Regiões Ricas em Polipirimidinas/antagonistas & inibidores , Proteína de Ligação a Regiões Ricas em Polipirimidinas/genética , Interferência de RNA , RNA Mensageiro/metabolismo , RNA Interferente Pequeno/metabolismo , Proteínas de Ligação a RNA/antagonistas & inibidores , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Proteína 1 de Ligação a Y-Box/metabolismo
16.
J Proteomics ; 88: 129-40, 2013 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-23523639

RESUMO

Prediction of protein sub-cellular localisation by employing quantitative mass spectrometry experiments is an expanding field. Several methods have led to the assignment of proteins to specific subcellular localisations by partial separation of organelles across a fractionation scheme coupled with computational analysis. Methods developed to analyse organelle data have largely employed supervised machine learning algorithms to map unannotated abundance profiles to known protein-organelle associations. Such approaches are likely to make association errors if organelle-related groupings present in experimental output are not included in data used to create a protein-organelle classifier. Currently, there is no automated way to detect organelle-specific clusters within such datasets. In order to address the above issues we adapted a phenotype discovery algorithm, originally created to filter image-based output for RNAi screens, to identify putative subcellular groupings in organelle proteomics experiments. We were able to mine datasets to a deeper level and extract interesting phenotype clusters for more comprehensive evaluation in an unbiased fashion upon application of this approach. Organelle-related protein clusters were identified beyond those sufficiently annotated for use as training data. Furthermore, we propose avenues for the incorporation of observations made into general practice for the classification of protein-organelle membership from quantitative MS experiments. BIOLOGICAL SIGNIFICANCE: Protein sub-cellular localisation plays an important role in molecular interactions, signalling and transport mechanisms. The prediction of protein localisation by quantitative mass-spectrometry (MS) proteomics is a growing field and an important endeavour in improving protein annotation. Several such approaches use gradient-based separation of cellular organelle content to measure relative protein abundance across distinct gradient fractions. The distribution profiles are commonly mapped in silico to known protein-organelle associations via supervised machine learning algorithms, to create classifiers that associate unannotated proteins to specific organelles. These strategies are prone to error, however, if organelle-related groupings present in experimental output are not represented, for example owing to the lack of existing annotation, when creating the protein-organelle mapping. Here, the application of a phenotype discovery approach to LOPIT gradient-based MS data identifies candidate organelle phenotypes for further evaluation in an unbiased fashion. Software implementation and usage guidelines are provided for application to wider protein-organelle association experiments. In the wider context, semi-supervised organelle discovery is discussed as a paradigm with which to generate new protein annotations from MS-based organelle proteomics experiments.


Assuntos
Proteínas de Arabidopsis/análise , Proteínas de Drosophila/análise , Espectrometria de Massas/métodos , Organelas/química , Proteômica/métodos , Animais , Arabidopsis , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Proteínas de Drosophila/química , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Células HEK293 , Humanos , Organelas/metabolismo
17.
Microbiology (Reading) ; 155(Pt 3): 687-698, 2009 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-19246740

RESUMO

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes acute and chronic infections in immunocompromised individuals. It is also a model organism for bacterial biofilm formation. Acute infections are often associated with planktonic or free-floating cells, high virulence and fast growth. Conversely, chronic infections are often associated with the biofilm mode of growth, low virulence and slow growth that resembles that of planktonic cells in stationary phase. Biofilm formation and type III secretion have been shown to be reciprocally regulated, and it has been suggested that factors related to acute infection may be incompatible with biofilm formation. In a previous proteomic study of the interrelationships between planktonic cells, colonies and continuously grown biofilms, we showed that biofilms under the growth conditions applied are more similar to planktonic cells in exponential phase than to those in stationary phase. In the current study, we investigated how these conditions influence the production of virulence factors using a transcriptomic approach. Our results show that biofilms express the type III secretion system, whereas planktonic cells do not. This was confirmed by the detection of PcrV in the cellular and secreted fractions of biofilms, but not in those of planktonic cells. We also detected the type III effector proteins ExoS and ExoT in the biofilm effluent, but not in the supernatants of planktonic cells. Biofilm formation and type III secretion are therefore not mutually exclusive in P. aeruginosa, and biofilms could play a more active role in virulence than previously thought.


Assuntos
Biofilmes/crescimento & desenvolvimento , Pseudomonas aeruginosa/crescimento & desenvolvimento , Pseudomonas aeruginosa/metabolismo , Fatores de Virulência/biossíntese , Proteínas de Bactérias/metabolismo , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Análise de Sequência com Séries de Oligonucleotídeos , Pseudomonas aeruginosa/genética , RNA Bacteriano/metabolismo
18.
J Bacteriol ; 189(6): 2411-6, 2007 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-17220232

RESUMO

Pseudomonas aeruginosa is a gram-negative bacterium and an opportunistic human pathogen that causes chronic infections in immunocompromised individuals. These infections are hard to treat, partly due to the high intrinsic resistance of the bacterium to clinically used antibiotics and partly due to the formation of antibiotic-tolerant biofilms. The three most common ways of growing bacteria in vitro are as planktonic cultures, colonies on agar plates, and biofilms in continuous-flow systems. Biofilms are known to express genes different from those of planktonic cells, and biofilm cells are generally believed to closely resemble planktonic cells in stationary phase. However, few, if any, studies have examined global gene expression in colonies. We used a proteomic approach to investigate the interrelationships between planktonic cells, colonies, and biofilms under comparable conditions. Our results show that protein profiles in colonies resemble those of planktonic cells. Furthermore, contrary to what has been reported previously, the protein profiles of biofilms were found to more closely resemble those of exponentially growing planktonic cells than those of planktonic cells in the stationary phase. These findings raise some intriguing questions about the true nature of biofilms.


Assuntos
Proteínas de Bactérias/metabolismo , Biofilmes/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Plâncton/crescimento & desenvolvimento , Proteoma , Pseudomonas aeruginosa/crescimento & desenvolvimento , Ágar , Análise de Variância , Proteínas de Bactérias/genética , Técnicas Bacteriológicas , Meios de Cultura , Eletroforese em Gel Bidimensional , Fluorescência , Humanos , Plâncton/genética , Plâncton/metabolismo , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo
19.
J Mater Sci Mater Med ; 16(12): 1185-90, 2005 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-16362220

RESUMO

Nanocrystalline hydroxyapatite (nHA) can be mixed with phosphoric acid to form a brushite cement; a degradable inorganic bone filling material. nHA was precipitated from reactants of calcium to phosphate (Ca/P) ratio 0.8 to 2.0 and mixed with phosphoric acid, which resulted in the formation of a brushite cement. Cement was also formed by mixing microcrystalline calcium phosphates, beta-tricalcium phosphate, hydroxyapatite and tetracalcium phosphate with phosphoric acid solution. Cement produced with nHA was stronger in compression than that formed with crystalline calcium phosphate phases. Setting time, strength and composition of cement produced with nHA was dependant on both the Ca/P ratio of nHA and the concentration of phosphoric acid in cement slurry. Increasing phosphoric acid concentration increased compressive strength whilst reducing the initial setting time of cement. Reducing the Ca/P ratio of nHA precipitation reactants retarded the setting and increased the extent of reaction of cements. This finding was unexpected and suggests that Ca/P ratio may strongly affect dissolution behaviour and this parameter is more important than stoichiometry in determining extent of reaction in this system. This study demonstrated that the wide variation in stoichiometry that may be attained in nanocrystalline apatite may be utilised to change cement performance and setting behaviour.


Assuntos
Cimentos Ósseos , Fosfatos de Cálcio/química , Durapatita , Nanotecnologia , Difração de Raios X
20.
J Mater Sci Mater Med ; 16(5): 455-60, 2005 May.
Artigo em Inglês | MEDLINE | ID: mdl-15875256

RESUMO

Brushite cement may be used as a bone graft material and is more soluble than apatite in physiological conditions. Consequently it is considerably more resorbable in vivo than apatite forming cements. Brushite cement formation has previously been reported by our group following the mixture of nanocrystalline hydroxyapatite and phosphoric acid. In this study, brushite cement was formed from the reaction of nanocrystalline magnesium-substituted hydroxyapatite with phosphoric acid in an attempt to produce a magnesium substituted brushite cement. The presence of magnesium was shown to have a strong effect on cement composition and strength. Additionally the presence of magnesium in brushite cement was found to reduce the extent of brushite hydrolysis resulting in the formation of HA. By incorporating magnesium ions in the apatite reactant structure the concentration of magnesium ions in the liquid phase of the cement was controlled by the dissolution rate of the apatite. This approach may be used to supply other ions to cement systems during setting as a means to manipulate the clinical performance and characteristics of brushite cements.


Assuntos
Cimentos Ósseos/química , Cristalização/métodos , Durapatita/química , Magnésio/química , Nanoestruturas/química , Cimentos Ósseos/análise , Força Compressiva , Durapatita/análise , Dureza , Magnésio/análise , Teste de Materiais , Peso Molecular , Nanoestruturas/análise , Tamanho da Partícula
SELEÇÃO DE REFERÊNCIAS
Detalhe da pesquisa