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1.
RNA Biol ; 18(4): 563-575, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-32893724

RESUMEN

Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.


Asunto(s)
Enzimas/genética , Agregado de Proteínas/genética , Biosíntesis de Proteínas/genética , ARN de Transferencia/metabolismo , Saccharomyces cerevisiae , Codón/genética , Mutación , Organismos Modificados Genéticamente , Proteostasis/genética , Procesamiento Postranscripcional del ARN/genética , ARN de Transferencia/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
2.
Int J Mol Sci ; 22(6)2021 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-33799331

RESUMEN

Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5'tRNA-derived stress-induced RNAs (5'tiRNAs), namely 5'tiRNA-GlyGCC and 5'tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.


Asunto(s)
Estrés Oxidativo/genética , ARN de Transferencia/genética , Ribonucleasa Pancreática/genética , ARNt Metiltransferasas/genética , Humanos , División del ARN/genética , Procesamiento Postranscripcional del ARN/genética , Estabilidad del ARN/genética , ARN Pequeño no Traducido/genética , ARN de Transferencia/química , Estrés Fisiológico/genética , Uridina/análogos & derivados , Uridina/genética
3.
Molecules ; 26(21)2021 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-34770818

RESUMEN

Studying aging is important to further understand the molecular mechanisms underlying this physiological process and, ideally, to identify a panel of aging biomarkers. Animals, in particular mice, are often used in aging studies, since they mimic important features of human aging, age quickly, and are easy to manipulate. The present work describes the use of Fourier Transform Infrared (FTIR) spectroscopy to identify an age-related spectroscopic profile of the cardiac and skeletal muscle tissues of C57BL/6J female mice. We acquired ATR-FTIR spectra of cardiac and skeletal muscle at four different ages: 6; 12; 17 and 24 months (10 samples at each age) and analyzed the data using multivariate statistical tools (PCA and PLS) and peak intensity analyses. The results suggest deep changes in protein secondary structure in 24-month-old mice compared to both tissues in 6-month-old mice. Oligomeric structures decreased with age in both tissues, while intermolecular ß-sheet structures increased with aging in cardiac muscle but not in skeletal muscle. Despite FTIR spectroscopy being unable to identify the proteins responsible for these conformational changes, this study gives insights into the potential of FTIR to monitor the aging process and identify an age-specific spectroscopic signature.


Asunto(s)
Envejecimiento , Miocardio/citología , Proteínas/análisis , Animales , Femenino , Ratones , Ratones Endogámicos C57BL , Músculo Esquelético/citología , Músculo Esquelético/metabolismo , Miocardio/metabolismo , Conformación Proteica en Lámina beta , Proteínas/metabolismo , Espectroscopía Infrarroja por Transformada de Fourier
4.
RNA Biol ; 17(1): 135-149, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31570039

RESUMEN

Deregulation of tRNAs, aminoacyl-tRNA synthetases (aaRS) or tRNA modifying enzymes, increase the level of protein synthesis errors (PSE) and are associated with several diseases, but the cause-effect mechanisms of these pathologies remain elusive. To clarify the role of PSE in human biology, we have engineered a HEK293 cell line to overexpress a wild type (Wt) tRNASer and two tRNASer mutants that misincorporate serine at non-cognate codon sites. Then, we followed long-term adaptation to PSE of such recombinant cells by analysing cell viability, protein synthesis rate and activation of protein quality control mechanisms (PQC). Engineered cells showed higher level of misfolded and aggregated proteins; activated the ubiquitin-proteasome system (UPS) and the unfolded protein response (UPR), indicative of proteotoxic stress. Adaptation to PSE involved increased protein turnover, UPR up-regulation and altered protein synthesis rate. Gene expression analysis showed that engineered cells presented recurrent alterations in the endoplasmic reticulum, cell adhesion and calcium homeostasis. Herein, we unveil new phenotypic consequences of protein synthesis errors in human cells and identify the protein quality control processes that are necessary for long-term adaptation to PSE and proteotoxic stress. Our data provide important insight on how chronic proteotoxic stress may cause disease and highlight potential biological pathways that support the association of PSE with disease.


Asunto(s)
Adaptación Biológica , Regulación de la Expresión Génica , Mutación , Biosíntesis de Proteínas , Biología Computacional/métodos , Ontología de Genes , Células HEK293 , Humanos , Chaperonas Moleculares/metabolismo , Complejo de la Endopetidasa Proteasomal , Procesamiento Proteico-Postraduccional , ARN de Transferencia/genética , Ubiquitina/metabolismo , Respuesta de Proteína Desplegada
5.
Microb Ecol ; 76(1): 144-155, 2018 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-29255936

RESUMEN

Increases in the terrestrial export of dissolved organic carbon (C) to rivers may be associated with additional loading of organic nitrogen (N) and phosphorus (P) to the coastal zone. However, little is known about how these resources interact in the regulation of heterotrophic bacterioplankton metabolism in boreal coastal ecosystems. Here, we measured changes in bacterioplankton production (BP) and respiration (BR) in response to full-factorial (C, N, and P) enrichment experiments at two sites within the Öre estuary, northern Sweden. The BR was stimulated by single C additions and further enhanced by combined additions of C and other nutrients. Single addition of N or P had no effect on BR rates. In contrast, BP was primarily limited by P at the site close to the river mouth and did not respond to C or N additions. However, at the site further away from the near the river mouth, BP was slightly stimulated by single additions of C. Possibly, the natural inflow of riverine bioavailable dissolved organic carbon induced local P limitation of BP near the river mouth, which was then exhausted and resulted in C-limited BP further away from the river mouth. We observed positive interactions between all elements on all responses except for BP at the site close to the river mouth, where P showed an independent effect. In light of predicted increases in terrestrial P and C deliveries, we expect future increases in BP and increases of BR of terrestrially delivered C substrates at the Öre estuary and similar areas.


Asunto(s)
Bacterias/crecimiento & desarrollo , Bacterias/metabolismo , Carbono/metabolismo , Estuarios , Nutrientes/metabolismo , Agua de Mar/microbiología , Carbono/química , Ecosistema , Monitoreo del Ambiente , Agua Dulce/química , Procesos Heterotróficos , Nutrientes/química , Fósforo/metabolismo , Plancton/crecimiento & desarrollo , Plancton/metabolismo , Ríos/química , Salinidad , Estaciones del Año , Suecia
6.
Extremophiles ; 20(6): 811-820, 2016 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-27502056

RESUMEN

Gimesia maris and Rubinisphaera brasiliensis are slightly halophilic representatives of the deep-branching phylum Planctomycetes. For osmoadaptation both species accumulated α-glutamate, sucrose, ectoine and hydroxyectoine. A major role was found for ectoine, hydroxyectoine as well as sucrose under hyper-osmotic shock conditions. Nevertheless, the levels of sucrose were up-regulated by the increased salinity levels and also by low nitrogen availability. Additionally, G. maris accumulated glucosylglycerate (GG) as major solute specifically under low nitrogen levels, which prompted us to analyse the transcript abundance of two homologues genes known for the biosynthesis of GG, namely glucosyl-3-phosphoglycerate synthase (GpgS) and glucosyl-3-phosphoglycerate phosphatase (GpgP). By qPCR using a suitable reference gene selected in this study, the transcript abundance of the biosynthetic genes was quantified in G. maris cells under hyper-osmotic shock or under low nitrogen conditions. The gpgS gene was induced under nitrogen-limiting conditions suggesting that GG synthesis is regulated primarily at the transcription level. Moreover, the expression of a gene coding for a putative sucrose-phosphorylase (Spase) located upstream the gpgS and gpgP genes was up-regulated, predicting a metabolic role of Spase probably related to GG synthesis.


Asunto(s)
Bacterias/genética , Glucósidos/metabolismo , Ácidos Glicéricos/metabolismo , Presión Osmótica , Tolerancia a la Sal , Bacterias/enzimología , Bacterias/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Glucosiltransferasas/genética , Glucosiltransferasas/metabolismo , Nitrógeno/metabolismo , Monoéster Fosfórico Hidrolasas/genética , Monoéster Fosfórico Hidrolasas/metabolismo , Plancton/enzimología , Plancton/genética , Plancton/metabolismo
7.
RNA Biol ; 11(9): 1199-213, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25483040

RESUMEN

Mutations in genes that encode tRNAs, aminoacyl-tRNA syntheases, tRNA modifying enzymes and other tRNA interacting partners are associated with neuropathies, cancer, type-II diabetes and hearing loss, but how these mutations cause disease is unclear. We have hypothesized that levels of tRNA decoding error (mistranslation) that do not fully impair embryonic development can accelerate cell degeneration through proteome instability and saturation of the proteostasis network. To test this hypothesis we have induced mistranslation in zebrafish embryos using mutant tRNAs that misincorporate Serine (Ser) at various non-cognate codon sites. Embryo viability was affected and malformations were observed, but a significant proportion of embryos survived by activating the unfolded protein response (UPR), the ubiquitin proteasome pathway (UPP) and downregulating protein biosynthesis. Accumulation of reactive oxygen species (ROS), mitochondrial and nuclear DNA damage and disruption of the mitochondrial network, were also observed, suggesting that mistranslation had a strong negative impact on protein synthesis rate, ER and mitochondrial homeostasis. We postulate that mistranslation promotes gradual cellular degeneration and disease through protein aggregation, mitochondrial dysfunction and genome instability.


Asunto(s)
Codón/genética , Embrión no Mamífero/citología , Mutación/genética , Biosíntesis de Proteínas , Proteínas/metabolismo , ARN de Transferencia/genética , Pez Cebra/genética , Animales , Northern Blotting , Western Blotting , Núcleo Celular/genética , Daño del ADN/genética , ADN Mitocondrial/genética , Embrión no Mamífero/fisiología , Retículo Endoplásmico/metabolismo , Estrés Oxidativo , Complejo de la Endopetidasa Proteasomal/genética , Procesamiento Proteico-Postraduccional , Proteoma/análisis , Especies Reactivas de Oxígeno/metabolismo , Respuesta de Proteína Desplegada/fisiología , Pez Cebra/embriología
8.
Rapid Commun Mass Spectrom ; 27(9): 1019-26, 2013 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-23592205

RESUMEN

RATIONALE: Glycophthalocyanines have a great promising potential in many scientific areas. However, their structural characterization is not an easy task. To overcome this drawback, it is urgent to develop simple and efficient methodologies to characterize this type of compounds. In this work, we describe the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and MALDI-MS/MS of the [M+H](+) to distinguish between two isomeric glycophatholocyanines bearing four galactose units with protected (1a and 2a) or unprotected hydroxyl groups (1b and 2b). METHODS: The MALDI-MS and MALDI-MS/MS spectra were acquired using a MALDI-TOF/TOF Applied Biosystems 4800 Proteomics Analyzer instrument equipped with a nitrogen laser and using dithranol as matrix. Computational studies were performed in order to gain insights into the mechanisms underlying the different fragmentation pathways observed for the isomeric species. RESULTS: The fragmentation pattern observed in MALDI-MS/MS spectra of the [M+H](+) ion was dependent on the peripheral distribution of the sugar units. Phthalocyanines (Pcs) with a sugar unit in each isoindole ring show the typical loss of sugar units (cleavage of C6-O bond) while Pcs with the four sugar units linked to the same isoindole ring show a major and unusual fragmentation pathway corresponding to the cleavage of the C5-C6 bond of the sugar units. This type of fragmentation is not usually observed in the MS/MS of oligosaccharides. CONCLUSIONS: MALDI-MS is a valuable tool for the structural characterization/differentiation of isomeric glycophthalocyanines.

9.
Chemistry ; 18(11): 3210-9, 2012 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-22331806

RESUMEN

The synthesis and photophysical properties of several porphyrin (P)-phthalocyanine (Pc) conjugates (P-Pc; 1-3) are described, in which the phthalocyanines are directly linked to the ß-pyrrolic position of a meso-tetraphenylporphyrin. Photoinduced energy- and electron-transfer processes were studied through the preparation of H(2)P-ZnPc, ZnP-ZnPc, and PdP-ZnPc conjugates, and their assembly through metal coordination with two different pyridylfulleropyrrolidines (4 and 5). The resulting electron-donor-acceptor hybrids, which were formed by axial coordination of compounds 4 and 5 with the corresponding phthalocyanines, mimicked the fundamental processes of photosynthesis; that is, light harvesting, the transduction of excited-state energy, and unidirectional electron transfer. In particular, photophysical studies confirmed that intramolecular energy-transfer resulted from the S(2) excited state as well as from the S(1) excited state of the porphyrins to the energetically lower-lying phthalocyanines, followed by an intramolecular charge-transfer to yield P-Pc(.+)⋅C(60)(.-). This unique sequence of processes opens the way for solar-energy-conversion processes.


Asunto(s)
Fulerenos/química , Indoles/química , Porfirinas/química , Piridinas/química , Transporte de Electrón , Indoles/síntesis química , Isoindoles , Espectroscopía de Resonancia Magnética , Estructura Molecular , Procesos Fotoquímicos , Porfirinas/síntesis química , Espectrometría de Fluorescencia
10.
Chem Res Toxicol ; 25(4): 940-51, 2012 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-22394248

RESUMEN

Photodynamic therapy (PDT) is a treatment modality for different forms of cancer based on the combination of light, molecular oxygen, and a photosensitizer (PS) compound. When activated by light, the PS generates reactive oxygen species leading to tumor destruction. Phthalocyanines are compounds that have already shown to be efficient PSs for PDT. Several examples of carbohydrate substituted phthalocyanines have been reported, assuming that the presence of carbohydrate moieties could improve their tumor selectivity. This work describes the photoeffects of symmetric and asymmetric phthalocyanines with D-galactose (so-called GPh1, GPh2, and GPh3) on HeLa carcinoma cells and their involvement in cell death. Photophysical properties and in vitro photodynamic activities for the compounds considered revealed that the asymmetric glycophthalocyanine GPh3 is very efficient and selective, producing higher photocytotoxicity on cancer cells than in nonmalignat HaCaT. The cell toxiticy after PDT treatment was dependent upon light exposure level and GPh3 concentration. GPh3 causes cell cycle arrest at the metaphase stage leading to multiple spindle poles, mitotic catastrophe, followed by apoptosis in cancer cells. These effects were partially negated by the pancaspase inhibitor Z-VAD-FMK. Together, these results indicate that GPh3 is an excellent candidate drug for PDT, able to induce selective tumor cell death.


Asunto(s)
Apoptosis/efectos de los fármacos , Indoles/toxicidad , Mitosis/efectos de los fármacos , Fármacos Fotosensibilizantes/toxicidad , Clorometilcetonas de Aminoácidos/farmacología , Inhibidores de Caspasas , Caspasas/metabolismo , Línea Celular , Citoesqueleto/efectos de los fármacos , Galactosa/química , Células HeLa , Humanos , Indoles/química , Isoindoles , Fármacos Fotosensibilizantes/química
11.
G3 (Bethesda) ; 12(7)2022 07 06.
Artículo en Inglés | MEDLINE | ID: mdl-35532173

RESUMEN

The pathogenic yeast Candida glabrata is intrinsically resilient to azoles and rapidly acquires resistance to these antifungals, in vitro and in vivo. In most cases azole-resistant C. glabrata clinical strains encode hyperactive CgPdr1 variants, however, resistant strains encoding wild-type CgPDR1 alleles have also been isolated, although remaining to be disclosed the underlying resistance mechanism. In this study, we scrutinized the mechanisms underlying resistance to azoles of 8 resistant clinical C. glabrata strains, identified along the course of epidemiological surveys undertaken in Portugal. Seven of the strains were found to encode CgPdr1 gain-of-function variants (I392M, E555K, G558C, and I803T) with the substitutions I392M and I803T being herein characterized as hyper-activating mutations for the first time. While cells expressing the wild-type CgPDR1 allele required the mediator subunit Gal11A to enhance tolerance to fluconazole, this was dispensable for cells expressing the I803T variant indicating that the CgPdr1 interactome is shaped by different gain-of-function substitutions. Genomic and transcriptomic profiling of the sole azole-resistant C. glabrata isolate encoding a wild-type CgPDR1 allele (ISTB218) revealed that under fluconazole stress this strain over-expresses various genes described to provide protection against this antifungal, while also showing reduced expression of genes described to increase sensitivity to these drugs. The overall role in driving the azole-resistance phenotype of the ISTB218 C. glabrata isolate played by these changes in the transcriptome and genome of the ISTB218 isolate are discussed shedding light into mechanisms of resistance that go beyond the CgPdr1-signalling pathway and that may alone, or in combination, pave the way for the acquisition of resistance to azoles in vivo.


Asunto(s)
Azoles , Candida glabrata , Alelos , Antifúngicos/farmacología , Azoles/farmacología , Farmacorresistencia Fúngica/genética , Fluconazol/farmacología , Mutación con Ganancia de Función , Regulación Fúngica de la Expresión Génica , Genómica , Pruebas de Sensibilidad Microbiana , Transcriptoma
12.
Phys Chem Chem Phys ; 13(25): 11858-63, 2011 Jul 07.
Artículo en Inglés | MEDLINE | ID: mdl-21614392

RESUMEN

In the current work, we report on the synthesis and photophysical features of supramolecular hybrid systems that are based on newly fused porphyrin-phthalocyanine (P-Pc) conjugates and a pyridylfullerene. The ZnP-ZnPc conjugate was synthesized in three steps starting with a Diels-Alder reaction between ß-vinylporphyrin and fumaronitrile. The resulting mixture of isomeric adducts was then dehydrogenated to yield the corresponding benzo[b]porphyrin-2(1),2(2)-dicarbonitrile. In the final step, cyclotetramerization with 4-tert-butylphthalonitrile, in the presence of zinc acetate, afforded the bis-metalated conjugate. Selective demetallation of ZnP led to the H(2)P-ZnPc conjugate. For both conjugates steric hindrance is the inception to a bent configuration, which does, however, not preclude enlargement of the π-conjugated system, that is, the porphyrins and the phthalocyanines. The two conjugates coordinate N-(4-pyridyl)fullero[c]pyrrolidine giving rise to the corresponding supramolecular porphyrin-phthalocyanine-fullerene systems. Photophysical measurements corroborate a sequential deactivation in the excited state, namely an initial intramolecular energy transfer from ZnP or H(2)P to ZnPc followed by an intramolecular charge transfer to yield ZnP-(ZnPc)˙(+)-(C(60))˙(-) and H(2)P-(ZnPc)˙(+)-(C(60))˙(-), respectively.


Asunto(s)
Fulerenos/química , Indoles/química , Porfirinas/química , Transferencia de Energía , Isoindoles , Espectrometría de Fluorescencia , Zinc/química
13.
Aging (Albany NY) ; 13(14): 18150-18190, 2021 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-34330884

RESUMEN

Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.


Asunto(s)
Envejecimiento/genética , Encéfalo/metabolismo , Corazón/fisiología , Hígado/metabolismo , Músculo Esquelético/metabolismo , Páncreas/metabolismo , Transcriptoma , Envejecimiento/metabolismo , Envejecimiento/fisiología , Aminoácidos/metabolismo , Animales , Correlación de Datos , Ácidos Grasos/metabolismo , Femenino , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Redes Reguladoras de Genes , Inmunidad/genética , Inflamación/genética , Metabolismo de los Lípidos/genética , Masculino , Ratones Endogámicos C57BL , Análisis de Secuencia por Matrices de Oligonucleótidos , RNA-Seq , Regeneración/genética , Análisis de Regresión
14.
Photochem Photobiol Sci ; 9(7): 1027-32, 2010 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-20508890

RESUMEN

Complementary experiments, that is, femtosecond up-conversion fluorescence, conventional fluorescence lifetime measurements, and transient absorption measurements, imply efficient porphyrin-to-phthalocyanine energy transfer phenomena in NH-connected porphyrin/phthalocyanine conjugates.


Asunto(s)
Transferencia de Energía , Indoles/química , Porfirinas/química , Absorción , Isoindoles , Espectrometría de Fluorescencia , Temperatura
15.
BMC Genomics ; 10: 195, 2009 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-19397817

RESUMEN

BACKGROUND: MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification, however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. RESULTS: We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from miRNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics. Twenty five novel miRNAs were predicted, 107 miRNA star sequences and also 41 candidate miRNA targets were identified. A miRNA expression profile built on the basis of pyrosequencing read numbers showed high expression of most miRNAs throughout zebrafish development and identified tissue specific miRNAs. CONCLUSION: This study increases the number of zebrafish miRNAs from 192 to 217 and demonstrates that a single DNA mini-chip pyrosequencing run is effective in miRNA identification in zebrafish. This methodology also produced sufficient information to elucidate miRNA expression patterns during development and in differentiated organs. Moreover, some zebrafish miRNA star sequences were more abundant than their corresponding miRNAs, suggesting a functional role for the former in gene expression control in this vertebrate model organism.


Asunto(s)
MicroARNs/genética , Análisis de Secuencia de ADN/métodos , Pez Cebra/genética , Animales , Secuencia de Bases , Biología Computacional , Perfilación de la Expresión Génica , Biblioteca de Genes , Estadios del Ciclo de Vida/genética , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Pez Cebra/crecimiento & desarrollo
16.
Mar Environ Res ; 148: 39-45, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-31078961

RESUMEN

Increasing loading of terrestrially derived dissolved organic matter tends to enhance bacterioplankton respiration (BR) in boreal estuaries, but knowledge on the mechanisms behind this effect is not complete. We determined the stable isotopic signature of the reactive estuarine dissolved organic carbon (DOC) in the Öre estuary (Baltic Sea) by using the Keeling plot method. The δ13C ratio of the estuarine labile DOC varied from -26.0‰ to -18.7‰ with most values resembling those typical for DOC of coastal phytoplanktonic origin (-18 to -24‰), while being distinctly higher than those of DOC from ter-res-trial sources (-28‰ to -27‰). Furthermore, the δ13C of the respired carbon was positively correlated to DOC concentrations, indicating that carbon of marine origin increasingly dominated the reactive substrates when input of organic matter into the estuary became higher. This suggests that riverine organic matter mainly affects BR indirectly, by providing nutrients that stimulate the production of phytoplankton-derived reactive DOC in the estuary. Thus, riverine derived DOC per se may not be as important for coastal CO2 emissions as previously thought.


Asunto(s)
Organismos Acuáticos/química , Carbono , Estuarios , Bacterias Aerobias/metabolismo , Países Bálticos , Ciclo del Carbono , Isótopos de Carbono , Monitoreo del Ambiente , Ríos/química , Algas Marinas/química
17.
Sci Rep ; 9(1): 14897, 2019 10 17.
Artículo en Inglés | MEDLINE | ID: mdl-31624278

RESUMEN

Inland waters transport, transform and retain significant amounts of dissolved organic carbon (DOC) that may be biologically reactive (bioreactive) and thus potentially degraded into atmospheric CO2. Despite its global importance, relatively little is known about environmental controls on bioreactivity of DOC as it moves through river systems with varying water residence time (WRT). Here we determined the influence of WRT and landscape properties on DOC bioreactivity in 15 Swedish catchments spanning a large geographical and environmental gradient. We found that the short-term bioreactive pools (0-6 d of decay experiments) were linked to high aquatic primary productivity that, in turn, was stimulated by phosphorus loading from forested, agricultural and urban areas. Unexpectedly, the percentage of long-term bioreactive DOC (determined in 1-year experiments) increased with WRT, possibly due to photo-transformation of recalcitrant DOC from terrestrial sources into long-term bioreactive DOC with relatively lower aromaticity. Thus, despite overall decreases in DOC during water transit through the inland water continuum, DOC becomes relatively more bioreactive on a long time-scale. This increase in DOC bioreactivity with increasing WRT along the freshwater continuum has previously been overlooked. Further studies are needed to explain the processes and mechanisms behind this pattern on a molecular level.

18.
Genes Brain Behav ; 18(6): e12542, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-30488664

RESUMEN

Chronic pain is frequently accompanied by the manifestation of emotional disturbances and cognitive deficits. While a causality relation between pain and emotional/cognitive disturbances is generally assumed, several observations suggest a temporal dissociation and independent mechanisms. We therefore studied Sprague-Dawley rats that presented a natural resistance to pain manifestation in a neuropathy model (spared nerve injury [SNI]) and compared their performance in a battery of behavioral paradigms-anxiety, depression and fear memory-with animals that presented a pain phenotype. Afterward, we performed an extensive volumetric analysis across prefrontal, orbitofrontal and insular cortical areas. The majority of SNI animals manifested mechanical allodynia (low threshold [LT]), but 13% were similar to Sham controls (high threshold [HT]). Readouts of spontaneous hypersensivity (paw flinches) were also significantly reduced in HT and correlated with allodynia. To increase the specificity of our findings, we segregated the SNI animals in those with left (SNI-L) and right (SNI-R) lesions and the lack of association between pain and behavior still remains. Left-lesioned animals, independent of the LT or HT phenotype, presented increased anxiety-like behaviors and decreased well-being. In contrast, we found that the insular cortex (agranular division) was significantly smaller in HT than in LT. To conclude, pain and emotional disturbances observed following nerve injury are to some extent segregated phenomena. Also, HT and LT SNI presented differences in insular volumes, an area vastly implicated in pain perception, suggesting a supraspinal involvement in the manifestation of these phenotypes.


Asunto(s)
Trastornos del Humor/fisiopatología , Neuralgia/fisiopatología , Ciática/fisiopatología , Animales , Corteza Cerebral/patología , Corteza Cerebral/fisiopatología , Masculino , Trastornos del Humor/etiología , Neuralgia/complicaciones , Neuralgia/psicología , Ratas , Ratas Sprague-Dawley , Ciática/complicaciones , Ciática/psicología
19.
Biotechnol J ; 13(4): e1700676, 2018 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-29345424

RESUMEN

Protein conformational disorders are characterized by disruption of protein folding and toxic accumulation of protein aggregates. Here we describe a sensitive and simple method to follow and monitor general protein aggregation in human cells. Heat shock protein 27 (HSP27) is an oligomeric small heat shock protein that binds and keeps unfolded proteins in a folding competent state. This high specificity of HSP27 for aggregated proteins can be explored to monitor aggregation in living cells by fusing it to a fluorescent protein as Green Fluorescent Protein (GFP). We have constructed a HeLa stable cell line expressing a HSP27:GFP chimeric reporter protein and after validation, this stable cell line is exposed to different agents that interfere with proteostasis, namely Arsenite, MG132, and Aß-peptide. Exposure to proteome destabilizers lead to re-localization of HSP27:GFP fluorescence to foci, confirming that our reporter system is functional and can be used to detect and follow protein aggregation in living cells. This reporter is a valuable tool to setup wide-genetic screens to identify genes and pathways involved in protein misfolding and aggregation.


Asunto(s)
Proteínas Fluorescentes Verdes/genética , Proteínas de Choque Térmico HSP27/genética , Proteolisis , Proteoma/metabolismo , Péptidos beta-Amiloides/efectos adversos , Arsenitos/efectos adversos , Proteínas Fluorescentes Verdes/metabolismo , Proteínas de Choque Térmico HSP27/metabolismo , Células HeLa , Proteínas de Choque Térmico , Humanos , Leupeptinas/efectos adversos , Chaperonas Moleculares , Agregado de Proteínas , Unión Proteica , Pliegue de Proteína , Proteoma/química , Proteínas Recombinantes/metabolismo
20.
Org Lett ; 9(8): 1557-60, 2007 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-17378573

RESUMEN

[structure: see text] Two types of covalently NH-linked porphyrin-phthalocyanine dyads, connected either through the meso phenyl group or the beta-pyrrolic position of the porphyrin, have been synthesized following statistical condensation methodologies for phthalocyanine preparation and palladium-catalyzed amination methods. Photophysical studies have revealed that energy transfer from the porphyrin to the phthalocyanine prevails regardless of linkage.

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