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1.
Plant Cell ; 33(10): 3348-3366, 2021 10 11.
Artículo en Inglés | MEDLINE | ID: mdl-34323976

RESUMEN

Carbohydrate partitioning from leaves to sink tissues is essential for plant growth and development. The maize (Zea mays) recessive carbohydrate partitioning defective28 (cpd28) and cpd47 mutants exhibit leaf chlorosis and accumulation of starch and soluble sugars. Transport studies with 14C-sucrose (Suc) found drastically decreased export from mature leaves in cpd28 and cpd47 mutants relative to wild-type siblings. Consistent with decreased Suc export, cpd28 mutants exhibited decreased phloem pressure in mature leaves, and altered phloem cell wall ultrastructure in immature and mature leaves. We identified the causative mutations in the Brittle Stalk2-Like3 (Bk2L3) gene, a member of the COBRA family, which is involved in cell wall development across angiosperms. None of the previously characterized COBRA genes are reported to affect carbohydrate export. Consistent with other characterized COBRA members, the BK2L3 protein localized to the plasma membrane, and the mutants condition a dwarf phenotype in dark-grown shoots and primary roots, as well as the loss of anisotropic cell elongation in the root elongation zone. Likewise, both mutants exhibit a significant cellulose deficiency in mature leaves. Therefore, Bk2L3 functions in tissue growth and cell wall development, and this work elucidates a unique connection between cellulose deposition in the phloem and whole-plant carbohydrate partitioning.


Asunto(s)
Metabolismo de los Hidratos de Carbono , Pared Celular/metabolismo , Proteínas de Plantas/genética , Zea mays/genética , Proteínas de Plantas/metabolismo , Zea mays/metabolismo
2.
Glycobiology ; 31(7): 859-872, 2021 08 07.
Artículo en Inglés | MEDLINE | ID: mdl-33403396

RESUMEN

N-glycosylated proteins produced in human embryonic kidney 293 (HEK 293) cells often carry terminal N-acetylgalactosamine (GalNAc) and only low levels of sialylation. On therapeutic proteins, such N-glycans often trigger rapid clearance from the patient's bloodstream via efficient binding to asialoglycoprotein receptor (ASGP-R) and mannose receptor (MR). This currently limits the use of HEK 293 cells for therapeutic protein production. To eliminate terminal GalNAc, we knocked-out GalNAc transferases B4GALNT3 and B4GALNT4 by CRISPR/Cas9 in FreeStyle 293-F cells. The resulting cell line produced a coagulation factor VII-albumin fusion protein without GalNAc but with increased sialylation. This glyco-engineered protein bound less efficiently to both the ASGP-R and MR in vitro and it showed improved recovery, terminal half-life and area under the curve in pharmacokinetic rat experiments. By overexpressing sialyltransferases ST6GAL1 and ST3GAL6 in B4GALNT3 and B4GALNT4 knock-out cells, we further increased factor VII-albumin sialylation; for ST6GAL1 even to the level of human plasma-derived factor VII. Simultaneous knock-out of B4GALNT3 and B4GALNT4 and overexpression of ST6GAL1 further lowered factor VII-albumin binding to ASGP-R and MR. This novel glyco-engineered cell line is well-suited for the production of factor VII-albumin and presumably other therapeutic proteins with fully human N-glycosylation and superior pharmacokinetic properties.


Asunto(s)
Glicoproteínas , Sialiltransferasas , Animales , Técnicas de Inactivación de Genes , Glicoproteínas/biosíntesis , Glicoproteínas/genética , Glicoproteínas/farmacocinética , Glicosilación , Células HEK293 , Humanos , Ratas , Sialiltransferasas/genética , Sialiltransferasas/metabolismo
3.
Sensors (Basel) ; 21(13)2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-34209063

RESUMEN

BACKGROUND AND OBJECTIVE: The reliability of low-cost mobile systems for recording Electrocardiographic (ECG) data is mostly unknown, posing questions regarding the quality of the recorded data and the validity of the extracted physiological parameters. The present study compared the BITalino toolkit with an established medical-grade ECG system (BrainAmp-ExG). METHODS: Participants underwent simultaneous ECG recordings with the two instruments while watching pleasant and unpleasant pictures of the "International Affective Picture System" (IAPS). Common ECG parameters were extracted and compared between the two systems. The Intraclass Correlation Coefficients (ICCs) and the Bland-Altman Limits of Agreement (LoA) method served as criteria for measurement agreement. RESULTS: All but one parameter showed an excellent agreement (>80%) between both devices in the ICC analysis. No criteria for Bland-Altman LoA and bias were found in the literature regarding ECG parameters. CONCLUSION: The results of the ICC and Bland-Altman methods demonstrate that the BITalino system can be considered as an equivalent recording device for stationary ECG recordings in psychophysiological experiments.


Asunto(s)
Electrocardiografía , Psicofisiología , Frecuencia Cardíaca , Humanos , Reproducibilidad de los Resultados
4.
Plant Cell ; 25(8): 2783-97, 2013 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-23922207

RESUMEN

DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, genetic changes such as transposon insertions can also lead to changes in DNA methylation. Genome-wide profiles of DNA methylation for 20 maize (Zea mays) inbred lines were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize or teosinte genotypes, resulting in the discovery of 1966 common DMRs and 1754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with single nucleotide polymorphisms found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the variation in DNA methylation. Analysis of gene expression in the same samples used for DNA methylation profiling identified over 300 genes with expression patterns that are significantly associated with DNA methylation variation. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic changes that are often stably inherited and can influence the expression of nearby genes.


Asunto(s)
Metilación de ADN/genética , Epigénesis Genética , Variación Genética , Zea mays/genética , Análisis por Conglomerados , Genotipo , Endogamia , Patrón de Herencia/genética , Modelos Genéticos , Recombinación Genética/genética , Reproducibilidad de los Resultados
5.
Plant J ; 80(1): 136-48, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-25039268

RESUMEN

We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.


Asunto(s)
Variación Genética , Genoma de Planta/genética , Solanum lycopersicum/genética , Cruzamiento , Mapeo Cromosómico , ADN de Plantas/química , ADN de Plantas/genética , Frutas/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Datos de Secuencia Molecular , Fenotipo , Filogenia , Polimorfismo de Nucleótido Simple , Alineación de Secuencia , Análisis de Secuencia de ADN , Especificidad de la Especie
6.
PLoS Pathog ; 9(10): e1003671, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-24204256

RESUMEN

Disassembly of the nuclear lamina is essential in mitosis and apoptosis requiring multiple coordinated enzymatic activities in nucleus and cytoplasm. Activation and coordination of the different activities is poorly understood and moreover complicated as some factors translocate between cytoplasm and nucleus in preparatory phases. Here we used the ability of parvoviruses to induce nuclear membrane breakdown to understand the triggers of key mitotic enzymes. Nuclear envelope disintegration was shown upon infection, microinjection but also upon their application to permeabilized cells. The latter technique also showed that nuclear envelope disintegration was independent upon soluble cytoplasmic factors. Using time-lapse microscopy, we observed that nuclear disassembly exhibited mitosis-like kinetics and occurred suddenly, implying a catastrophic event irrespective of cell- or type of parvovirus used. Analyzing the order of the processes allowed us to propose a model starting with direct binding of parvoviruses to distinct proteins of the nuclear pore causing structural rearrangement of the parvoviruses. The resulting exposure of domains comprising amphipathic helices was required for nuclear envelope disintegration, which comprised disruption of inner and outer nuclear membrane as shown by electron microscopy. Consistent with Ca⁺⁺ efflux from the lumen between inner and outer nuclear membrane we found that Ca⁺⁺ was essential for nuclear disassembly by activating PKC. PKC activation then triggered activation of cdk-2, which became further activated by caspase-3. Collectively our study shows a unique interaction of a virus with the nuclear envelope, provides evidence that a nuclear pool of executing enzymes is sufficient for nuclear disassembly in quiescent cells, and demonstrates that nuclear disassembly can be uncoupled from initial phases of mitosis.


Asunto(s)
Señalización del Calcio , Caspasa 3/metabolismo , Quinasa 2 Dependiente de la Ciclina/metabolismo , Parvovirus H-1/metabolismo , Mitosis , Membrana Nuclear/enzimología , Infecciones por Parvoviridae/enzimología , Proteína Quinasa C/metabolismo , Animales , Calcio/metabolismo , Caspasa 3/genética , Quinasa 2 Dependiente de la Ciclina/genética , Parvovirus H-1/genética , Células HeLa , Humanos , Membrana Nuclear/genética , Membrana Nuclear/patología , Membrana Nuclear/virología , Infecciones por Parvoviridae/genética , Infecciones por Parvoviridae/patología , Proteína Quinasa C/genética , Xenopus laevis
7.
Proc Natl Acad Sci U S A ; 109(29): 11878-83, 2012 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-22753482

RESUMEN

Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.


Asunto(s)
Productos Agrícolas/genética , Evolución Molecular , Redes Reguladoras de Genes/genética , Selección Genética/genética , Transcriptoma/genética , Zea mays/genética , Perfilación de la Expresión Génica , Genes de Plantas/genética , Genética de Población , Genotipo , Análisis por Micromatrices , Anotación de Secuencia Molecular
8.
Plant Cell ; 23(12): 4221-33, 2011 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-22198147

RESUMEN

Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm, including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted, while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.


Asunto(s)
Metilación de ADN , Endospermo/genética , Impresión Genómica , Zea mays/genética , Alelos , Arabidopsis/química , Arabidopsis/genética , Cromosomas de las Plantas/química , Cromosomas de las Plantas/genética , Secuencia Conservada , Endospermo/química , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Sitios Genéticos , Patrón de Herencia , Oryza/química , Oryza/genética , Polinización , Polimorfismo Genético , Análisis de Secuencia de ARN , Zea mays/química
9.
PLoS Genet ; 7(11): e1002372, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22125494

RESUMEN

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs). Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic variation, may contribute to complex trait variation.


Asunto(s)
Citosina/metabolismo , Metilación de ADN/genética , Epigénesis Genética , Regulación de la Expresión Génica de las Plantas , Zea mays/genética , Hibridación Genómica Comparativa , Variaciones en el Número de Copia de ADN , Genoma de Planta , Genotipo , Endogamia , Análisis de Secuencia por Matrices de Oligonucleótidos , Población
10.
Plant J ; 72(3): 390-9, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22731681

RESUMEN

A careful analysis of two maize recombinant inbred lines (RILs) relative to their inbred parents revealed the presence of several hundred apparently de novo copy number variants (CNVs). These changes in genome content were validated via both PCR and whole exome-array capture-and-sequencing experiments. One hundred and eighty-five genomic regions, which overlap with 38 high-confidence genes, exhibited apparently de novo copy number variation (CNV) in these two RILs and in many instances the same apparently de novo CNV events were observed in multiple RILs. Further analyses revealed that these recurrent apparently de novo CNVs were caused by segregation of single-copy homologous sequences that are located in non-allelic positions in the two parental inbred lines. F(1) individuals derived from these inbred lines will be hemizygous for each of these non-allelic homologs but RIL genotypes will contain these sequences at zero, one or two genomic loci. Hence, the segregation of non-allelic homologs may contribute to transgressive segregation. Indeed, statistical associations between phenotypic quantitative trait loci and genomic losses were observed for two of 14 tested pairs of non-allelic homologs.


Asunto(s)
Segregación Cromosómica/genética , Variaciones en el Número de Copia de ADN/genética , ADN de Plantas/genética , Genoma de Planta/genética , Zea mays/genética , Mapeo Cromosómico , Hibridación Genómica Comparativa , Exoma , Exones , Dosificación de Gen/genética , Genotipo , Modelos Genéticos , Análisis de Secuencia por Matrices de Oligonucleótidos , Fenotipo , Sitios de Carácter Cuantitativo
11.
Genome Res ; 20(12): 1689-99, 2010 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-21036921

RESUMEN

Individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. Array comparative genomic hybridization (CGH) was used to compare gene content and copy number variation among 19 diverse maize inbreds and 14 genotypes of the wild ancestor of maize, teosinte. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes present in B73, but missing from other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes, and the majority of events are observed in both maize and teosinte, suggesting that these variants predate domestication and that there is not strong selection acting against them. Many of the genes affected by CNV/PAV are either maize specific (thus possible annotation artifacts) or members of large gene families, suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.


Asunto(s)
Dosificación de Gen/genética , Genes de Plantas/genética , Variación Genética , Zea mays/genética , Mapeo Cromosómico , Hibridación Genómica Comparativa , Genotipo , Recombinación Genética/genética , Especificidad de la Especie
12.
J Virol ; 86(17): 9163-74, 2012 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22696661

RESUMEN

Adeno-associated virus type 2 (AAV2) has gained much interest as a gene delivery vector. A hallmark of AAV2-mediated gene transfer is an intracellular conformational change of the virus capsid, leading to the exposure of infection-relevant protein domains. These protein domains, which are located on the N-terminal portion of the structural proteins VP1 and VP2, include a catalytic phospholipase A(2) domain and three clusters of basic amino acids. We have identified additional protein sequence motifs located on the VP1/2 N terminus that also proved to be obligatory for virus infectivity. These motifs include signals that are known to be involved in protein interaction, endosomal sorting and signal transduction in eukaryotic cells. Among different AAV serotypes they are highly conserved and mutation of critical amino acids of the respective motifs led to a severe infection-deficient phenotype. In particular, mutation of a YXXQ-sequence motif significantly reduced accumulation of virus capsids around the nucleus in comparison to wild-type AAV2. Interestingly, intracellular trafficking of AAV2 was shown to be independent of PLA(2) activity. Moreover, mutation of three PDZ-binding motifs, which are located consecutively at the very tip of the VP1 N terminus, revealed a nuclear transport-defective phenotype, suggesting a role in nuclear uptake of the virus through an as-yet-unknown mechanism.


Asunto(s)
Proteínas de la Cápside/química , Proteínas de la Cápside/metabolismo , Núcleo Celular/virología , Dependovirus/metabolismo , Infecciones por Parvoviridae/virología , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Proteínas de la Cápside/genética , Línea Celular , Núcleo Celular/metabolismo , Dependovirus/química , Dependovirus/genética , Humanos , Datos de Secuencia Molecular , Infecciones por Parvoviridae/metabolismo , Transporte de Proteínas , Alineación de Secuencia
13.
J Virol ; 86(23): 13038-48, 2012 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-23015698

RESUMEN

Adeno-associated virus (AAV) capsid assembly requires expression of the assembly-activating protein (AAP) together with capsid proteins VP1, VP2, and VP3. AAP is encoded by an alternative open reading frame of the cap gene. Sequence analysis and site-directed mutagenesis revealed that AAP contains two hydrophobic domains in the N-terminal part of the molecule that are essential for its assembly-promoting activity. Mutation of these sequences reduced the interaction of AAP with the capsid proteins. Deletions and a point mutation in the capsid protein C terminus also abolished capsid assembly and strongly reduced the interaction with AAP. Interpretation of these observations on a structural basis suggests an interaction of AAP with the VP C terminus, which forms the capsid protein interface at the 2-fold symmetry axis. This interpretation is supported by a decrease in the interaction of monoclonal antibody B1 with VP3 under nondenaturing conditions in the presence of AAP, indicative of steric hindrance of B1 binding to its C-terminal epitope by AAP. In addition, AAP forms high-molecular-weight oligomers and changes the conformation of nonassembled VP molecules as detected by conformation-sensitive monoclonal antibodies A20 and C37. Combined, these observations suggest a possible scaffolding activity of AAP in the AAV capsid assembly reaction.


Asunto(s)
Proteínas de la Cápside/genética , Cápside/metabolismo , Dependovirus/metabolismo , Ensamble de Virus/genética , Anticuerpos Monoclonales , Cápside/ultraestructura , Proteínas de la Cápside/metabolismo , Dependovirus/ultraestructura , Immunoblotting , Inmunoprecipitación , Microscopía Electrónica , Mutagénesis Sitio-Dirigida , Estructura Terciaria de Proteína , Análisis de Secuencia de ADN
14.
J Virol ; 86(15): 7739-51, 2012 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-22593150

RESUMEN

Adeno-associated viruses (AAVs) are small single-stranded DNA viruses that can package and deliver nongenomic DNA for therapeutic gene delivery. AAV8, a liver-tropic vector, has shown great promise for the treatment of hemophilia A and B. However, as with other AAV vectors, host anti-capsid immune responses are a deterrent to therapeutic success. To characterize the antigenic structure of this vector, cryo-electron microscopy and image reconstruction (cryo-reconstruction) combined with molecular genetics, biochemistry, and in vivo approaches were used to define an antigenic epitope on the AAV8 capsid surface for a neutralizing monoclonal antibody, ADK8. Docking of the crystal structures of AAV8 and a generic Fab into the cryo-reconstruction for the AAV8-ADK8 complex identified a footprint on the prominent protrusions that flank the 3-fold axes of the icosahedrally symmetric capsid. Mutagenesis and cell-binding studies, along with in vitro and in vivo transduction assays, showed that the major ADK8 epitope is formed by an AAV variable region, VRVIII (amino acids 586 to 591 [AAV8 VP1 numbering]), which lies on the surface of the protrusions facing the 3-fold axis. This region plays a role in AAV2 and AAV8 cellular transduction. Coincidently, cell binding and trafficking assays indicate that ADK8 affects a postentry step required for successful virus trafficking to the nucleus, suggesting a probable mechanism of neutralization. This structure-directed strategy for characterizing the antigenic regions of AAVs can thus generate useful information to help re-engineer vectors that escape host neutralization and are hence more efficacious.


Asunto(s)
Anticuerpos Antivirales/química , Antígenos Virales/química , Proteínas de la Cápside/química , Dependovirus/química , Mapeo Epitopo , Fragmentos Fab de Inmunoglobulinas/química , Transporte Activo de Núcleo Celular , Animales , Anticuerpos Antivirales/genética , Anticuerpos Antivirales/inmunología , Antígenos Virales/genética , Antígenos Virales/inmunología , Proteínas de la Cápside/genética , Proteínas de la Cápside/inmunología , Núcleo Celular/genética , Núcleo Celular/inmunología , Núcleo Celular/virología , Cristalografía por Rayos X , Dependovirus/genética , Dependovirus/inmunología , Femenino , Técnicas de Transferencia de Gen , Células HEK293 , Células HeLa , Células Hep G2 , Humanos , Fragmentos Fab de Inmunoglobulinas/genética , Fragmentos Fab de Inmunoglobulinas/inmunología , Ratones , Estructura Terciaria de Proteína , Relación Estructura-Actividad
15.
J Gen Virol ; 93(Pt 10): 2131-2141, 2012 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-22764318

RESUMEN

Vectors based on adeno-associated virus serotype 2 (AAV2) belong to today's most promising and most frequently used viral vectors in human gene therapy. Like in many other vector systems, the broad but non-specific tropism limits their use for certain cell types or tissues. One approach to screen for transduction-improved vectors is the selection of random peptide libraries displayed directly on the AAV2 capsid. Although the AAV2 library system has been widely applied for the successful selection of improved gene therapy vectors, it remains unknown which steps of the transduction process are most affected and therefore critical for the selection of targeting peptides. Attachment to the cell surface is the first essential step of AAV-mediated gene transduction; however, our experiments challenge the conventional belief that enhanced gene transfer is equivalent to more efficient cell binding of recombinant AAV2 vectors. A comparison of the various steps of gene transfer by vectors carrying a wild-type AAV2 capsid or displaying two exemplary peptide ligands selected from AAV2 random libraries on different human tumour cell lines demonstrated strong alterations in cell binding, cellular uptake, as well as intracellular processing of these vectors. Combined, our results suggest that entry and post-entry events are decisive for the selection of the peptides NDVRSAN and GPQGKNS rather than their cell binding efficiency.


Asunto(s)
Proteínas de la Cápside/genética , Proteínas de la Cápside/metabolismo , Cápside/metabolismo , Dependovirus/genética , Dependovirus/metabolismo , Péptidos/genética , Péptidos/metabolismo , Línea Celular Tumoral , Técnicas de Transferencia de Gen , Terapia Genética/métodos , Vectores Genéticos/genética , Vectores Genéticos/metabolismo , Glioblastoma/genética , Glioblastoma/metabolismo , Glioblastoma/virología , Células HEK293 , Humanos , Ligandos , Melanoma/genética , Melanoma/metabolismo , Melanoma/virología , Biblioteca de Péptidos , Transducción Genética , Replicación Viral/genética
16.
J Gen Virol ; 93(Pt 9): 1887-1898, 2012 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22694902

RESUMEN

Adeno-associated virus (AAV) capsid assembly occurs in the nucleus. Newly synthesized capsid proteins VP1, VP2 and VP3 contain several basic regions (BRs), which may act as nuclear localization signals (NLSs). Mutation of BR2 and BR3, located at the VP1 and VP2 N termini, marginally reduced nuclear uptake of VP1 or VP2, but not of VP3, when expressed in the context of the whole AAV type 2 (AAV2) genome. Combined mutation of BR1, BR2 and BR3 resulted in capsids with slightly reduced amounts of VP1. Expression of isolated VP1/2 N termini revealed an influence of BR3 on nuclear transport, whilst BR1 or BR2 had no effect. However, deletion of an N-terminal fragment in front of the BR elements strongly reduced nuclear uptake of VP1/2 N termini. Mutation of BR4, present in all three capsid proteins, led to their retention in the cytoplasm and to the formation of speckles, resulting in a lack of capsid formation and a significant reduction in VP levels. In a VP fragment comprising BR2, BR3 and BR4, the BR4 element was not necessary for nuclear localization. Mutation of BR5 in the C-terminal part of the VPs resulted in a speckled protein distribution in the nucleus, strongly reduced capsid assembly, and low VP1 and VP2 levels. Taken together, these results showed that BR2 and BR3 have a weak influence on nuclear transport of VP1 and VP2, whilst combined mutation of BR1, BR2 and BR3 influences the stoichiometry of VPs in assembled capsids. BR4 and BR5 play a crucial role in capsid assembly but have no NLS activity.


Asunto(s)
Proteínas de la Cápside/metabolismo , Núcleo Celular/virología , Dependovirus/fisiología , Infecciones por Parvoviridae/virología , Virión/fisiología , Ensamble de Virus , Transporte Activo de Núcleo Celular , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Proteínas de la Cápside/química , Proteínas de la Cápside/genética , Núcleo Celular/metabolismo , Dependovirus/química , Dependovirus/genética , Datos de Secuencia Molecular , Señales de Localización Nuclear , Infecciones por Parvoviridae/metabolismo , Alineación de Secuencia , Virión/química , Virión/genética
17.
Plant J ; 62(5): 898-909, 2010 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-20230488

RESUMEN

Sequence capture technologies, pioneered in mammalian genomes, enable the resequencing of targeted genomic regions. Most capture protocols require blocking DNA, the production of which in large quantities can prove challenging. A blocker-free, two-stage capture protocol was developed using NimbleGen arrays. The first capture depletes the library of repetitive sequences, while the second enriches for target loci. This strategy was used to resequence non-repetitive portions of an approximately 2.2 Mb chromosomal interval and a set of 43 genes dispersed in the 2.3 Gb maize genome. This approach achieved approximately 1800-3000-fold enrichment and 80-98% coverage of targeted bases. More than 2500 SNPs were identified in target genes. Low rates of false-positive SNP predictions were obtained, even in the presence of captured paralogous sequences. Importantly, it was possible to recover novel sequences from non-reference alleles. The ability to design novel repeat-subtraction and target capture arrays makes this technology accessible in any species.


Asunto(s)
Genoma de Planta , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Análisis de Secuencia de ADN/métodos , Hibridación Genómica Comparativa , ADN de Plantas/genética , Genes de Plantas , Polimorfismo de Nucleótido Simple , Zea mays/genética
18.
Sci Data ; 8(1): 50, 2021 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-33558550

RESUMEN

We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.


Asunto(s)
Genoma de Planta , Glycine max/genética , Polimorfismo de Nucleótido Simple , Productos Agrícolas/genética , Fabaceae/genética , Genotipo , Geografía , Desequilibrio de Ligamiento , Selección Genética
19.
J Clin Med ; 8(9)2019 Sep 02.
Artículo en Inglés | MEDLINE | ID: mdl-31480798

RESUMEN

Studies have shown that pain acceptance is associated with a better pain outcome. The current study explored whether changes in pain acceptance in the very early treatment phase of an interdisciplinary cognitive-behavioral therapy (CBT)-based treatment program for chronic pain predict pain outcomes. A total of 69 patients with chronic, non-malignant pain (at least 6 months) were treated in a day-clinic for four-weeks. Pain acceptance was measured with the Chronic Pain Acceptance Questionnaire (CPAQ), pain outcomes included pain intensity (Numeric Rating Scale, NRS) as well as affective and sensory pain perception (Pain Perception Scale, SES-A and SES-S). Regression analyses controlling for the pre-treatment values of the pain outcomes, age, and gender were performed. Early changes in pain acceptance predicted pain intensity at post-treatment measured with the NRS (B = -0.04 (SE = 0.02); T = -2.28; p = 0.026), affective pain perception at post-treatment assessed with the SES-A (B = -0.26 (SE = 0.10); T = -2.79; p = 0.007), and sensory pain perception at post-treatment measured with the SES-S (B = -0.19 (SE = 0.08); T = -2.44; p = 0.017) . Yet, a binary logistic regression analysis revealed that early changes in pain acceptance did not predict clinically relevant pre-post changes in pain intensity (at least 2 points on the NRS). Early changes in pain acceptance were associated with pain outcomes, however, the impact was beneath the threshold defined as clinically relevant.

20.
Mol Plant ; 12(9): 1278-1293, 2019 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-31102785

RESUMEN

To sustain plant growth, development, and crop yield, sucrose must be transported from leaves to distant parts of the plant, such as seeds and roots. To identify genes that regulate sucrose accumulation and transport in maize (Zea mays), we isolated carbohydrate partitioning defective33 (cpd33), a recessive mutant that accumulated excess starch and soluble sugars in mature leaves. The cpd33 mutants also exhibited chlorosis in the leaf blades, greatly diminished plant growth, and reduced fertility. Cpd33 encodes a protein containing multiple C2 domains and transmembrane regions. Subcellular localization experiments showed the CPD33 protein localized to plasmodesmata (PD), the plasma membrane, and the endoplasmic reticulum. We also found that a loss-of-function mutant of the CPD33 homolog in Arabidopsis, QUIRKY, had a similar carbohydrate hyperaccumulation phenotype. Radioactively labeled sucrose transport assays showed that sucrose export was significantly lower in cpd33 mutant leaves relative to wild-type leaves. However, PD transport in the adaxial-abaxial direction was unaffected in cpd33 mutant leaves. Intriguingly, transmission electron microscopy revealed fewer PD at the companion cell-sieve element interface in mutant phloem tissue, providing a possible explanation for the reduced sucrose export in mutant leaves. Collectively, our results suggest that CPD33 functions to promote symplastic transport into sieve elements.


Asunto(s)
Hojas de la Planta/metabolismo , Sacarosa/metabolismo , Zea mays/metabolismo , Transporte Biológico/genética , Transporte Biológico/fisiología , Regulación de la Expresión Génica de las Plantas/genética , Regulación de la Expresión Génica de las Plantas/fisiología , Floema/metabolismo , Plasmodesmos/metabolismo
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