RESUMEN
Oculocutaneous albinism (OCA) is a rare disorder of pigment production. Affected individuals have variably decreased global pigmentation and visual-developmental changes that lead to low vision. OCA is notable for significant missing heritability, particularly among individuals with residual pigmentation. Tyrosinase (TYR) is the rate-limiting enzyme in melanin pigment biosynthesis and mutations that decrease enzyme function are one of the most common causes of OCA. We present the analysis of high-depth short-read TYR sequencing data for a cohort of 352 OCA probands, â¼50% of whom were previously sequenced without yielding a definitive diagnostic result. Our analysis identified 66 TYR single-nucleotide variants (SNVs) and small insertion/deletions (indels), 3 structural variants, and a rare haplotype comprised of two common frequency variants (p.Ser192Tyr and p.Arg402Gln) in cis-orientation, present in 149/352 OCA probands. We further describe a detailed analysis of the disease-causing haplotype, p.[Ser192Tyr; Arg402Gln] ("cis-YQ"). Haplotype analysis suggests that the cis-YQ allele arose by recombination and that multiple cis-YQ haplotypes are segregating in OCA-affected individuals and control populations. The cis-YQ allele is the most common disease-causing allele in our cohort, representing 19.1% (57/298) of TYR pathogenic alleles in individuals with type 1 (TYR-associated) OCA. Finally, among the 66 TYR variants, we found several additional alleles defined by a cis-oriented combination of minor, potentially hypomorph-producing alleles at common variant sites plus a second, rare pathogenic variant. Together, these results suggest that identification of phased variants for the full TYR locus are required for an exhaustive assessment for potentially disease-causing alleles.
Asunto(s)
Albinismo Oculocutáneo , Humanos , Haplotipos/genética , Albinismo Oculocutáneo/genética , Albinismo Oculocutáneo/diagnóstico , Mutación , AlelosRESUMEN
BACKGROUND: Down syndrome is associated with several comorbidities, including intellectual disability, growth restriction, and congenital heart defects. The prevalence of Down syndrome-associated comorbidities is highly variable, and intellectual disability, although fully penetrant, ranges from mild to severe. Understanding the basis of this interindividual variability might identify predictive biomarkers of in utero and postnatal outcomes that could be used as endpoints to test the efficacy of future therapeutic interventions. OBJECTIVE: The main objective of this study was to examine if antenatal interindividual variability exists in mouse models of Down syndrome and whether applying statistical approaches to clinically relevant measurements (ie, the weights of the embryo, placenta, and brain) could define cutoffs that discriminate between subgroups of trisomic embryos. STUDY DESIGN: Three commonly used mouse models of Down syndrome (Dp(16)1/Yey, Ts65Dn, and Ts1Cje) and a new model (Ts66Yah) were used in this study. Trisomic and euploid littermate embryos were used from each model with total numbers of 102 for Ts66Yah, 118 for Dp(16)1/Yey, 92 for Ts65Dn, and 126 for Ts1Cje. Placental, embryonic, and brain weights and volumes at embryonic day 18.5 were compared between genotypes in each model. K-mean clustering analysis was applied to embryonic and brain weights to identify severity classes in trisomic embryos, and brain and placental volumetric measurements were compared between genotypes and classes for each strain. In addition, Ts66Yah embryos were examined for malformations because embryonic phenotypes have never been examined in this model. RESULTS: Reduced body and brain weights were present in Ts66Yah, Dp(16)1/Yey, and Ts65Dn embyos. Cluster analysis identified 2 severity classes in trisomic embryos-mild and severe-in all 4 models that were distinguishable using a putative embryonic weight cutoff of <0.5 standard deviation below the mean. Ts66Yah trisomic embryos develop congenital anomalies that are also found in humans with Down syndrome, including congenital heart defects and renal pelvis dilation. CONCLUSION: Statistical approaches applied to clinically relevant measurements revealed 2 classes of phenotypic severity in trisomic mouse models of Down syndrome. Analysis of severely affected trisomic animals may facilitate the identification of biomarkers and endpoints that can be used to prenatally predict outcomes and the efficacy of treatments.
Asunto(s)
Síndrome de Down , Cardiopatías Congénitas , Discapacidad Intelectual , Animales , Ratones , Femenino , Humanos , Embarazo , Síndrome de Down/genética , Placenta , Fenotipo , Cardiopatías Congénitas/genética , Biomarcadores , Modelos Animales de Enfermedad , Ratones Endogámicos C57BLRESUMEN
The rare, fatal neurodegenerative disorder Niemann-Pick disease type C1 (NPC1) arises from lysosomal accumulation of unesterified cholesterol and glycosphingolipids. These subcellular pathologies lead to phenotypes of hepatosplenomegaly, neurological degeneration and premature death. The timing and severity of NPC1 clinical presentation is extremely heterogeneous. This study analyzed RNA-Seq data from 42 NPC1 patient-derived, primary fibroblast cell lines to determine transcriptional changes induced by treatment with 2-hydroxypropyl-ß-cyclodextrin (HPßCD), a compound currently under investigation in clinical trials. A total of 485 HPßCD-responsive genes were identified. Pathway enrichment analysis of these genes showed significant involvement in cholesterol and lipid biosynthesis. Furthermore, immunohistochemistry of the cerebellum as well as measurements of plasma from Npc1m1N null mice treated with HPßCD and adeno-associated virus gene therapy suggests that one of the identified genes, GPNMB, may serve as a useful biomarker of treatment response in NPC1 disease. Overall, this large NPC1 patient-derived dataset provides a comprehensive foundation for understanding the genomic response to HPßCD treatment.
Asunto(s)
Enfermedad de Niemann-Pick Tipo C , 2-Hidroxipropil-beta-Ciclodextrina , Animales , Biomarcadores , Modelos Animales de Enfermedad , Proteínas del Ojo/genética , Humanos , Glicoproteínas de Membrana/genética , Ratones , Ratones Noqueados , Enfermedad de Niemann-Pick Tipo C/tratamiento farmacológico , Enfermedad de Niemann-Pick Tipo C/genética , Enfermedad de Niemann-Pick Tipo C/patología , TranscriptomaRESUMEN
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.
Asunto(s)
Relojes Circadianos , Medicago truncatula , Sinorhizobium meliloti , Cisteína/metabolismo , Regulación de la Expresión Génica de las Plantas , Medicago truncatula/metabolismo , Fijación del Nitrógeno/fisiología , Péptidos/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Nodulación de la Raíz de la Planta/genética , Nódulos de las Raíces de las Plantas/metabolismo , SimbiosisRESUMEN
Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3-19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.
Asunto(s)
Albinismo Oculocutáneo , Estudio de Asociación del Genoma Completo , Albinismo Oculocutáneo/diagnóstico , Albinismo Oculocutáneo/genética , Alelos , Humanos , Proteínas de Transporte de Membrana/genética , MutaciónRESUMEN
In Arabidopsis thaliana, changes in metabolism and gene expression drive increased drought tolerance and initiate diverse drought avoidance and escape responses. To address regulatory processes that link these responses, we set out to identify genes that govern early responses to drought. To do this, a high-resolution time series transcriptomics data set was produced, coupled with detailed physiological and metabolic analyses of plants subjected to a slow transition from well-watered to drought conditions. A total of 1815 drought-responsive differentially expressed genes were identified. The early changes in gene expression coincided with a drop in carbon assimilation, and only in the late stages with an increase in foliar abscisic acid content. To identify gene regulatory networks (GRNs) mediating the transition between the early and late stages of drought, we used Bayesian network modeling of differentially expressed transcription factor (TF) genes. This approach identified AGAMOUS-LIKE22 (AGL22), as key hub gene in a TF GRN. It has previously been shown that AGL22 is involved in the transition from vegetative state to flowering but here we show that AGL22 expression influences steady state photosynthetic rates and lifetime water use. This suggests that AGL22 uniquely regulates a transcriptional network during drought stress, linking changes in primary metabolism and the initiation of stress responses.
Asunto(s)
Ácido Abscísico/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas , Reguladores del Crecimiento de las Plantas/metabolismo , Factores de Transcripción/metabolismo , Arabidopsis/crecimiento & desarrollo , Arabidopsis/fisiología , Proteínas de Arabidopsis/genética , Teorema de Bayes , Análisis por Conglomerados , Sequías , Redes Reguladoras de Genes , Mutación , Fenotipo , Fotosíntesis/fisiología , Estrés Fisiológico , Factores de Transcripción/genéticaRESUMEN
OBJECTIVES: To develop a focused panel of somatic mutations (SMs) present in the majority of urothelial bladder cancers (UBCs), to investigate the diagnostic and prognostic utility of this panel, and to compare the identification of SMs in urinary cell-pellet (cp)DNA and cell-free (cf)DNA as part of the development of a non-invasive clinical assay. PATIENTS AND METHODS: A panel of SMs was validated by targeted deep-sequencing of tumour DNA from 956 patients with UBC. In addition, amplicon and capture-based targeted sequencing measured mutant allele frequencies (MAFs) of SMs in 314 urine cpDNAs and 153 urine cfDNAs. The association of SMs with grade, stage, and clinical outcomes was investigated by univariate and multivariate Cox models. Concordance between SMs detected in tumour tissue and cpDNA and cfDNA was assessed. RESULTS: The panel comprised SMs in 23 genes: TERT (promoter), FGFR3, PIK3CA, TP53, ERCC2, RHOB, ERBB2, HRAS, RXRA, ELF3, CDKN1A, KRAS, KDM6A, AKT1, FBXW7, ERBB3, SF3B1, CTNNB1, BRAF, C3orf70, CREBBP, CDKN2A, and NRAS; 93.5-98.3% of UBCs of all grades and stages harboured ≥1 SM (mean: 2.5 SMs/tumour). RAS mutations were associated with better overall survival (P = 0.04). Mutations in RXRA, RHOB and TERT (promoter) were associated with shorter time to recurrence (P < 0.05). MAFs in urinary cfDNA and cpDNA were highly correlated; using a capture-based approach, >94% of tumour SMs were detected in both cpDNA and cfDNA. CONCLUSIONS: SMs are reliably detected in urinary cpDNA and cfDNA. The technical capability to identify very low MAFs is essential to reliably detect UBC, regardless of the use of cpDNA or cfDNA. This 23-gene panel shows promise for the non-invasive diagnosis and risk stratification of UBC.
Asunto(s)
ADN de Neoplasias/orina , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Mutación/genética , Neoplasias de la Vejiga Urinaria/diagnóstico , Neoplasias de la Vejiga Urinaria/genética , Adulto , Anciano , Anciano de 80 o más Años , Bases de Datos Genéticas , Femenino , Humanos , Masculino , Persona de Mediana Edad , Pronóstico , Medición de Riesgo , Análisis de Secuencia de ADNRESUMEN
Genome-wide analyses of the effector- and toxin-encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry (Prunus avium), including pathovars P. syringae pv morsprunorum (Psm) races 1 and 2, P. syringae pv syringae (Pss) and P. syringae pv avii. Phylogenetic analyses revealed Psm races and P. syringae pv avii clades were distinct and were each monophyletic, whereas cherry-pathogenic strains of Pss were interspersed amongst strains from other host species. A maximum likelihood approach was used to predict effectors associated with pathogenicity on cherry. Pss possesses a smaller repertoire of type III effectors but has more toxin biosynthesis clusters than Psm and P. syringae pv avii. Evolution of cherry pathogenicity was correlated with gain of genes such as hopAR1 and hopBB1 through putative phage transfer and horizontal transfer respectively. By contrast, loss of the avrPto/hopAB redundant effector group was observed in cherry-pathogenic clades. Ectopic expression of hopAB and hopC1 triggered the hypersensitive reaction in cherry leaves, confirming computational predictions. Cherry canker provides a fascinating example of convergent evolution of pathogenicity that is explained by the mix of effector and toxin repertoires acting on a common host.
Asunto(s)
Genes Bacterianos , Genómica , Prunus avium/microbiología , Pseudomonas syringae/genética , Alelos , Sistemas de Secreción Bacterianos , Transferencia de Gen Horizontal/genética , Modelos Biológicos , Filogenia , Enfermedades de las Plantas/microbiología , Pseudomonas syringae/clasificación , Pseudomonas syringae/patogenicidad , Análisis de Secuencia de ADN , Virulencia/genética , Factores de Virulencia/metabolismoRESUMEN
Transcriptional reprogramming is integral to effective plant defense. Pathogen effectors act transcriptionally and posttranscriptionally to suppress defense responses. A major challenge to understanding disease and defense responses is discriminating between transcriptional reprogramming associated with microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and that orchestrated by effectors. A high-resolution time course of genome-wide expression changes following challenge with Pseudomonas syringae pv tomato DC3000 and the nonpathogenic mutant strain DC3000hrpA- allowed us to establish causal links between the activities of pathogen effectors and suppression of MTI and infer with high confidence a range of processes specifically targeted by effectors. Analysis of this information-rich data set with a range of computational tools provided insights into the earliest transcriptional events triggered by effector delivery, regulatory mechanisms recruited, and biological processes targeted. We show that the majority of genes contributing to disease or defense are induced within 6 h postinfection, significantly before pathogen multiplication. Suppression of chloroplast-associated genes is a rapid MAMP-triggered defense response, and suppression of genes involved in chromatin assembly and induction of ubiquitin-related genes coincide with pathogen-induced abscisic acid accumulation. Specific combinations of promoter motifs are engaged in fine-tuning the MTI response and active transcriptional suppression at specific promoter configurations by P. syringae.
Asunto(s)
Arabidopsis/inmunología , Terapia de Inmunosupresión , Moléculas de Patrón Molecular Asociado a Patógenos/metabolismo , Inmunidad de la Planta/genética , Hojas de la Planta/inmunología , Pseudomonas syringae/fisiología , Transcripción Genética , Arabidopsis/genética , Arabidopsis/microbiología , Secuencia de Bases , Cromatina/metabolismo , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Ontología de Genes , Redes Reguladoras de Genes , Genes de Plantas , Datos de Secuencia Molecular , Motivos de Nucleótidos/genética , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/inmunología , Enfermedades de las Plantas/microbiología , Hojas de la Planta/genética , Hojas de la Planta/microbiología , Regiones Promotoras Genéticas/genética , Pseudomonas syringae/crecimiento & desarrollo , Factores de Transcripción/metabolismoRESUMEN
Comparison of the genome of the Gram negative human pathogen Haemophilus quentini MP1 with other species of Haemophilus revealed that, although it is more closely related to Haemophilus haemolyticus than Haemophilus influenzae, the pathogen is in fact genetically distinct, a finding confirmed by phylogenetic analysis using the H. influenzae multilocus sequence typing genes. Further comparison with two other H. quentini strains recently identified in Canada revealed that these three genomes are more closely related than any other species of Haemophilus; however, there is still some sequence variation. There was no evidence of acquired antimicrobial resistance within the H. quentini MP1 genome nor any mutations within the DNA gyrase or topoisomerase IV genes known to confer resistance to fluoroquinolones, which has been previously identified in other H. quentini isolates. We hope by presenting the annotation and genetic comparison of the H. quentini MP1 genome it will aid the future molecular detection of this potentially emerging pathogen via the identification of unique genes that differentiate it from other species of Haemophilus.
Asunto(s)
Girasa de ADN/genética , Topoisomerasa de ADN IV/genética , Genoma Bacteriano , Haemophilus influenzae/genética , Haemophilus/genética , Girasa de ADN/metabolismo , Topoisomerasa de ADN IV/metabolismo , Expresión Génica , Variación Genética , Haemophilus/clasificación , Haemophilus/metabolismo , Haemophilus influenzae/clasificación , Haemophilus influenzae/metabolismo , Tipificación de Secuencias Multilocus , Filogenia , Secuenciación Completa del GenomaAsunto(s)
ADN de Neoplasias/orina , Recurrencia Local de Neoplasia/orina , Neoplasias de la Vejiga Urinaria/terapia , Neoplasias de la Vejiga Urinaria/orina , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Biomarcadores de Tumor/orina , Cetuximab/administración & dosificación , Quimioradioterapia , Ensayos Clínicos Fase I como Asunto , Ensayos Clínicos Fase II como Asunto , ADN de Neoplasias/análisis , Fluorouracilo/administración & dosificación , Humanos , Biopsia Líquida , Mitomicina/administración & dosificación , Músculo Liso/patología , Mutación , Invasividad Neoplásica , Recurrencia Local de Neoplasia/genética , Proyectos Piloto , Receptor Tipo 3 de Factor de Crecimiento de Fibroblastos/genética , Análisis de Secuencia de ADN , Telomerasa/genética , Resultado del Tratamiento , Proteína p53 Supresora de Tumor/genética , Neoplasias de la Vejiga Urinaria/genética , Neoplasias de la Vejiga Urinaria/patologíaRESUMEN
Severe longitudinally extensive transverse myelitis (LETM) can cause quadriplegia, marked sensory dysfunction, and respiratory failure. Some patients are unresponsive to conventional immune therapy. We report two cases of severe immune-mediated LETM requiring intensive care admission that failed to respond to high-dose corticosteroids, plasma exchange, intravenous immunoglobulin, and rituximab. Disease cessation and significant recovery was achieved after cyclophosphamide induction. In patients with severe acute immune-mediated LETM who fail to respond to corticosteroids and plasma exchange, cyclophosphamide induction should be considered. This agent and regimen provides a robust immunosuppressive response and can be induced rapidly. Cyclophosphamide effects and supportive evidence are discussed.
Asunto(s)
Ciclofosfamida/uso terapéutico , Inmunosupresores/uso terapéutico , Mielitis Transversa/tratamiento farmacológico , Neuromielitis Óptica/tratamiento farmacológico , Femenino , Humanos , Imagen por Resonancia Magnética/métodos , Mielitis Transversa/diagnóstico , Mielitis Transversa/patología , Neuromielitis Óptica/diagnóstico , Neuromielitis Óptica/patología , Columna Vertebral/patología , Resultado del Tratamiento , Adulto JovenRESUMEN
The ribosome is an evolutionarily conserved organelle essential for cellular function. Ribosome construction requires assembly of approximately 80 different ribosomal proteins (RPs) and four different species of rRNA. As RPs co-assemble into one multi-subunit complex, mutation of the genes that encode RPs might be expected to give rise to phenocopies, in which the same phenotype is associated with loss-of-function of each individual gene. However, a more complex picture is emerging in which, in addition to a group of shared phenotypes, diverse RP gene-specific phenotypes are observed. Here we report the first two mouse mutations (Rps7(Mtu) and Rps7(Zma)) of ribosomal protein S7 (Rps7), a gene that has been implicated in Diamond-Blackfan anemia. Rps7 disruption results in decreased body size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations. These phenotypes are reported in other murine RP mutants and, as demonstrated for some other RP mutations, are ameliorated by Trp53 deficiency. Interestingly, Rps7 mutants have additional overt malformations of the developing central nervous system and deficits in working memory, phenotypes that are not reported in murine or human RP gene mutants. Conversely, Rps7 mouse mutants show no anemia or hyperpigmentation, phenotypes associated with mutation of human RPS7 and other murine RPs, respectively. We provide two novel RP mouse models and expand the repertoire of potential phenotypes that should be examined in RP mutants to further explore the concept of RP gene-specific phenotypes.
Asunto(s)
Anemia de Diamond-Blackfan , Sistema Nervioso Central , Morfogénesis/genética , Proteínas Ribosómicas/genética , Anemia de Diamond-Blackfan/genética , Anemia de Diamond-Blackfan/patología , Animales , Tamaño Corporal/genética , Sistema Nervioso Central/crecimiento & desarrollo , Sistema Nervioso Central/patología , Modelos Animales de Enfermedad , Humanos , Memoria a Corto Plazo/fisiología , Ratones , Mutación , Fenotipo , Proteínas Ribosómicas/fisiología , Ribosomas/genéticaRESUMEN
Niemann-Pick disease, type C1 (NPC1), which arises from a mutation in the NPC1 gene, is characterized by abnormal cellular storage and transport of cholesterol and other lipids that leads to hepatic disease and progressive neurological impairment. Oxidative stress has been hypothesized to contribute to the NPC1 disease pathological cascade. To determine whether treatments reducing oxidative stress could alleviate NPC1 disease phenotypes, the in vivo effects of the antioxidant N-acetylcysteine (NAC) on two mouse models for NPC1 disease were studied. NAC was able to partially suppress phenotypes in both antisense-induced (NPC1ASO) and germline (Npc1-/-) knockout genetic mouse models, confirming the presence of an oxidative stress-related mechanism in progression of NPC1 phenotypes and suggesting NAC as a potential molecule for treatment. Gene expression analyses of NAC-treated NPC1ASO mice suggested NAC affects pathways distinct from those initially altered by Npc1 knockdown, data consistent with NAC achieving partial disease phenotype suppression. In a therapeutic trial of short-term NAC administration to NPC1 patients, no significant effects on oxidative stress in these patients were identified other than moderate improvement of the fraction of reduced CoQ10, suggesting limited efficacy of NAC monotherapy. However, the mouse model data suggest that the distinct antioxidant effects of NAC could provide potential treatment of NPC1 disease, possibly in concert with other therapeutic molecules at earlier stages of disease progression. These data also validated the NPC1ASO mouse as an efficient model for candidate NPC1 drug screening, and demonstrated similarities in hepatic phenotypes and genome-wide transcript expression patterns between the NPC1ASO and Npc1-/- models.
Asunto(s)
Acetilcisteína/farmacología , Acetilcisteína/uso terapéutico , Enfermedad de Niemann-Pick Tipo C/tratamiento farmacológico , Enfermedad de Niemann-Pick Tipo C/genética , Estrés Oxidativo/efectos de los fármacos , Acetilcisteína/administración & dosificación , Adolescente , Adulto , Animales , Niño , Preescolar , Estudios Cruzados , Modelos Animales de Enfermedad , Método Doble Ciego , Femenino , Expresión Génica , Humanos , Hígado/metabolismo , Hígado/patología , Masculino , Ratones , Ratones Noqueados , Enfermedad de Niemann-Pick Tipo C/metabolismo , Enfermedad de Niemann-Pick Tipo C/fisiopatología , Estrés Oxidativo/genética , Ubiquinona/análogos & derivados , Ubiquinona/metabolismo , Adulto JovenRESUMEN
Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.
Asunto(s)
Arabidopsis/genética , Carica/genética , ADN de Plantas/química , Regulación de la Expresión Génica de las Plantas , Redes Reguladoras de Genes , Populus/genética , Vitis/genética , Sitios de Unión , Secuencia Conservada , Genómica , Nucleosomas/metabolismo , Análisis de Secuencia de ADN , Programas InformáticosRESUMEN
Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.
Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Botrytis/fisiología , Regulación de la Expresión Génica de las Plantas/genética , Genoma de Planta/genética , Enfermedades de las Plantas/inmunología , Arabidopsis/inmunología , Arabidopsis/metabolismo , Arabidopsis/microbiología , Botrytis/crecimiento & desarrollo , Perfilación de la Expresión Génica , Redes Reguladoras de Genes , Modelos Genéticos , Mutación , Motivos de Nucleótidos , Análisis de Secuencia por Matrices de Oligonucleótidos , Enfermedades de las Plantas/microbiología , Inmunidad de la Planta , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Hojas de la Planta/microbiología , Regiones Promotoras Genéticas/genética , Transducción de Señal , Factores de Tiempo , Factores de Transcripción/genética , TranscriptomaRESUMEN
Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Asunto(s)
Genoma/genética , Phytophthora infestans/genética , Enfermedades de las Plantas/microbiología , Solanum tuberosum/microbiología , Proteínas Algáceas/genética , Elementos Transponibles de ADN/genética , ADN Intergénico/genética , Evolución Molecular , Interacciones Huésped-Patógeno/genética , Humanos , Irlanda , Datos de Secuencia Molecular , Necrosis , Fenotipo , Phytophthora infestans/patogenicidad , Enfermedades de las Plantas/inmunología , Solanum tuberosum/inmunología , InaniciónRESUMEN
SUMMARY: Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. Although there are tools for ab initio discovery of transcription factor-binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets. AVAILABILITY: MEME-LaB is freely accessible at: http://wsbc.warwick.ac.uk/wsbcToolsWebpage/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)
Regiones Promotoras Genéticas , Programas Informáticos , Factores de Transcripción/metabolismo , Algoritmos , Sitios de Unión , Análisis por Conglomerados , Internet , Motivos de Nucleótidos , Análisis de Secuencia de ADNRESUMEN
Honeybees, Apis mellifera, show age-related division of labor in which young adults perform maintenance ("housekeeping") tasks inside the colony before switching to outside foraging at approximately 23 days old. Disease resistance is an important feature of honeybee biology, but little is known about the interaction of pathogens and age-related division of labor. We tested a hypothesis that older forager bees and younger "house" bees differ in susceptibility to infection. We coupled an infection bioassay with a functional analysis of gene expression in individual bees using a whole genome microarray. Forager bees treated with the entomopathogenic fungus Metarhizium anisopliae s.l. survived for significantly longer than house bees. This was concomitant with substantial differences in gene expression including genes associated with immune function. In house bees, infection was associated with differential expression of 35 candidate immune genes contrasted with differential expression of only two candidate immune genes in forager bees. For control bees (i.e. not treated with M. anisopliae) the development from the house to the forager stage was associated with differential expression of 49 candidate immune genes, including up-regulation of the antimicrobial peptide gene abaecin, plus major components of the Toll pathway, serine proteases, and serpins. We infer that reduced pathogen susceptibility in forager bees was associated with age-related activation of specific immune system pathways. Our findings contrast with the view that the immunocompetence in social insects declines with the onset of foraging as a result of a trade-off in the allocation of resources for foraging. The up-regulation of immune-related genes in young adult bees in response to M. anisopliae infection was an indicator of disease susceptibility; this also challenges previous research in social insects, in which an elevated immune status has been used as a marker of increased disease resistance and fitness without considering the effects of age-related development.
Asunto(s)
Abejas/inmunología , Resistencia a la Enfermedad/inmunología , Metarhizium/inmunología , Factores de Edad , Animales , Péptidos Catiónicos Antimicrobianos/biosíntesis , Péptidos Catiónicos Antimicrobianos/genética , Abejas/microbiología , Expresión Génica/inmunología , Perfilación de la Expresión Génica , Proteínas de Insectos/biosíntesis , Proteínas de Insectos/genética , Serina Proteasas/biosíntesis , Serpinas/biosíntesis , Medio Social , Receptores Toll-Like/biosíntesisRESUMEN
Consumers have become interested in plant-based alternatives to animal-based products. One of the under-studied alternatives is plant-based eggs (PBEs). This research investigated PBEs relative to conventional eggs and tofu scramble-another plant-based alternative. Firstly, participants (n = 93) completed a word association task asking them about PBEs. Participants then evaluated the different food samples using hedonic scales, check-all-that-apply (CATA), and temporal check-all-that-apply (TCATA), as well as identified their emotional response and proposed use for PBEs. Participants were interested in plant-based alternatives, including PBEs, but they were concerned about the sensory properties. When they evaluated the different samples, the flavour and texture of the PBEs were disliked in comparison to the eggs. This result may be due to the beany, bitterness, and off-flavour attributes associated with the PBEs. Participants also associated the PBEs with negative emotions. The liking of tofu scramble was not significantly different from the eggs, and the eggs and tofu scramble were mainly associated with positive emotions. During the TCATA evaluation, the participants focused on the flavour attributes of PBEs, while their evaluation of the eggs was dominated by the textural attributes. Whether following a plant-based diet or not, consumers are interested in PBEs, but the sensory properties of PBEs need to be improved before they are willing to adopt them into their diet. This study is one of the first to evaluate the sensory properties of PBEs, as well as consumers' emotional response to them and their attitudes about PBEs.