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1.
Nature ; 479(7374): 487-92, 2011 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-22113690

RESUMO

The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.


Assuntos
Adaptação Fisiológica/genética , Genoma/genética , Herbivoria/genética , Tetranychidae/genética , Tetranychidae/fisiologia , Adaptação Fisiológica/fisiologia , Animais , Ecdisterona/análogos & derivados , Ecdisterona/genética , Evolução Molecular , Fibroínas/genética , Regulação da Expressão Gênica , Transferência Genética Horizontal/genética , Genes Homeobox/genética , Genômica , Herbivoria/fisiologia , Dados de Sequência Molecular , Muda/genética , Família Multigênica/genética , Nanoestruturas/química , Plantas/parasitologia , Seda/biossíntese , Seda/química , Transcriptoma/genética
2.
BMC Genomics ; 17(1): 853, 2016 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-27806710

RESUMO

BACKGROUND: Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages. RESULTS: Using this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs. CONCLUSION: Our analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells.


Assuntos
Evolução Molecular , Regulação da Expressão Gênica de Plantas , Inativação Gênica , Pequeno RNA não Traduzido/genética , Volvox/genética , Proteínas Argonautas/metabolismo , Sequência de Bases , Sítios de Ligação , Biologia Computacional/métodos , Elementos de DNA Transponíveis , Perfilação da Expressão Gênica , MicroRNAs/genética , Anotação de Sequência Molecular , Motivos de Nucleotídeos , Ligação Proteica , Reprodutibilidade dos Testes , Transcriptoma
3.
EMBO J ; 31(15): 3323-33, 2012 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-22781127

RESUMO

Precise gene expression is a fundamental aspect of organismal function and depends on the combinatorial interplay of transcription factors (TFs) with cis-regulatory DNA elements. While much is known about TF function in general, our understanding of their cell type-specific activities is still poor. To address how widely expressed transcriptional regulators modulate downstream gene activity with high cellular specificity, we have identified binding regions for the Hox TF Deformed (Dfd) in the Drosophila genome. Our analysis of architectural features within Hox cis-regulatory response elements (HREs) shows that HRE structure is essential for cell type-specific gene expression. We also find that Dfd and Ultrabithorax (Ubx), another Hox TF specifying different morphological traits, interact with non-overlapping regions in vivo, despite their similar DNA binding preferences. While Dfd and Ubx HREs exhibit comparable design principles, their motif compositions and motif-pair associations are distinct, explaining the highly selective interaction of these Hox proteins with the regulatory environment. Thus, our results uncover the regulatory code imprinted in Hox enhancers and elucidate the mechanisms underlying functional specificity of TFs in vivo.


Assuntos
Drosophila/genética , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/fisiologia , Elementos de Resposta/genética , Fatores de Transcrição/metabolismo , Animais , Animais Geneticamente Modificados , Sítios de Ligação/genética , Drosophila/embriologia , Proteínas de Drosophila/metabolismo , Proteínas de Drosophila/fisiologia , Embrião não Mamífero , Regulação da Expressão Gênica no Desenvolvimento , Genes Homeobox , Genes de Insetos , Código das Histonas/genética , Código das Histonas/fisiologia , Proteínas de Homeodomínio/metabolismo , Modelos Biológicos , Ligação Proteica , Fatores de Transcrição/fisiologia , Ativação Transcricional
4.
Bioinformatics ; 30(22): 3264-5, 2014 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-25075116

RESUMO

MOTIVATION: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. RESULT: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k-mer spectrum. With high-quality k-mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. AVAILABILITY AND IMPLEMENTATION: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net. CONTACT: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Software , Algoritmos
5.
BMC Genomics ; 15: 400, 2014 May 26.
Artigo em Inglês | MEDLINE | ID: mdl-24886435

RESUMO

BACKGROUND: Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this divergence in the presence of variable sex-determination mechanisms of recent origin. The guppy, Poecilia reticulata, displays sexual dimorphism in size, ornaments, and behavior, traits shaped by natural and sexual selection in the wild. RESULTS: To gain insight into molecular mechanisms underlying the guppy's sexual dimorphism, we assembled a reference transcriptome combining genome-independent as well as genome-guided assemblies and analyzed sex-biased gene expression between different tissues of adult male and female guppies. We found tissue-associated sex-biased expression of genes related to pigmentation, signal transduction, and spermatogenesis in males; and growth, cell-division, extra-cellular matrix organization, nutrient transport, and folliculogenesis in females. While most sex-biased genes were randomly distributed across linkage groups, we observed accumulation of ovary-biased genes on the sex linkage group, LG12. Both testis-biased and ovary-biased genes showed a significantly higher rate of non-synonymous to synonymous substitutions (dN/dS) compared to unbiased genes. However, in somatic tissues only female-biased genes, including those co-expressed in multiple tissues, showed elevated ratios of non-synonymous substitutions. CONCLUSIONS: Our work identifies a set of annotated gene products that are candidate factors affecting sexual dimorphism in guppies. The differential genomic distribution of gonad-biased genes provides evidence for sex-specific selection pressures acting on the nascent sex chromosomes of the guppy. The elevated rates of evolution of testis-biased and female-biased genes indicate differing evolution under distinct selection pressures on the reproductive versus non-reproductive tissues.


Assuntos
Genômica/métodos , Poecilia/genética , Caracteres Sexuais , Animais , Feminino , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Masculino , Taxa de Mutação , Especificidade de Órgãos , Poecilia/classificação , Poecilia/fisiologia , Seleção Genética , Cromossomos Sexuais , Transcriptoma
7.
Genome Res ; 21(2): 325-41, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21177967

RESUMO

The C. elegans genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning-based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total C. elegans genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Examination of known tissue- and cell-specific transcripts validates these data sets and suggests that newly identified TARs may exercise cell-specific functions. Additionally, we used self-organizing maps to define groups of coregulated transcripts and applied regulatory element analysis to identify known transcription factor- and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation.


Assuntos
Caenorhabditis elegans/genética , Regulação da Expressão Gênica no Desenvolvimento , Animais , Biologia Computacional , Bases de Dados Genéticas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento/genética , Masculino , Meiose/genética , Dados de Sequência Molecular , Oogênese/genética , Fases de Leitura Aberta/genética , Transcrição Gênica , Regiões não Traduzidas/genética , Inativação do Cromossomo X/genética
8.
Proc Natl Acad Sci U S A ; 108(1): 254-9, 2011 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-21173231

RESUMO

CO(2) is both a critical regulator of animal physiology and an important sensory cue for many animals for host detection, food location, and mate finding. The free-living soil nematode Caenorhabditis elegans shows CO(2) avoidance behavior, which requires a pair of ciliated sensory neurons, the BAG neurons. Using in vivo calcium imaging, we show that CO(2) specifically activates the BAG neurons and that the CO(2)-sensing function of BAG neurons requires TAX-2/TAX-4 cyclic nucleotide-gated ion channels and the receptor-type guanylate cyclase GCY-9. Our results delineate a molecular pathway for CO(2) sensing and suggest that activation of a receptor-type guanylate cyclase is an evolutionarily conserved mechanism by which animals detect environmental CO(2).


Assuntos
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/fisiologia , Dióxido de Carbono/metabolismo , Quimiotaxia/fisiologia , Guanilato Ciclase/metabolismo , Canais Iônicos/metabolismo , Neurônios/metabolismo , Receptores Acoplados a Guanilato Ciclase/metabolismo , Olfato/fisiologia , Animais , Sequência de Bases , Evolução Biológica , Caenorhabditis elegans/enzimologia , Dióxido de Carbono/toxicidade , Quimiotaxia/efeitos dos fármacos , Análise por Conglomerados , Primers do DNA/genética , Componentes do Gene , Microscopia Confocal , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Olfato/genética , Transgenes/genética
9.
Proc Natl Acad Sci U S A ; 108(25): 10249-54, 2011 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-21646520

RESUMO

We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.


Assuntos
Arabidopsis/genética , Genoma de Planta , Algoritmos , Sequência de Bases , Polimorfismo Genético , Alinhamento de Sequência , Análise de Sequência de DNA
10.
Nat Genet ; 37(5): 501-6, 2005 May.
Artigo em Inglês | MEDLINE | ID: mdl-15806101

RESUMO

Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.


Assuntos
Arabidopsis/crescimento & desenvolvimento , Arabidopsis/genética , Perfilação da Expressão Gênica , Expressão Gênica/fisiologia , Marcadores Genéticos
11.
Proc Natl Acad Sci U S A ; 107(41): 17466-73, 2010 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-20870966

RESUMO

In Arabidopsis thaliana, four different dicer-like (DCL) proteins have distinct but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and siRNAs from longer, noncoding precursor RNAs. To analyze the impact of different components of the small RNA biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in small RNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. Our analysis revealed a surprising number of common targets in dcl1 and dcl2 dcl3 dcl4 triple mutants. Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Ciclo Celular/metabolismo , Regulação da Expressão Gênica de Plantas/fisiologia , MicroRNAs/biossíntese , Ribonuclease III/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Ciclo Celular/genética , Metilação de DNA , Elementos de DNA Transponíveis/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Mutação/genética , Análise Serial de Proteínas , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Ribonuclease III/genética
12.
Plant Physiol ; 152(2): 487-99, 2010 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-20032078

RESUMO

Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strands, with on average one 25mer probe per 35-bp genome sequence window. In addition, the new AGRONOMICS1 array contains all perfect match probes from the original ATH1 array, allowing for seamless integration of the very large existing ATH1 knowledge base. The AGRONOMICS1 array can be used for diverse functional genomics applications such as reliable expression profiling of more than 30,000 genes, detection of alternative splicing, and chromatin immunoprecipitation coupled to microarrays (ChIP-chip). Here, we describe the design of the array and compare its performance with that of the ATH1 array. We find results from both microarrays to be of similar quality, but AGRONOMICS1 arrays yield robust expression information for many more genes, as expected. Analysis of the ATH1 probes on AGRONOMICS1 arrays produces results that closely mirror those of ATH1 arrays. Finally, the AGRONOMICS1 array is shown to be useful for ChIP-chip experiments. We show that heterochromatic H3K9me2 is strongly confined to the gene body of target genes in euchromatic chromosome regions, suggesting that spreading of heterochromatin is limited outside of pericentromeric regions.


Assuntos
Arabidopsis/genética , Perfilação da Expressão Gênica/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Imunoprecipitação da Cromatina , Biologia Computacional , Sondas de DNA , Genes de Plantas , Genômica , RNA de Plantas/genética , Análise de Sequência de DNA
13.
Plant J ; 58(6): 1068-82, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19222804

RESUMO

The responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Perfilação da Expressão Gênica/métodos , Genoma de Planta , Ácido Abscísico/farmacologia , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Temperatura Baixa , Regulação da Expressão Gênica de Plantas , Temperatura Alta , Análise de Sequência com Séries de Oligonucleotídeos/métodos , RNA de Plantas/genética , Cloreto de Sódio/farmacologia , Estresse Fisiológico
14.
J Pharm Sci ; 109(1): 818-829, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31689430

RESUMO

Specifically tailored amino acid-based formulations were previously shown to have a high potential to avoid stress-mediated degradation of complex molecules such as monoclonal antibodies and viral vectors. By using adenovirus 5 (Ad5) as a model, we studied whether such formulations may also efficiently protect viral vectors in thermal stress experiments and during long-term liquid storage. Algorithm-based amino acid preselection using an excipient database and subsequent application of design of experiments (DoE) in combination with a 37°C challenging model enabled the prediction of long-term storage stability of Ad5. By statistical analysis of the Ad5 infectivity, amino acids with significant influence on Ad5 stability were detected after 2 and 3 weeks of liquid storage at 37°C. Ad5 formulations comprising positively selected amino acids did not reveal any loss of infectivity after 24 months in liquid storage at 5°C. By contrast, a 2 log reduction after 3 months and complete loss of infectivity after 18 months was observed with a standard viral vector formulation. By an optimization round, we designed a simple and well-balanced formulation avoiding MgCl2, previously considered essential in Ad5 formulations. This work demonstrates the efficacy of an algorithm-based development approach in the formulation development for viral vectors.


Assuntos
Adenovírus Humanos/genética , Algoritmos , Aminoácidos/química , DNA Viral/química , Excipientes/química , Técnicas de Transferência de Genes , Vetores Genéticos , DNA Viral/metabolismo , Células HEK293 , Humanos , Desnaturação de Ácido Nucleico , Temperatura , Fatores de Tempo
15.
BMC Genomics ; 8: 269, 2007 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-17686157

RESUMO

BACKGROUND: The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available. RESULTS: With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes. CONCLUSION: Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.


Assuntos
Etiquetas de Sequências Expressas , Filogenia , Poecilia/genética , Polimorfismo de Nucleotídeo Único , Animais , Sequência de Bases , Primers do DNA , DNA Complementar , Bases de Dados Genéticas , Poecilia/classificação , Cromossomos Sexuais
16.
Proc Biol Sci ; 274(1606): 33-42, 2007 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-17015333

RESUMO

Identification of genes that control variation in adaptive characters is a prerequisite for understanding the processes that drive sexual and natural selection. Male coloration and female colour perception play important roles in mate choice in the guppy (Poecilia reticulata), a model organism for studies of natural and sexual selection. We examined a potential source for the known variation in colour perception, by analysing genomic and complementary DNA sequences of genes that code for visual pigment proteins. We find high sequence variability, both within and between populations, and expanded copy number for long-wave sensitive (LWS) opsin genes. Alleles with non-synonymous changes that suggest dissimilar spectral tuning properties occur in the same population and even in the same individual, and the high frequency of non-synonymous substitutions argues for diversifying selection acting on these proteins. Therefore, variability in tuning amino acids is partitioned within individuals and populations of the guppy, in contrast to variability for LWS at higher taxonomic levels in cichlids, a second model system for differentiation owing to sexual selection. Since opsin variability parallels the extreme male colour polymorphism within guppy populations, we suggest that mate choice has been a major factor driving the coevolution of opsins and male ornaments in this species.


Assuntos
Duplicação Gênica , Modelos Genéticos , Poecilia/genética , Opsinas de Bastonetes/genética , Alelos , Sequência de Aminoácidos , Animais , Clonagem Molecular , Percepção de Cores/genética , Evolução Molecular , Dosagem de Genes , Haplótipos , Dados de Sequência Molecular , Filogenia , Polimorfismo Genético , Opsinas de Bastonetes/química , Opsinas de Bastonetes/fisiologia , Seleção Genética , Alinhamento de Sequência
17.
Endocrinology ; 158(8): 2503-2521, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28582497

RESUMO

Type 1 diabetes is a chronic autoimmune disease characterized by pancreatic islet inflammation and ß-cell destruction by proinflammatory cytokines and other mediators. Based on RNA sequencing and protein-protein interaction analyses of human islets exposed to proinflammatory cytokines, we identified complement C3 as a hub for some of the effects of cytokines. The proinflammatory cytokines interleukin-1ß plus interferon-γ increase C3 expression in rodent and human pancreatic ß-cells, and C3 is detected by histology in and around the islets of diabetic patients. Surprisingly, C3 silencing exacerbates apoptosis under both basal condition and following exposure to cytokines, and it increases chemokine expression upon cytokine treatment. C3 exerts its prosurvival effects via AKT activation and c-Jun N-terminal kinase inhibition. Exogenously added C3 also protects against cytokine-induced ß-cell death and partially rescues the deleterious effects of inhibition of endogenous C3. These data suggest that locally produced C3 is an important prosurvival mechanism in pancreatic ß-cells under a proinflammatory assault.


Assuntos
Complemento C3/metabolismo , Citocinas/metabolismo , Células Secretoras de Insulina/fisiologia , Animais , Apoptose , Linhagem Celular , Sobrevivência Celular , Complemento C3/genética , Regulação da Expressão Gênica/efeitos dos fármacos , Regulação da Expressão Gênica/fisiologia , Inativação Gênica , Glucose/farmacologia , Humanos , Insulina/metabolismo , Ligação Proteica , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ratos
18.
BMC Bioinformatics ; 7: 350, 2006 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-16854218

RESUMO

BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called delta value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS: Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. delta values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION: Using the most treelike distance matrices, as judged by their delta values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. delta values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference.


Assuntos
Biologia Computacional/métodos , DNA Mitocondrial/genética , Genoma/genética , Filogenia , Plastídeos/genética , Algoritmos , Animais , DNA de Cloroplastos/genética , Bases de Dados Genéticas , Humanos , Análise de Regressão , Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos
19.
Cell Host Microbe ; 16(3): 364-75, 2014 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-25211078

RESUMO

While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Ascomicetos/metabolismo , Proteínas de Bactérias/metabolismo , Evolução Biológica , Proteínas Fúngicas/metabolismo , Oomicetos/metabolismo , Pseudomonas syringae/metabolismo , Arabidopsis/genética , Arabidopsis/microbiologia , Arabidopsis/parasitologia , Proteínas de Arabidopsis/genética , Ascomicetos/genética , Proteínas de Bactérias/genética , Proteínas Fúngicas/genética , Interações Hospedeiro-Patógeno , Oomicetos/genética , Doenças das Plantas/microbiologia , Doenças das Plantas/parasitologia , Pseudomonas syringae/genética
20.
Nat Genet ; 45(7): 831-5, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23749190

RESUMO

The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.


Assuntos
Capsella/genética , Evolução Molecular , Fertilização/genética , Genoma de Planta , Polinização/genética , Arabidopsis/genética , Fertilização/fisiologia , Genes de Plantas , Genoma de Planta/fisiologia , Dados de Sequência Molecular , Polinização/fisiologia , Autofertilização/genética , Análise de Sequência de DNA , Fatores de Tempo
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