Melampsora americana strain:R15-033-03
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA501628 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8246752_1.fastq.gz | Fastqsanger.gz | |||
| SRR8246752_2.fastq.gz | Fastqsanger.gz | |||
| SRR8246753_1.fastq.gz | Fastqsanger.gz | |||
| SRR8246753_2.fastq.gz | Fastqsanger.gz | |||
| SRR8246754_1.fastq.gz | Fastqsanger.gz |
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Project description:Melampsora Americana R15-033-03 Standard Draft genome sequencing
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Project description:Despite the advances in our understanding of aging-associated behavioral decline, we know relatively little about how aging affect neural circuits that underlie specific behaviors. Specifically, we know little about how aging affect expression of genes in specific neural circuits. We have now addressed this problem by exploring a cholinergic neuron R15, an identified neuron of marine snail Aplysia. R15 is characterized by bursting action potentials and is implicated in reproduction, osmoregulation and locomotion.
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Project description:Despite the advances in our understanding of aging-associated behavioral decline, we know relatively little about how aging affect neural circuits that underlie specific behaviors. Specifically, we know little about how aging affect expression of genes in specific neural circuits. We have now addressed this problem by exploring a cholinergic neuron R15, an identified neuron of marine snail Aplysia. R15 is characterized by bursting action potentials and is implicated in reproduction, osmoregulation and locomotion. We examined changes in gene expression in R15 neurons during aging by microarray analyses of RNAs prepared from two different age groups, mature and old animals. Specifically we find that 1083 ESTs are differentially regulated in mature and old R15 neurons. Bioinformatics analyses of these genes have identified specific biological pathways and molecular processes that are up or down regulated in mature and old neurons. Comparison with human signaling networks using pathway analyses have identified three major networks that are altered in old R15 neurons. Furthermore, by single neuron qRTPCR we examined expression levels of candidate regulators involved in transcription (CREB1) and translation (S6 kinase) and find that aging is associated with a decrease in expression of these regulators. We next studied expression of CREB1 and S6 kinase in two different motor neurons (L7 and L11) and another cholinergic neuron R2 and find that these neurons have characteristic changes in gene expression during aging
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Project description:Background: Germ-free or axenic organisms are valuable tools for studying immunity, digestion, and development in different hosts. Although most of these studies have been conducted on mice, recently, germ-free invertebrate models (e.g. Drosophila and Apis) are used due to their easy husbandry, low cost for production, maintenance and the high number of individuals per generation they produce. However, a limitation of using these insects is the simple bacterial community present in their guts. The gut of the American cockroach Periplaneta americana displays a complex gut bacterial community composed of hundreds of species. Using P. americana, we developed a germ-free omnivorous invertebrate model to investigate how gut bacteria stimulate and shape normal gut development and metabolism. To determine if the insect host is directly affected by the presence of specific members of their bacterial community, gnotobiotic cockroaches were generated by inoculating a set of various P. americana gut-endemic Gram-negative (Bacteroidetes; n=11) and Gram-positive (Firmicutes; n=2) bacterial strains into germ-free insects. Additionally, we were able to recover the ‘normal’ bacterial-induced gut phenotype by co-housing germ-free cockroaches with wildtype P. americana to produce gut-bacteria conventionalized insects. Changes in gene expression profiles from two distinct regions (midgut and hindgut) of P. americana guts were quantified by RNA-Seq analysis of the germfree, gnotobiotic and conventionalized insects. Basic transcriptomics description: High-resolution transcriptome profiling of germ-free, gnotobiotic, and conventionalized treated P. americana midgut and hindguts. Ca. 43 million reads were obtained for each treatment. A de-novo assembly of all sequence reads was performed by Trinity assembler. Transcriptome assembly yielded 369,082 gene models and 554,155 isoforms. After running Trinotate pipeline, 65,047 (12 %) these transcripts matched an annotated product in at least one of the reference databases used (Uniprot, pfam, KEGG, COG). Additionally, 1,008 putative bacterial genes were annotated in the P. americana genome and ultimately excluded from these analyses. After bacteria decontamination, 553,147 assembled isoforms were used for transcript quantification and differential expression analysis using the DESeq2 pipeline. DESeq2 analysis detected 6,730 and 3,958 differentially expressed transcripts among the germ-free, gnotobiotic and conventionalized treatments in P. americana hindgut and midgut, respectively.
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Project description:The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and during poplar leaf infection. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression profiles during poplar leaf infection and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.
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Project description:The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and infected Poplar leaves. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression at different developmental stages and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.
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Project description:Persea americana var. americana Genome sequencing and assembly
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