The first fifty microarray studies in filamentous fungi

Breakspear, Andrew; Momany, Michelle

doi:10.1099/mic.0.2006/002592-0

Cited by 66 publications

(43 citation statements)

References 72 publications

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“…This allowed a comparison between equivalent growth stages, with the caveat that nuclear abundance differed between the wt and the ⌬cgrA mutant. The alternative approach of normalizing to nuclear number was not employed because any comparison between the wt and the slower growing ⌬cgrA strain would be confounded by stage-specific effects (7).…”

Section: Methodsmentioning

confidence: 99%

Impaired Ribosome Biogenesis Disrupts the Integration between Morphogenesis and Nuclear Duplication during the Germination of Aspergillus fumigatus

et al. 2008

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Aspergillus fumigatus is an important opportunistic fungal pathogen that is responsible for high mortality rates in the immunosuppressed population. CgrA, the A. fumigatus ortholog of a Saccharomyces cerevisiae nucleolar protein involved in ribosome biogenesis, contributes to the virulence of this fungus by supporting rapid growth at 37°C. To determine how CgrA affects ribosome biogenesis in A. fumigatus, polysome profile and ribosomal subunit analyses were performed on both wild-type A. fumigatus and a ⌬cgrA mutant. The loss of CgrA was associated with a reduction in the level of 80S monosomes as well as an imbalance in the 60S:40S subunit ratio and the appearance of half-mer ribosomes. The gene expression profile in the ⌬cgrA mutant revealed increased abundance of a subset of translational machinery mRNAs relative to the wild type, suggesting a potential compensatory response to CgrA deficiency. Although ⌬cgrA conidia germinated normally at 22°C, they swelled excessively when incubated at 37°C and accumulated abnormally high numbers of nuclei. This hypernucleated phenotype could be replicated pharmacologically by germinating wild-type conidia under conditions of reductive stress. These findings indicate that the germination process is particularly vulnerable to global disruption of protein synthesis and suggest that CgrA is involved in both ribosome biogenesis and polarized cell growth in A. fumigatus.

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Section: Methodsmentioning

confidence: 99%

Impaired Ribosome Biogenesis Disrupts the Integration between Morphogenesis and Nuclear Duplication during the Germination of Aspergillus fumigatus

et al. 2008

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“…After that a good number of studies have been published on fungal proteomics [9]. This review focus on the genus Colletotrichum.…”

Section: The Kingdom Fungimentioning

confidence: 99%

Pathogen to Endophytic Transmission in Fungi- A Proteomics Approach

Pillai¹

2017

SOJMID

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Fungi are a model organism for eukaryotic kingdom. Endophytic fungi have important role in plant microbiome. The endophytic fungi are thought to have evolved from parasites or pathogens through an extension of latency periods and reduction of virulence. The endophytic fungi, Colletotrichum are source of valuable compounds, useful in pharmaceutical/agricultural industry. The genus Colletotrichum consists of 29 to 700 species. It is a wellknown pathogen for long period and at the same time a well-known endophyte. This transition of the fungus from one state to another is interesting. The mechanism of transition from pathogen to endophyte is not yet studied. Chances of genetic drift were proposed earlier but not yet studied. In this review, we try to apply protein profiling as a powerful tool to study the transition of the fungi as a pathogen to endophyte (Parasitism to mutualism).

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“…Compared to EST sequencing and SAGE, both of which also rely on the sequencing of cDNAs or cDNA tags, the much higher throughput and consequently the increased sequencing depth of RNA-seq provides a much better resolution that allows not only the quantification of expression levels but the identification of transcript boundaries at the single-nucleotide level (80,115). During the last decade, microarrays were the most widely used method to determine transcript levels at a whole-genome scale, and they have greatly contributed to our knowledge about gene expression in eukaryotic microbes (10,27,83). However, using microarrays, transcripts can be detected only when there is a corresponding probe on the chip, and arrays for most organisms were designed to cover only the annotated coding (or, if known, transcribed) regions of a genome.…”

Section: -35mentioning

confidence: 99%

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

Nowrousian

2010

Eukaryot Cell

124

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Over the past 5 years, large-scale sequencing has been revolutionized by the development of several so-called next-generation sequencing (NGS) technologies. These have drastically increased the number of bases obtained per sequencing run while at the same time decreasing the costs per base. Compared to Sanger sequencing, NGS technologies yield shorter read lengths; however, despite this drawback, they have greatly facilitated genome sequencing, first for prokaryotic genomes and within the last year also for eukaryotic ones. This advance was possible due to a concomitant development of software that allows the de novo assembly of draft genomes from large numbers of short reads. In addition, NGS can be used for metagenomics studies as well as for the detection of sequence variations within individual genomes, e.g., single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), or structural variants. Furthermore, NGS technologies have quickly been adopted for other high-throughput studies that were previously performed mostly by hybridization-based methods like microarrays. This includes the use of NGS for transcriptomics (RNA-seq) or the genome-wide analysis of DNA/protein interactions (ChIP-seq). This review provides an overview of NGS technologies that are currently available and the bioinformatics analyses that are necessary to obtain information from the flood of sequencing data as well as applications of NGS to address biological questions in eukaryotic microorganisms.The first report on the sequence of 10 consecutive bases in a DNA strand was published in 1968 (117), but methods to reliably obtain longer DNA sequences, namely, Sanger and Maxam-Gilbert sequencing, were not available until 1977 (71, 96). Of these, only Sanger sequencing underwent improvements that led to automation and therefore, for the next 30 years, large-scale sequencing projects, e.g., whole-genome sequencing for various species, relied on this technology (41). However, despite (or indeed because of) much progress in the area of genome sequencing, it became clear that even more information was to be gained not only from sequencing one genome per species but rather from sequencing and comparing the genomes of different individuals or strains/lines from the same species. This would enable a better grasp of genetic diversity and, in the case of humans, allow "personalized medicine" approaches. To make this feasible, novel techniques were needed that overcame current limitations of Sanger sequencing with respect to throughput and costs (98), and in the last decade, a number of different methods were developed that not only have revolutionized the field of genome sequencing but also can be applied to other biological questions not previously addressed by sequencing-based approaches. This review provides an overview of these so-called second-generation or next-generation sequencing (NGS) technologies and their applications with a special focus on addressing questions relevant to the biology of eukaryotic microorganisms. NEXT-GENERATIO...

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The first fifty microarray studies in filamentous fungi

Cited by 66 publications

References 72 publications

Impaired Ribosome Biogenesis Disrupts the Integration between Morphogenesis and Nuclear Duplication during the Germination of Aspergillus fumigatus

Impaired Ribosome Biogenesis Disrupts the Integration between Morphogenesis and Nuclear Duplication during the Germination of Aspergillus fumigatus

Pathogen to Endophytic Transmission in Fungi- A Proteomics Approach

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

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