Trimorphodon tau

Number of Pages: 2Integrative BiologyGeological Science

Intronization, de-intronization and intron sliding are rare in Cryptococcus

<p>Abstract</p> <p>Background</p> <p>Eukaryotic pre-mRNA gene transcripts are processed by the spliceosome to remove portions of the transcript, called spliceosomal introns. The spliceosome recognizes intron boundaries by the presence of sequence signals (motifs) contained in the actual transcript, thus sequence changes in the genome that affect existing splicing signals or create new signals may lead to changes in transcript splicing patterns. Such changes may lead to previously excluded (intronic) transcript regions being included (exonic) or vice versa. Such changes can affect the encoded protein sequence and/or post-transcriptional regulation, and are thus a potentially important source of genomic and phenotypic novelty. Two recent papers suggest that such changes may be a major force in remodeling of eukaryotic gene structures, however the rate of occurrence of such changes has not been assessed at the genomic level.</p> <p>Results</p> <p>I studied four closely related species of <it>Cryptoccocus </it>fungi. Among 28,256 studied introns, canonical GT/C...AG boundaries are nearly universally conserved across all four species. Among only 40 observed cases of cDNA-confirmed non-conserved intron boundaries, most are likely to involve alternative splicing. I find only five cases of "intronization," intron creation from an internal exonic region by de novo emergence of new splicing boundaries, and no cases of the reverse process, "de-intronization." I find no more than ten clear cases of true movement of an intron boundary of a possibly constitutively spliced intron, and no clear cases of true "intron sliding," in which changes in the positions of both intron boundaries could lead to a movement of the intron position along the coding sequence.</p> <p>Conclusion</p> <p>These results suggest that intronization, de-intronization, and intron boundary movement are rare events in evolution.</p

Analyses of Alternatively Processed Genes in Ciliates Provide Insights into the Origins of Scrambled Genomes and may Provide a Mechanism for Speciation

Chromosome rearrangements occur in a variety of eukaryotic life cycles, including during the development of the somatic macronuclear genome in ciliates. Previous work on the phyllopharyngean ciliate Chilodonella uncinata revealed that macronuclear β-tubulin and protein kinase gene families share alternatively processed germ line segments nested within divergent regions. To study genome evolution in this ciliate further, we characterized two additional alternatively processed gene families from two cryptic species of the ciliate morphospecies C. uncinata: those encoding histidine acid phosphatase protein (Hap) and leishmanolysin family protein (Lei). Analyses of the macronuclear Hap and Lei sequences reveal that each gene family consists of three members in the macronucleus that are marked by identical regions nested among highly divergent regions. Investigation of the micronuclear Hap sequences revealed a complex pattern in which the three macronuclear sequences are derived either from a single micronuclear region or from a combination of this shared region recombined with additional duplicate micronuclear copies of Hap.We propose a model whereby gene scrambling evolves by gene duplication followed by partial and reciprocal degradation of the duplicate sequences. In this model, alternative processing represents an intermediate step in the evolution of scrambled genes. Finally, we speculate on the possible role of genome architecture in speciation in ciliates by describing what might happen if changes in alternatively processed loci occur in subdivided populations. IMPORTANCE Genome rearrangements occur in a variety of eukaryotic cells and serve as an important mechanism for generating genomic diversity. The unusual genome architecture of ciliates with separate germline and somatic nuclei in each cell, provides an ideal system to study further principles of genome evolution. Previous analyses revealed complex forms of chromosome rearrangements, including gene scrambling and alternative processing of germ line chromosomes. Here we describe more complex rearrangements between germ line and somatic chromosomes than previously seen in alternatively processed gene families. Drawing on the present and previous findings, we propose a model in which alternative processing of duplicated micronuclear regions represents an intermediate stage in the evolution of scrambled genes. Under this model, alternative processing may provide insights into a mechanism for speciation in ciliates. Our data on gene scrambling and alternative processing also enhance views on the dynamic nature of genomes across the eukaryotic tree of life

Comparative genomic analysis of fungal genomes reveals intron-rich ancestors

Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor

Chondrosarcoma of the Thorax

Although a rare entity, chondrosarcoma is the most common malignant tumor of the chest wall. Most patients present with an enlarging, painful anterior chest wall mass arising from the costochondrosternal junction. CT scan with intravenous contrast is the gold standard radiographic study for diagnosis and operative planning. Contrary to previous dictum, resection may be performed in an appropriate surgical candidate based on imaging characteristics or image-guided percutaneous biopsy results; incisional biopsy is rarely required. The keys to successful treatment are early recognition and radical excision with adequate margins, as chondrosarcoma is relatively resistant to radiotherapy and conventional cytotoxic chemotherapy. Overall survival is excellent in most surgical series from experienced centers. Complete excision with widely negative microscopic margins at the initial operation is of the utmost importance, as local recurrence portends systemic metastasis and eventual tumor-related mortality. This paper summarizes data from relevant surgical series and thereupon draws conclusions regarding preoperative, intraoperative, and postoperative management of thoracic chondrosarcoma

Multi-D CFD Modeling of Free-Piston Stirling Convertor at NASA GRC

A high efficiency Stirling Radioisotope Generator (SRG) is being developed for possible use in long duration space science missions. NASA s advanced technology goals for next generation Stirling convertors include increasing the Carnot efficiency and percent of Carnot efficiency. To help achieve these goals, a multidimensional Computational Fluid Dynamics (CFD) code is being developed to numerically model unsteady fluid flow and heat transfer phenomena of the oscillating working gas inside Stirling convertors. Simulations of the Stirling convertors for the SRG will help characterize the thermodynamic losses resulting from fluid flow and heat transfer between the working gas and solid walls. The current CFD simulation represents approximated 2-dimensional convertor geometry. The simulation solves the Navier Stokes equations for an ideal helium gas oscillating at low speeds. The current simulation results are discussed

Multi-D CFD Modeling of Free-Piston Stirling Convertor at NASA GRC

A high efficiency Stirling Radioisotope Generator (SRG) is being developed for possible use in long duration space science missions. NASA s advanced technology goals for next generation Stirling convertors include increasing the Carnot efficiency and percent of Carnot efficiency. To help achieve these goals, a multidimensional Computational Fluid Dynamics (CFD) code is being developed to numerically model unsteady fluid flow and heat transfer phenomena of the oscillating working gas inside Stirling convertors. Simulations of the Stirling convertors for the SRG will help characterize the thermodynamic losses resulting from fluid flow and heat transfer between the working gas and solid walls. The current CFD simulation represents approximated 2-dimensional convertor geometry. The simulation solves the Navier Stokes equations for an ideal helium gas oscillating at low speeds. The current simulation results are discussed