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1.  Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta) 
AoB Plants  2011;2011:plr001.
Despite the fact that brown algae are critical components of marine ecosystems around the world only one species has had its genome sequenced. To facilitate genome studies in the class we report data for 12 of the 19 recognized orders.
Background and aims
Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class.
The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and the red blood cell (chicken erythrocyte) standard were used to estimate 2C values by static microspectrophotometry.
Principal results
2C DNA contents are reported for 98 species of brown algae, almost doubling the number of estimates available for the class. The present results also expand the reported DNA content range to 0.2–3.6 pg, with several species of Fucales and Laminariales containing apparent polyploid genomes with 2C = 1.8–3.6 pg.
The data provide DNA content values for 12 of the 19 recognized orders of brown algae spanning the breadth of the class. Despite earlier contentions concerning DNA content and the presence of oogamy, the present results do not support a correlation between phylogenetic placement and genome size. The closest sister groups to the brown algae have genome sizes on the order of 0.3 pg (e.g. Schizocladiophyceae), suggesting that this may be the ancestral genome size. However, DNA content ranges widely across the class.
PMCID: PMC3064507  PMID: 22476472
2.  Tropomodulin isoforms regulate thin filament pointed-end capping and skeletal muscle physiology 
The Journal of Cell Biology  2010;189(1):95-109.
In skeletal muscle fibers, tropomodulin 1 (Tmod1) can be compensated for, structurally but not functionally, by Tmod3 and -4.
During myofibril assembly, thin filament lengths are precisely specified to optimize skeletal muscle function. Tropomodulins (Tmods) are capping proteins that specify thin filament lengths by controlling actin dynamics at pointed ends. In this study, we use a genetic targeting approach to explore the effects of deleting Tmod1 from skeletal muscle. Myofibril assembly, skeletal muscle structure, and thin filament lengths are normal in the absence of Tmod1. Tmod4 localizes to thin filament pointed ends in Tmod1-null embryonic muscle, whereas both Tmod3 and -4 localize to pointed ends in Tmod1-null adult muscle. Substitution by Tmod3 and -4 occurs despite their weaker interactions with striated muscle tropomyosins. However, the absence of Tmod1 results in depressed isometric stress production during muscle contraction, systemic locomotor deficits, and a shift to a faster fiber type distribution. Thus, Tmod3 and -4 compensate for the absence of Tmod1 structurally but not functionally. We conclude that Tmod1 is a novel regulator of skeletal muscle physiology.
PMCID: PMC2854367  PMID: 20368620
3.  Disease Severity and Thin Filament Regulation in M9R TPM3 Nemaline Myopathy 
The mechanism of muscle weakness was investigated in an Australian family with a M9R mutation in TPM3 (α-tropomyosinslow). Detailed protein analyses of five muscle samples from two patients showed that nemaline bodies are restricted to atrophied type 1 (slow) fibers in which the TPM3 gene is expressed. Developmental expression studies showed that α-tropomyosinslow is not expressed at significant levels until after birth, thereby likely explaining the childhood (rather than congenital) disease onset in TPM3 nemaline myopathy. Isoelectric focusing demonstrated that α-tropomyosinslow dimers, comprised of equal ratios of wild-type and M9R-α-tropomyosinslow, are the dominant tropomyosin species in three separate muscle groups from an affected patient. These findings suggest that myopathy-related slow fiber predominance likely contributes to the severity of weakness in TPM3 nemaline myopathy because of increased proportions of fibers that express the mutant protein. Using recombinant proteins and far Western blot we demonstrated a higher affinity of tropomodulin for α-tropomyosinslow compared to β-tropomyosin; the M9R substitution within α-tropomyosinslow greatly reduced this interaction. Finally, transfection of the M9R mutated and wild-type α-tropomyosinslow into myoblasts revealed reduced incorporation into stress fibers and disruption of the filamentous actin network by the mutant protein. Collectively, these results provide insights into the clinical features and pathogenesis of M9R-TPM3 nemaline myopathy.
PMCID: PMC2746243  PMID: 18716557
Disease severity; Nemaline myopathy; Skeletal muscle; Tropomodulin; Tropomyosin
4.  PTB/hnRNP I Is Required for RNP Remodeling during RNA Localization in Xenopus Oocytes▿  
Molecular and Cellular Biology  2007;28(2):678-686.
Transport of specific mRNAs to defined regions within the cell cytoplasm is a fundamental mechanism for regulating cell and developmental polarity. In the Xenopus oocyte, Vg1 RNA is transported to the vegetal cytoplasm, where localized expression of the encoded protein is critical for embryonic polarity. The Vg1 localization pathway is directed by interactions between key motifs within Vg1 RNA and protein factors recognizing those RNA sequences. We have investigated how RNA-protein interactions could be modulated to trigger distinct steps in the localization pathway and found that the Vg1 RNP is remodeled during cytoplasmic RNA transport. Our results implicate two RNA-binding proteins with key roles in Vg1 RNA localization, PTB/hnRNP I and Vg1RBP/vera, in this process. We show that PTB/hnRNP I is required for remodeling of the interaction between Vg1 RNA and Vg1RBP/vera. Critically, mutations that block this remodeling event also eliminate vegetal localization of the RNA, suggesting that RNP remodeling is required for localization.
PMCID: PMC2223416  PMID: 18039852
5.  Localization of RNAs to the Mitochondrial Cloud in Xenopus Oocytes through Entrapment and Association with Endoplasmic ReticulumV⃞ 
Molecular Biology of the Cell  2004;15(10):4669-4681.
The germ cell lineage in Xenopus is specified by the inheritance of germ plasm, which originates within a distinct “mitochondrial cloud” (MC) in previtellogenic oocytes. Germ plasm contains localized RNAs implicated in germ cell development, including Xcat2 and Xdazl. To understand the mechanism of the early pathway through which RNAs localize to the MC, we applied live confocal imaging and photobleaching analysis to oocytes microinjected with fluorescent Xcat2 and Xdazl RNA constructs. These RNAs dispersed evenly throughout the cytoplasm through diffusion and then became progressively immobilized and formed aggregates in the MC. Entrapment in the MC was not prevented by microtubule disruption and did not require localization to germinal granules. Immobilized RNA constructs codistributed and showed coordinated movement with densely packed endoplasmic reticulum (ER) concentrated in the MC, as revealed with Dil16(3) labeling and immunofluorescence analysis. Vg1RBP/Vera protein, which has been implicated in linking late pathway RNAs to vegetal ER, was shown to bind specifically both wild-type Xcat2 3′ untranslated region and localization-defective constructs. We found endogenous Vg1RBP/Vera and Vg1RBP/Vera-green fluorescent protein to be largely excluded from the MC but subsequently to codistribute with Xcat2 and ER at the vegetal cortex. We conclude that germ line RNAs localize into the MC through a diffusion/entrapment mechanism involving Vg1RBP/Vera-independent association with ER.
PMCID: PMC519158  PMID: 15292452

Results 1-5 (5)