POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons

Background: The existence of exons and introns has been known for thirty years. Despite this knowledge, there is a lack of formal research into the categorization of exons. Exon taxonomies used by researchers tend to be selected ad hoc or based on an information poor de-facto standard. Exons have been shown to have specific properties and functions based on among other things their location and order. These factors should play a role in the naming to increase specificity about which exon type(s) are in question.

Results: POEM (Protein Oriented Exon Monikers) is a new taxonomy focused on protein proximal exons. It integrates three dimensions of information (Global Position, Regional Position and Region), thus its exon categories are based on known statistical exon features. POEM is applied to two congruent untranslated exon datasets resulting in the following statistical properties. Using the POEM taxonomy previous wide ranging estimates of initial 5' untranslated region exons are resolved. According to our datasets, 29–36% of genes have wholly untranslated first exons. Untranslated exon containing sequences are shown to have consistently up to 6 times more 5' untranslated exons than 3' untranslated exons. Finally, three exon patterns are determined which account for 70% of untranslated exon genes.

Conclusion: We describe a thorough three-dimensional exon taxonomy called POEM, which is biologically and statistically relevant. No previous taxonomy provides such fine grained information and yet still includes all valid information dimensions. The use of POEM will improve the accuracy of genefinder comparisons and analysis by means of a common taxonomy. It will also facilitate unambiguous communication due to its fine granularity

3-dimensional characterization of membrane with nanoporous structure using TEM tomography and image analysis

The nanoporous structure of membrane varies in 3-dimensional (3-D) space and has remarkable influences on the filtration or desalination achieved, fouling potentials and therefore, the quality of yielded water. Knowledge of the 3-D nanoporous structure is thus vital to understanding and predicting its performance. A novel method by incorporating transmission electronic microtomography, image processing and 3-D reconstruction is introduced to characterize membranes with nano structures. The reconstruction algorithm allows for the visualization of 3-D nanoporous structure in a non-destructive way from any directions. This novel technique Ieads to in-depth understanding and accurate prediction of filtration performance.

3-dimensional characterization of membrane with nanoporous structure using TEM tomography and image analysis

The nanoporous structure of a membrane varies in a 3-dimensional (3-D) space and has remarkable influences on the filtration or desalination achieved, fouling potentials and therefore, the quality of yielded water. Knowledge of the 3-D nanoporous structure is thus vital to understanding and predicting its performance. A novel method by incorporating transmission electronic microtomography, image processing and 3-D reconstruction is introduced to characterize membranes with nano structures. The reconstruction algorithm allows for the visualization of 3-D nanoporous structure in a non-destructive way from any directions. This novel technique leads to in-depth understanding and accurate prediction of filtration performance.

Super-resolution of a 3-dimensional scene from novel viewpoints

Super-resolution is a method of post-processing image enhancement that increases the spatial resolution of video or images. Existing super-resolution techniques apply only to images captured of a planar scene. This paper aims to extend super-resolution concepts from the 2D domain to the 3D domain, drawing on ideas from both superresolution and multi-view geometry, two fields of research that until now have predominantly been studied in isolation. 2D super-resolution methods are not without their complexities and limitations. However, once multiple views of a scene are considered within a super-resolution framework, a new range of issues arise that must also be resolved. For example, when input images of a scene with variation in depth are considered, it is no longer clear how and where the images should be registered. This paper describes the use of sparse 3D reconstruction in order to ‘register’ the input images, which are then transferred to a novel image plane and combined to increase the perceived detail in the scene. Experimental results using real images captured from generally positioned input cameras are presented.

Super-resolution of 3-dimensional scenes

Super-resolution is an image enhancement method that increases the resolution of images and video. Previously this technique could only be applied to 2D scenes. The super-resolution algorithm developed in this thesis creates high-resolution views of 3-dimensional scenes, using low-resolution images captured from varying, unknown positions.

Validating the relationship between 3-dimensional body acceleration and oxygen consumption in trained Steller sea lions

We tested the ability of overall dynamic body acceleration (ODBA) to predict the rate of oxygen consumption ([Formula: see text]) in freely diving Steller sea lions (Eumetopias jubatus) while resting at the surface and diving. The trained sea lions executed three dive types-single dives, bouts of multiple long dives with 4-6 dives per bout, or bouts of multiple short dives with 10-12 dives per bout-to depths of 40 m, resulting in a range of activity and oxygen consumption levels. Average metabolic rate (AMR) over the dive cycle or dive bout calculated was calculated from [Formula: see text]. We found that ODBA could statistically predict AMR when data from all dive types were combined, but that dive type was a significant model factor. However, there were no significant linear relationships between AMR and ODBA when data for each dive type were analyzed separately. The potential relationships between AMR and ODBA were not improved by including dive duration, food consumed, proportion of dive cycle spent submerged, or number of dives per bout. It is not clear whether the lack of predictive power within dive type was due to low statistical power, or whether it reflected a true absence of a relationship between ODBA and AMR. The average percent error for predicting AMR from ODBA was 7-11 %, and standard error of the estimated AMR was 5-32 %. Overall, the extensive range of dive behaviors and physiological conditions we tested indicated that ODBA was not suitable for estimating AMR in the field due to considerable error and the inconclusive effects of dive type.

Functional analysis of yeast snoRNA and snRNA 3' end formation mediated by uncoupling of cleavage and polyadenylation

Many nuclear and nucleolar small RNAs are accumulated as nonpolyadenylated species and require 3′-end processing for maturation. Here, we show that several genes coding for box C/D and H/ACA snoRNAs and for the U5 and U2 snRNAs contain sequences in their 3′ portions which direct cleavage of primary transcripts without being polyadenylated. Genetic analysis of yeasts with mutations in different components of the pre-mRNA cleavage and polyadenylation machinery suggests that this mechanism of 3"-end formation requires cleavage factor IA (CF IA) but not cleavage and polyadenylation factor activity. However, in vitro results indicate that other factors participate in the reaction besides CF IA. Sequence analysis of snoRNA genes indicated that they contain conserved motifs in their 3" noncoding regions, and mutational studies demonstrated their essential role in 3"-end formation. We propose a model in which CF IA functions in cleavage and polyadenylation of pre-mRNAs and, in combination with a different set of factors, in 3"-end formation of nonpolyadenylated polymerase II transcripts.

The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3' end formation

Cleavage and polyadenylation factor (CPF) is a multi‐protein complex that functions in pre‐mRNA 3′‐end formation and in the RNA polymerase II (RNAP II) transcription cycle. Ydh1p/Cft2p is an essential component of CPF but its precise role in 3′‐end processing remained unclear. We found that mutations in YDH1 inhibited both the cleavage and the polyadenylation steps of the 3′‐end formation reaction in vitro. Recently, we demonstrated that an important function of CPF lies in the recognition of poly(A) site sequences and RNA binding analyses suggesting that Ydh1p/Cft2p interacts with the poly(A) site region. Here we show that mutant ydh1 strains are deficient in the recognition of the ACT1 cleavage site in vivo. The C‐terminal domain (CTD) of RNAP II plays a major role in coupling 3′‐end processing and transcription. We provide evidence that Ydh1p/Cft2p interacts with the CTD of RNAP II, several other subunits of CPF and with Pcf11p, a component of CF IA. We propose that Ydh1p/Cft2p contributes to the formation of important interaction surfaces that mediate the dynamic association of CPF with RNAP II, the recognition of poly(A) site sequences and the assembly of the polyadenylation machinery on the RNA substrate.

Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation

Cordycepin (3′ deoxyadenosine) is a biologically active compound that, when incorporated during RNA synthesis in vitro, provokes chain termination due to the absence of a 3′ hydroxyl moiety. We were interested in the effects mediated by this drug in vivo and analyzed its impact on RNA metabolism of yeast. Our results support the view that cordycepin-triphosphate (CoTP) is the toxic component that is limiting cell growth through inhibition of RNA synthesis. Unexpectedly, cordycepin treatment modulated 3′ end heterogeneity of ACT1 and ASC1 mRNAs and rapidly induced extended transcripts derived from CYH2 and NEL025c loci. Moreover, cordycepin ameliorated the growth defects of poly(A) polymerase mutants and the pap1-1 mutation neutralized the effects of the drug on gene expression. Our observations are consistent with an epistatic relationship between poly(A) polymerase function and cordycepin action and suggest that a major mode of cordycepin activity reduces 3′ end formation efficiency independently of its potential to terminate RNA chain elongation. Finally, chemical-genetic profiling revealed genome-wide pathways linked to cordycepin activity and identified novel genes involved in poly(A) homeostasis.

Functions for S. cerevisiae Swd2p in 3' end formation of specific mRNAs and snoRNAs and global histone 3 lysine 4 methylation

The Saccharomyces cerevisiae WD-40 repeat protein Swd2p associates with two functionally distinct multiprotein complexes: the cleavage and polyadenylation factor (CPF) that is involved in pre-mRNA and snoRNA 3′ end formation and the SET1 complex (SET1C) that methylates histone 3 lysine 4. Based on bioinformatic analysis we predict a seven-bladed β-propeller structure for Swd2p proteins. Northern, transcriptional run-on and in vitro 3′ end cleavage analyses suggest that temperature sensitive swd2 strains were defective in 3′ end formation of specific mRNAs and snoRNAs. Protein–protein interaction studies support a role for Swd2p in the assembly of 3′ end formation complexes. Furthermore, histone 3 lysine 4 di-and tri-methylation were adversely affected and telomeres were shortened in swd2 mutants. Underaccumulation of the Set1p methyltransferase accounts for the observed loss of SET1C activity and suggests a requirement for Swd2p for the stability or assembly of this complex. We also provide evidence that the roles of Swd2p as component of CPF and SET1C are functionally independent. Taken together, our results establish a dual requirement for Swd2p in 3′ end formation and histone tail modification.

Multicellular spheroids in ovarian cancer metastases: Biology and pathology

Epithelial ovarian cancer (EOC) has a relatively high mortality rate (~55%). One of the presiding causes is that the current chemotherapeutic regimes are unable to achieve sustained remission, despite frequently producing a positive response at first treatment. One of the reasons that EOC is difficult to treat is that the mechanism of dissemination is unusual. EOC dissemination characteristically involves local invasion of pelvic and abdominal organs. Unlike many epithelial cancers, initial dissemination rarely requires the vasculature, although the vasculature is often implicated in the advanced stages of disease. Recently, it has become apparent that aggregates of malignant cells (spheroids) contained within malignant ascites represent a significant impediment to efficacious treatment of late stage EOC. In vivo, spheroids are present in the malignant ascites of EOC patients, while in vitro cultured spheroids are capable of tumorgenesis in vivo and display a reduced response to chemotherapeutic drugs when compared to monolayers. A major problem associated with the current generation of chemotherapy agents is that they do not address the anchorage and vascular-independent growth conditions associated with a 3-dimensional structure that has formed and/or grown in suspension. Thus, spheroid formation may represent a key component of platinum/taxanesensitive recurrence. If this is correct, a better understanding of spheroid biology may contribute to the identification of new treatment opportunities for the sustained treatment of metastatic EOC. This review article outlines the key biological features of spheroids, specifically discussing their role in EOC dissemination and chemo-response as well as providing insights into spheroid functionality.

The role of the putative 3′ end processing endonuclease Ysh1p in mRNA and snoRNA synthesis

Pre-mRNA 3′ end formation is tightly linked to upstream and downstream events of eukaryotic mRNA synthesis. The two-step reaction involves endonucleolytic cleavage of the primary transcript followed by poly(A) addition to the upstream cleavage product. To further characterize the putative 3′ end processing endonuclease Ysh1p/Brr5p, we isolated and analyzed a number of new temperature- and cold-sensitive mutant alleles. We show that Ysh1p plays a crucial role in 3′ end formation and in RNA polymerase II (RNAP II) transcription termination on mRNA genes. In addition, we observed a range of additional functional deficiencies in ysh1 mutant strains, which were partially allele-specific. Interestingly, snoRNA 3′ end formation and RNAP II termination were defective on specific snoRNAs in the cold-sensitive ysh1-12 strain. Moreover, we observed the accumulation of several mRNAs including the NRD1 transcript in this mutant. We provide evidence that NRD1 autoregulation is associated with endonucleolytic cleavage and that this process may involve Ysh1p. In addition, the ysh1-12 strain displayed defects in RNA splicing indicating that a functional link may exist between intron removal and 3′ end formation in yeast. These observations suggest that Ysh1p has multiple roles in RNA synthesis and processing.

Interobserver reliability of coronoid fracture classification : two-dimensional versus three-dimensional computed tomography

Purpose : This study tests the hypothesis that 3-dimensional computed tomography (CT) reconstructions improve interobserver agreement on classification and treatment of coronoid fractures compared with 2-dimensional CT.

Methods : A total of 29 orthopedic surgeons evaluated 10 coronoid fractures on 2 occasions (first with radiographs and 2-dimensional CT and then with radiographs and 3-dimensional CT), separated by a minimum of 2 weeks. Surgeons classified fractures according to the classifications of Regan and Morrey and of O'Driscoll et al., identified specific characteristics, recommended the most appropriate treatment approach, and made treatment recommendations. The kappa multirater measure (κ) was calculated to estimate agreement between observers.

Results : Regardless of the imaging modality used, there was fair to moderate agreement for most of the observations. Three-dimensional CT improved interobserver agreement in Regan and Morrey's classsication (κ3-dimensional = 0.51 vs κ2-dimensional = 0.40; p < .001) and O'Driscoll et al.'s classifications (κ3-dimensional = 0.48 vs κ2-dimensional = 0.42; p = .009). There were trends toward better reliability for 3-dimensional reconstruction in recognition of coronoid tip fractures (κ3-dimensional = 0.19, κ2-dimensional = 0.03; p = .268), comminution (κ3-dimensional = 0.41 vs κ2-dimensional = 0.29; p = .133), and impacted fragments (κ3-dimensional = 0.39 vs κ2-dimensional = 0.27; p = .094), and in surgeons' opinions on the need for something other than screws or plate for surgical fixation (κ3-dimensional = 0.31 vs κ2-dimensional = 0.15; p = .138). Interobserver agreement on treatment approach was better with 2-dimensional CT (κ3-dimensional = 0.27, κ2-dimensional = 0.32; p = .015).

Conclusions : Three-dimensional CT reconstructions improve interobserver agreement with respect to fracture classification compared with 2-dimensional CT.

High-resolution terrestrial permian-triassic eventostratigraphic boundary in western Guizhou and eastern Yunnan, southwestern China

The adjoining area of western Guizhou and eastern Yunnan Provinces in southwest China is an ideal place to investigate the feasibility of correlating marine and nonmarine Permian–Triassic boundary (PTB) sequences, as it contains outcrop sections of shallow marine, marginal marine (or paralic), and terrestrial PTB sections, all in close geographic proximity. This paper documents for the first time multiple stratigraphic data from several well-preserved terrestrial PTB sections in the area and attempts to use these data to define, locate, and correlate the PTB in the area. A study of the spores and pollen and vegetation types across the terrestrial PTB sections in the study area suggests three distinct evolutionary stages across the boundary: Stage 1 (Xuanwei Formation) is characterised by Late Permian or Paleozoic-type ferns and pteridosperms (85.0%), with a few gymnosperms (15.0%); stage 2 is marked by an abrupt drop of sporopollen elements of Late Permian aspects, coupled with the appearance of fungal spores and limited Early Triassic palynomorphs; stage 3 (top Xuanwei Formation and Kayitou Formation) is dominated by gymnosperm pollen (58.8%) of clearly Early Triassic aspect, although still retaining limited ferns and pteridosperms. The three biotic stages seem to well correspond with the changing trend of the δ13Corg curves from the same sections, which is characterized by a sharp drop just before the PTB, followed by a short term partial recovery across the boundary, and then succeeded by a gradual decline after the PTB in the Early Triassic. Combining evidence from eventostratigraphic (i.e., the succession of boundary clay beds), biostratigraphic (using both macroplants and palynomorphs), and chemostratigraphic (i.e., organic carbon isotope excursion signals), we propose that a high-resolution PTB succession, closely correlatable to its marine counterpart at the Meishan section in eastern China, is recognisable at the terrestrial PTB sections in the western Guizhou–eastern Yunnan area in southwest China.