Molecular identification of 16 Porphyra lines using sequence-related amplified polymorphism markers

Sequence-related amplified polymorphism (SRAP) is a novel molecular marker technique designed to amplify open reading frames (ORFs). The SRAP analytic system was set up and applied to Porphyra germplasm identification in this study for the first time. Sixteen Porphyra lines were screened by SRAP technique with 30 primer combinations. In the analysis, 14 primer combinations produced stable and reproducible amplification patterns in three repetitive experiments. Among the total 533 amplified fragments, 522 (98%) were polymorphic, with an average of 38 fragments for each primer combination, ranging in size from 50 to 500 bp. The 533 fragments were visually scored one by one and then used to develop a dendrogram with Unweighted Pair-Group Method Arithmetic Average (UPGMA), and the 16 Porphyra lines were divided into two major groups at the 0.68 similarity level. From the total 533 fragments, I I amplified by two primer combinations, ME1/EM1 and ME4/EM6, were used to develop the DNA fingerprints of the 16 Porphyra lines. The DNA fingerprints were then converted into binary codes, with I and 0 representing presence and absence of the corresponding amplified fragment, respectively. In the DNA fingerprints, each of the 16 Porphyra lines has its unique binary code and can be easily distinguished from the others. This is the first report on the development of SRAP technique and its utilization in germplasm identification of seaweeds. The results demonstrated that SRAP is a simple, stable, polymorphic and reproducible molecular marker technique for the classification and identification of Porphyra lines. (c) 2007 Elsevier B.V. All rights reserved.

Finding Edges and Lines in Images

The problem of detecting intensity changes in images is canonical in vision. Edge detection operators are typically designed to optimally estimate first or second derivative over some (usually small) support. Other criteria such as output signal to noise ratio or bandwidth have also been argued for. This thesis is an attempt to formulate a set of edge detection criteria that capture as directly as possible the desirable properties of an edge operator. Variational techniques are used to find a solution over the space of all linear shift invariant operators. The first criterion is that the detector have low probability of error i.e. failing to mark edges or falsely marking non-edges. The second is that the marked points should be as close as possible to the centre of the true edge. The third criterion is that there should be low probability of more than one response to a single edge. The technique is used to find optimal operators for step edges and for extended impulse profiles (ridges or valleys in two dimensions). The extension of the one dimensional operators to two dimentions is then discussed. The result is a set of operators of varying width, length and orientation. The problem of combining these outputs into a single description is discussed, and a set of heuristics for the integration are given.

Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.METHODS: the suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent nonneoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). the ranking of the best single and combination of reference genes was determined by NormFinder, geNorm (TM), BestKeeper, and DataAssist (TM). in addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. the relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. the level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested. (C) 2013 Baishideng Publishing Group Co., Limited. All rights reserved.

Using a prompt sheet to improve the reference interview in a health telephone helpline service

Price, T., Urquhart, C. & Cooper, J. (2007). Using a prompt sheet to improve the reference interview in a health telephone helpline service. Evidence Based Library and Information Practice, 2(3), 43-58 Open access journal

Construction of a Festuca pratensis BAC library for map-based cloning in IFestulolium substitution lines

Iain S. Donnison, Donal M. O Sullivan, Ann Thomas, Peter Canter, Beverley Moore, Ian Armstead, Howard Thomas, Keith J. Edwards and Ian P. King (2005). Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines. Theoretical and Applied Genetics, 110 (5) pp.846-851 Sponsorship: BBSRC;BBSRC RAE2008

Reading Between the Lines: The Potential of Popular Young Adult Fiction in Adolescent Spiritual Formation

Popular culture is a powerful, shaping force in the lives of teenagers between the ages of fourteen through eighteen in the United States today. This dissertation argues the importance of popular fiction for adolescent spiritual formation and it investigates that importance by exploring the significance of narrative for theology and moral formation. The dissertation employs mythic and archetypal criticism as a tool for informing the selection and critique of narratives for use in adolescent spiritual development and it also incorporates insights gained from developmental psychology to lay the groundwork for the development of a curriculum that uses young adult fiction in a program of spiritual formation for teenagers in a local church setting. The dissertation defends the power of narrative in Christian theology and concludes that narrative shapes the imagination in ways that alter perception and are important for the faith life of teenagers in particular. I go on to argue that not all narratives are created equal. In using literary myth criticism in concert with theology, I use the two disciplines’ different aims and methods to fully flesh out the potential of theologies intrinsic to works meant for a largely secular audience. The dissertation compares various works of young adult fiction (M.T. Anderson’s Feed and Terry Pratchett’s Nation in dialogue with a theology of creation; Marcus Zusak’s I am the Messenger and Jerry Spinelli’s Stargirl in dialogue with salvation and saviors; and the four novels of Stephanie Meyer’s Twilight saga in dialogue with a theology of hope (eschatology). The dissertation explores how each theme surfaces (even if only implicitly) from both literary and theological standpoints. The dissertation concludes with a sample four-week lesson plan that demonstrates one way the theological and literary critique can be formed into a practical curriculum for use in an adolescent spiritual development setting. Ultimately, this dissertation provides a framework for how practitioners of young adult formation can select, analyze, and develop materials for their teenagers using new works of popular young adult fiction. The dissertation comes to the conclusion that popular fiction contains a wealth of material that can challenge and shape young readers’ own emerging theology.

Problems with drawing lines: Theo-geographies of the Catholic parish in Ireland

While people in Catholic parishes in Ireland appear keenly aware of parish boundaries, these understandings are more often oral than cartographic. There is no digital map of all of the Catholic parishes in Ireland. However, the institutional Catholic Church insists that no square kilometre can exist outside of a parish boundary. In this paper, I explain a process whereby the Catholic parishes of Ireland were produced digitally. I will outline some of the technical challenges of digitizing such boundaries. In making these maps, it is not only a question of drawing lines but mapping people’s understanding of their locality. Through an example of one part of the digitisation project, I want to talk about how verifying maps with local people often complicates something which may have at first sight seemed simple. The paper ends on a comparison with how other communities of interest are territorialised in Ireland and elsewhere to draw out some broader theoretical and theological issues of concern.

Molecular characterization of chordoma xenografts generated from a novel primary chordoma cell source and two chordoma cell lines.

OBJECT: Chordoma cells can generate solid-like tumors in xenograft models that express some molecular characteristics of the parent tumor, including positivity for brachyury and cytokeratins. However, there is a dearth of molecular markers that relate to chordoma tumor growth, as well as the cell lines needed to advance treatment. The objective in this study was to isolate a novel primary chordoma cell source and analyze the characteristics of tumor growth in a mouse xenograft model for comparison with the established U-CH1 and U-CH2b cell lines. METHODS: Primary cells from a sacral chordoma, called "DVC-4," were cultured alongside U-CH1 and U-CH2b cells for more than 20 passages and characterized for expression of CD24 and brachyury. While brachyury is believed essential for driving tumor formation, CD24 is associated with healthy nucleus pulposus cells. Each cell type was subcutaneously implanted in NOD/SCID/IL2Rγ(null) mice. The percentage of solid tumors formed, time to maximum tumor size, and immunostaining scores for CD24 and brachyury (intensity scores of 0-3, heterogeneity scores of 0-1) were reported and evaluated to test differences across groups. RESULTS: The DVC-4 cells retained chordoma-like morphology in culture and exhibited CD24 and brachyury expression profiles in vitro that were similar to those for U-CH1 and U-CH2b. Both U-CH1 and DVC-4 cells grew tumors at rates that were faster than those for U-CH2b cells. Gross tumor developed at nearly every site (95%) injected with U-CH1 and at most sites (75%) injected with DVC-4. In contrast, U-CH2b cells produced grossly visible tumors in less than 50% of injected sites. Brachyury staining was similar among tumors derived from all 3 cell types and was intensely positive (scores of 2-3) in a majority of tissue sections. In contrast, differences in the pattern and intensity of staining for CD24 were noted among the 3 types of cell-derived tumors (p < 0.05, chi-square test), with evidence of intense and uniform staining in a majority of U-CH1 tumor sections (score of 3) and more than half of the DVC-4 tumor sections (scores of 2-3). In contrast, a majority of sections from U-CH2b cells stained modestly for CD24 (scores of 1-2) with a predominantly heterogeneous staining pattern. CONCLUSIONS: This is the first report on xenografts generated from U-CH2b cells in which a low tumorigenicity was discovered despite evidence of chordoma-like characteristics in vitro. For tumors derived from a primary chordoma cell and U-CH1 cell line, similarly intense staining for CD24 was observed, which may correspond to their similar potential to grow tumors. In contrast, U-CH2b tumors stained less intensely for CD24. These results emphasize that many markers, including CD24, may be useful in distinguishing among chordoma cell types and their tumorigenicity in vivo.

Absolute intensities of water vapor lines in the near ultraviolet and visible regions

Collection :Europto series, 6

Yields for four inbred lines and six F1 hybrid of silkworm in Argentina

p.61-65

The relationship between the distribution of genetically distinct inbred lines and upper lethal temperature in Lasaea rubra

Lasaea rubra is an inbreeding bivalve species, living at most heights on rocky shores. Freshly collected animals from different shore heights showed significantly different upper median lethal temperatures (MLTs), with upper shore animals having higher MLTs than lower shore specimens. Experiments with animals acclimated for at least one month to a single temperature (15°C) demonstrated that these differences in upper MLT were unaffected by thermal acclimation. Electrophoretic investigation showed that the differences in thermal response had a genetic basis. Homogeneous populations of the high-water inbred line (‘Inbred line A’) had a higher MLT than homogeneous populations of ‘Inbred line C’ which was found on the middle and lower shore. No differences were detected between the MLTs of separate populations of Inbred lines A or C. A third inbred line (‘Inbred line B’) was found on the middle shore, but no homogeneous populations were found. However, indirect evidence suggests that Inbred line B has a thermal response intermediate between those of Inbred lines A and C. Study of populations made up of mixtures of inbred lines confirmed the relationship between upper MLTs and genetic composition of the population.