The Potential Of High-Resolution BAC-FISH In Banana Breeding

Abstract The genetic complexity in the genus Musa has been subject of study in many breeding programs worldwide. Parthenocarpy, female sterility, polyploidy in different cultivars and limited amount of genetic and genomic information make the production of new banana cultivars difficult and time consuming. In addition, it is known that part of the cultivars and related wild species in the genus contain numerous chromosomal rearrangements. In order to produce new cultivars more effectively breeders must better understand the genetic differences of the potential crossing parents for introgression hybridization, but extensive genetic information is lacking. As an alternative to achieve information on genetic collinearity we make use of modern chromosome map technology known as high-resolution fluorescent in situ hybridization (FISH). This article presents the technical aspects and applications of such a technology in Musa species. The technique deals with BAC clone positioning on pachytene chromosomes of Calcutta 4 (Musa acuminata ssp. burmanicoides, A genome group, section Eumusa) and M. velutina (section Rodochlamys). Pollen mother cells digestion with pectolytic enzymes and maceration with acetic acid were optimized for making cell spread preparations appropriate for FISH. As an example of this approach we chose BAC clones that contain markers to known resistance genes and hybridize them for establishing their relative positions on the two species. Technical challenges for adapting existing protocols to the banana cells are presented. We also discuss how this technique can be instrumental for validating collinearity between potential crossing parents and how the method can be helpful in future mapping initiatives, and how this method allows identification of chromosomal rearrangements between related Musa species and cultivar

Thermodynamics of the S=1 spin ladder as a composite S=2 chain model

A special class of S=1 spin ladder hamiltonians, with second- neighbor exchange interactions and with anisotropies in the $z$-direction, can be mapped onto one-dimensional composite S=2 (tetrahedral S=1) models. We calculate the high temperature expansion of the Helmoltz free energy for the latter class of models, and show that their magnetization behaves closely to that of standard XXZ models with a suitable effective spin $S_{eff}$, such that $S_{eff}(1+S_{eff})=$, where ${\bf S}_i$ refers to the components of spin in the composite model. It is also shown that the specific heat per site of the composite model, on the other hand, can be very different from that of the effective spin model, depending on the parameters of the hamiltonian.Comment: 17 pages, 4 figures. Submitted for publicatio

The high temperature expansion of the classical XYZXYZ chain

We present the $\beta$-expansion of the Helmholtz free energy of the classical $XYZ$ model, with a single-ion anisotropy term and in the presence of an external magnetic field, up to order $\beta^{12}$. We compare our results to the numerical solution of Joyce's [Phys. Rev. Lett. 19, 581 (1967)] expression for the thermodynamics of the $XXZ$ classical model, with neither single-ion anisotropy term nor external magnetic field. This comparison shows that the derived analytical expansion is valid for intermediate temperatures such as $kT/J_x \approx 0.5$. We show that the specific heat and magnetic susceptibility of the spin-2 antiferromagnetic chain can be approximated by their respective classical results, up to $kT/J \approx 0.8$, within an error of 2.5%. In the absence of an external magnetic field, the ferromagnetic and antiferromagnetic chains have the same classical Helmholtz free energy. We show how this two types of media react to the presence of an external magnetic field

Kinase Inhibitor Profile For Human Nek1, Nek6, And Nek7 And Analysis Of The Structural Basis For Inhibitor Specificity

Human Neks are a conserved protein kinase family related to cell cycle progression and cell division and are considered potential drug targets for the treatment of cancer and other pathologies. We screened the activation loop mutant kinases hNek1 and hNek2, wild-type hNek7, and five hNek6 variants in different activation/phosphorylation statesand compared them against 85 compounds using thermal shift denaturation. We identified three compounds with significant Tm shifts: JNK Inhibitor II for hNek1(Ä262-1258)-(T162A), Isogranulatimide for hNek6(S206A), and GSK-3 Inhibitor XIII for hNek7wt. Each one of these compounds was also validated by reducing the kinases activity by at least 25%. The binding sites for these compounds were identified by in silico docking at the ATP-binding site of the respective hNeks. Potential inhibitors were first screened by thermal shift assays, had their efficiency tested by a kinase assay, and were finally analyzed by molecular docking. Our findings corroborate the idea of ATP-competitive inhibition for hNek1 and hNek6 and suggest a novel non-competitive inhibition for hNek7 in regard to GSK-3 Inhibitor XIII. Our results demonstrate that our approach is useful for finding promising general and specific hNekscandidate inhibitors, which may also function as scaffolds to design more potent and selective inhibitors.20111761191Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., Hariharan, I.K., Fortini, M.E., Fleischmann, W., Comparative genomics of the eukaryotes (2000) Science, 287, pp. 2204-2215Johnson, L.N., Lowe, E.D., Noble, M.E., Owen, D.J., The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases (1998) FEBS Lett., 430, pp. 1-11Hanks, S.K., Eukaryotic protein kinases (1991) Curr. Opin. Struct. 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Res.Commun., 360, pp. 56-62Roig, J., Mikhailov, A., Belham, C., Avruch, J., Nercc1, a mammalian NIMA-family kinase, binds the Ran GTPase and regulates mitotic progression (2002) Genes Dev., 16, pp. 1640-1658Upadhya, P., Birkenmeier, E.H., Birkenmeier, C.S., Barker, J.E., Mutations in a NIMA-related kinase gene, Nek1, cause pleiotropic effects including a progressive polycystic kidney disease in mice (2000) Proc. Natl. Acad. Sci. USA, 97, pp. 217-221Liu, S., Lu, W., Obara, T., Kuida, S., Lehoczky, J., Dewar, K., Drummond, I.A., Beier, D.R., A defect in a novel Nek-family kinase causes cystic kidney disease in the mouse and in zebrafish (2002) Development, 129, pp. 5839-5846Chen, J., Li, L., Zhang, Y., Yang, H., Wei, Y., Zhang, L., Liu, X., Yu, L., Interaction of Pin1 with Nek6 and characterization of their expression correlation in Chinese hepatocellular carcinoma patients (2006) Biochem. Biophys. Res. 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Monitoring Of Bcr-abl Levels In Chronic Myeloid Leukemia Patients Treated With Imatinib In The Chronic Phase - The Importance Of A Major Molecular Response

Background: Real time PCR has become the most common technique to monitor BCR-ABL transcript levels of patients treated with kinase inhibitors. The aim of this study was to evaluate BCR-ABL levels of chronic myeloid leukemia patients treated with imatinib in the chronic phase and correlate the response to therapy and event-free survival. Methods: BCR-ABL levels were measured in peripheral blood cell samples using Real time PCR at diagnosis and then every 3 months after starting therapy with imatinib. Major molecular response was defined as a three-log reduction from the standardized baseline value. Major molecular response values were adjusted to international scale using a conversion factor of 1.19. The results are reported as a BCR-ABL/ABL ratio (%). Results: Hematological, major cytogenetic and complete cytogenetic responses were achieved by 57 (95%), 45 (75%) and 38 (63%) patients, respectively. Twenty-four out of sixty patients achieved a major molecular response (40%) in a median time of 8.5 months. Overall survival and event free survival were higher for patients with (100%) versus patients without (77%) a complete cytogenetic response (p-value = 0.01) at 48 months. Patients with complete cytogenetic response and major molecular response had a higher event free survival compared to patients with complete cytogenetic response but without major molecular response (p-value = 0.007). Conclusion: In conclusion, the prognostic impact of achieving complete cytogenetic response and a major molecular response and also the importance of molecular monitoring in the follow-up of chronic myeloid leukemia patients were demonstrated.333211215Melo, J.V., The molecular biology of chronic myeloid leukaemia (1996) Leukemia, 10 (5), pp. 751-756Wang, L., Pearson, K., Pillitteri, L., Ferguson, J.E., Clark, R.E., Serial monitoring of BCR-ABL by peripheral blood real-time polymerase chain reaction predicts the marrow cytogenetic response to imatinib mesylate in chronic myeloid leukaemia (2002) Br J Haematol, 118 (3), pp. 771-777Muller, M.C., Gattermann, N., Lahaye, T., Deininger, M.W., Berndt, A., Fruehauf, S., Dynamics of BCR-ABL mRNA expression in firstline therapy of chronic myelogenous leukemia patients with imatinib or interferon alpha/ara-C (2003) Leukemia, 17 (12), pp. 2392-2400Branford, S., Hughes, T.P., Rudzki, Z., Monitoring chronic myeloid leukaemia therapy by real-time quantitative PCR in blood is a reliable alternative to bone marrow cytogenetics (1999) Br J Haematol, 107 (3), pp. 587-599Radich, J.P., Gooley, T., Bryant, E., Chauncey, T., Clift, R., Beppu, L., The significance of bcr-abl molecular detection in chronic myeloid leukemia patients late, 18 months or more after transplantation (2001) Blood, 98 (6), pp. 1701-1707Hughes, T.P., Kaeda, J., Branford, S., Rudzki, Z., Hochhaus, A., Hensley, M.L., Frequency of major molecular responses to imatinib or interferon-alpha plus cytarabine in newly diagnosed chronic myeloid leukemia (2003) N Engl J Med, 349 (15), pp. 1423-1432Press, R.D., Love, Z., Tronnes, A.A., Yang, R., Tran, T., Mongoue- tchokote, S., BCR-ABL mRNA levels at and after the time of a complete cytogenetic response predict the duration of CCR in imatinib mesylate-treated patients with CML (2006) Blood, 107 (11), pp. 4250-4256Cortes, J., Talpaz, M., O'Brien, S., Jones, D., Luthra, R., Shan, J., Molecular responses in patients with chronic myelogenous leukemia in chronic phase treated with imatinib mesylate (2005) Clin Cancer Res, 11 (9), pp. 3425-3432Iacobucci, I., Saglio, G., Rosti, G., Testoni, N., Pane, F., Amabile, M., Achieving a major molecular response at the time of a complete cytogenetic response (CCgR) predicts a better duration of CCgR in imatinib-treated chronic myeloid leukemia patients (2006) Clin Cancer Res, 12 (10), pp. 3037-3042Baccarani, M., Saglio, G., Goldman, J., Hochhaus, A., Simonsson, B., Appelbaum, F., Evolving concepts in the management of chronic myeloid leukemia: Recommendations from an expert panel on behalf of the European LeukemiaNet (2006) Blood, 108 (6), pp. 1809-1820Hughes, T., Deininger, M., Hochhaus, A., Branford, S., Radich, J., Kaeda, J., Monitoring CML patients responding to treatment with tyrosine kinase inhibitors: Review and recommendations for harmonizing current methodology for detecting BCR-ABL transcripts and kinase domain mutations and for expressing results (2006) Blood, 108 (1), pp. 28-37Branford, S., Cross, N.C., Hochhaus, A., Radich, J., Saglio, G., Kaeda, J., Rationale for the recommendations for harmonizing current methodology for detecting BCR-ABL transcripts in patients with chronic myeloid leukaemia (2006) Leukemia, 20 (11), pp. 1925-1930Cortes, J., Baccarani, M., Fea, G., (2008) A Phase III, Randomized, Openlabel Study of 400 Mg Versus 800 Mg of Imatinib Mesylate (IM) in Patients With Newly Diagnosed, Previously Untreated Chronic Myeloid Leukemia in Chronic Phase (CML-CP), Using Molecular Endpoints: One Year Results of TOPS (Tyrosine Kinase Inhibitor Optimization and Selectivity) Study, , 50th ASH Annual Meeting and Exposition Online program and Abstracts. San Francisco, CABranford, S., Fletcher, L., Cross, N.C., Muller, M.C., Hochhaus, A., Kim, D.W., Desirable performance characteristics for BCR-ABL measurement on an international reporting scale to allow consistent interpretation of individual patient response and comparison of response rates between clinical trials (2008) Blood, 112 (8), pp. 3330-3338O'Brien, S.G., Guilhot, F., Larson, R.A., Gathmann, I., Baccarani, M., Cervantes, F., Imatinib compared with interferon and lowdose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia (2003) N Engl J Med, 348 (11), pp. 994-1004Marin, D., Milojkovic, D., Olavarria, E., Khorashad, J.S., de Lavallade, H., Reid, A.G., European LeukemiaNet criteria for failure or suboptimal response reliably identify patients with CML in early chronic phase treated with imatinib whose eventual outcome is poor (2008) Blood, 112 (12), pp. 4437-444

Structure and Mechanism of Dimer-Monomer Transition of a Plant Poly(A)-Binding Protein upon RNA Interaction: Insights into Its Poly(A) Tail Assembly

Poly(A)-binding proteins (PABPs) play crucial roles in mRNA biogenesis, stability, transport and translational control in most eukaryotic cells. Although animal PABPs are well-studied proteins, the biological role, three-dimensional structure and RNA-binding mode of plant PABPs remain largely uncharacterized. Here, we report the structural features and RNA-binding mode of a Citrus sinensis PABP (CsPABPN1). CsPABPN1 has a domain architecture of nuclear PABPs (PABPNs) with a single RNA recognition motif (RRM) flanked by an acidic N-terminus and a GRPF-rich C-terminus. The RRM domain of CsPABPN1 displays virtually the same three-dimensional structure and poly(A)-binding mode of animal PABPNs. However, while the CsPABPN1 RRM domain specifically binds poly(A), the full-length protein also binds poly(U). CsPABPN1 localizes to the nucleus of plant cells and undergoes a dimer–monomer transition upon poly(A) interaction. We show that poly(A) binding by CsPABPN1 begins with the recognition of the RNA-binding sites RNP1 and RNP2, followed by interactions with residues of the β2 strands, which stabilize the dimer, thus leading to dimer dissociation. Like human PABPN1, CsPABPN1 also seems to form filaments in the presence of poly(A). Based on these data, we propose a structural model in which contiguous CsPABPN1 RRM monomers wrap around the RNA molecule creating a superhelical structure that could not only shield the poly(A) tail but also serve as a scaffold for the assembly of additional mRNA processing factors

A Comment on the beta-expansion of s=1/2 and s=1 Ising Models

The purpose of the present work is to apply the method recently developed in reference [chain_m] to the spin-1 Ising chain, showing how to obtain analytical $\beta$-expansions of thermodynamical functions through this formalism. In this method, we do not solve any transfer matrix-like equations. A comparison between the $\beta$-expansions of the specific heat and the magnetic susceptibility for the $s=1/2$ and $s=1$ one-dimensional Ising models is presented. We show that those expansions have poorer convergence when the auxiliary function of the model has singularities.Comment: 12 pages, 8 figure

Anisotropy studies around the galactic centre at EeV energies with the Auger Observatory

Data from the Pierre Auger Observatory are analyzed to search for anisotropies near the direction of the Galactic Centre at EeV energies. The exposure of the surface array in this part of the sky is already significantly larger than that of the fore-runner experiments. Our results do not support previous findings of localized excesses in the AGASA and SUGAR data. We set an upper bound on a point-like flux of cosmic rays arriving from the Galactic Centre which excludes several scenarios predicting sources of EeV neutrons from Sagittarius $A$. Also the events detected simultaneously by the surface and fluorescence detectors (the `hybrid' data set), which have better pointing accuracy but are less numerous than those of the surface array alone, do not show any significant localized excess from this direction.Comment: Matches published versio