The Degradome database: mammalian proteases and diseases of proteolysis

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes

Signals of CP Violation Beyond the MSSM in Higgs and Flavor Physics

We study an extension of the Higgs sector of the Minimal Supersymmetric Standard Model (MSSM), considering the effects of new degrees of freedom at the TeV scale, and allowing for sources of CP violation beyond the MSSM (BMSSM). We analyze the impact of the BMSSM sources of CP violation on the Higgs collider phenomenology and on low energy flavor and CP violating observables. We identify distinct Higgs collider signatures that cannot be realized, either in the case without CP violating phases or in the CP violating MSSM, and investigate the prospects to probe them at the Tevatron and the LHC. The most striking benchmark scenario has three neutral Higgs bosons that all decay dominantly into W boson pairs and that are well within the reach of the 7 TeV LHC run. On the other hand, we also present scenarios with three Higgs bosons that have masses M_Hi > 150 GeV and decay dominantly into b bbar. Such scenarios are much more challenging to probe and can even lie completely outside the reach of the 7 TeV LHC run. We explore complementary scenarios with standard MSSM Higgs signals that allow to accommodate a sizable B_s mixing phase as indicated by D0, as well as the excess in B_s --> mu+ mu- candidates recently reported by CDF. We find that, in contrast to the MSSM, a minimal flavor violating soft sector is sufficient to generate significant corrections to CP violating observables in meson mixing, compatible with EDM constraints. In particular, a sizable B_s mixing phase, S_psiphi < 0.4, can be achieved for specific regions of parameter space. Such a large B_s mixing phase would unambiguously imply a sizable suppression of S_psiKs with respect to the SM prediction and a BR(B_s --> mu+ mu-) close to the 95% C.L. upper bound reported by CDF.Comment: 58 pages, 15 figures, 2 tables, v2 matches published versio

Tariff At Risk: Can The Florida Citrus Industry Survive?

For over 70 years, the Florida citrus industry has been protected from foreign competition by a tariff on orange juice. The orange juice tariff is currently being threatened by negotiations over the Free Trade Area of the Americas (FTAA) agreement and the World Trade Organization (WTO). Brazil is the leading foreign competitor to the Florida citrus industry. The tariff prevents Brazil from becoming a large citrus cartel that could take control of the worlds orange juice market. The Florida citrus industry contributes $9.1 billion to Floridas economy and provides jobs for 90,000 Florida citizens. Orange juice production is a key to the strength of Floridas economy. Florida citrus growers argue that the tariff is the most important issue facing the industrys survival. Without the tariff, Florida citrus growers are in danger of going out of business. This could devastate Floridas economy. It is important that Florida citrus growers and FTAA negotiators unite and intensify efforts to protect the citrus tariff and ensure the survival of Floridas citrus industry

Supersymmetric approach to exactly solvable systems with position-dependent effective masses

We discuss the relationship between exact solvability of the Schr\"{o}dinger equation with a position-dependent mass and the ordering ambiguity in the Hamiltonian operator within the frame of supersymmetric quantum mechanics. The one-dimensional Schr\"{o}dinger equation, derived from the general form of the effective mass Hamiltonian, is solved exactly for a system with exponentially changing mass in the presence of a potential with similar behaviour, and the corresponding supersymmetric partner Hamiltonians are related to the effective-mass Hamiltonians proposed in the literature.Comment: 12 pages article in LaTEX (uses standard article.sty). Please check http://www1.gantep.edu.tr/~ozer for other studies of Nuclear Physics Group at University of Gaziantep. [arXiv admin note: excessive overlap with quant-ph/0306065 and "Supersymmetric approach to quantum systems with position-dependent effective mass" by A. R. Plastino, A. Rigo, M. Casas, F. Garcias, and A. Plastino - Phys. Rev. A 60, 4318 - 4325 (1999)

Ferromagneticlike Closure Domains in Ferroelectric Ultrathin Films: First-Principles Simulations

We simulate from first principles the energetic, structural, and electronic properties of ferroelectric domains in ultrathin SrRuO3/BaTiO3/SrRuO3 ferroelectric capacitors in short circuit. The domains are stabilized down to two unit cells at zero temperature, adopting the form of a domain of closure, common in ferromagnetic thin films. The domains are closed by the in-plane relaxation of the atoms in the first SrO layer of the electrode, which behaves more like SrO in highly polarizable SrTiO3 than in metallic SrRuO3. Even if small, these lateral displacements are very important to stabilize the domains and might provide some hints to explain why some systems break into domains while others remain in a monodomain configuration. An analysis of the electrostatic potential reveals preferential points of pinning for charged defects at the ferroelectric-electrode interface, possibly playing a major role in film fatigue

Counting Arithmetical Structures on Paths and Cycles

Let G be a finite, connected graph. An arithmetical structure on G is a pair of positive integer vectors d, r such that (diag (d) - A) r=0 , where A is the adjacency matrix of G. We investigate the combinatorics of arithmetical structures on path and cycle graphs, as well as the associated critical groups (the torsion part of the cokernels of the matrices (diag (d) - A)). For paths, we prove that arithmetical structures are enumerated by the Catalan numbers, and we obtain refined enumeration results related to ballot sequences. For cycles, we prove that arithmetical structures are enumerated by the binomial coefficients ((2n-1)/(n-1)) , and we obtain refined enumeration results related to multisets. In addition, we determine the critical groups for all arithmetical structures on paths and cycles

Tumour prothymosin alpha content, a potential prognostic marker for primary breast cancer

In a previous report we suggested that the estimation of prothymosin α (PTA) levels in primary breast tumours might be used to identify breast cancer patients at high risk for distant metastasis (Dominguez F et al (1993) Eur J Cancer29A: 893–897). Here the role of tumour PTA levels as predictor was investigated with respect to both disease-free survival (DFS) and survival. Tumours were obtained from a series of 210 consecutive female patients with ductal carcinoma who underwent surgery at the Hospital Xeral de Galicia (Santiago de Compostela, Spain). Characteristics including PTA tumour levels, number of positive axillary nodes, patient's age at surgery and tumour histological grade were significantly associated with DFS and survival, as determined by univariate analysis. Patients with tumours with low or moderate PTA levels demonstrated a statistically decreased rate of tumour recurrence and a statistically significant increased overall survival in comparison with those whose tumours had high PTA levels. Patient's relative risk of dying was 2.1 times greater for tumours with high PTA levels than for those tumours with low or moderate PTA levels. In conclusion, these data support the hypothesis that tumour high PTA levels is associated with a worse outcome. © 2000 Cancer Research Campaig

Counting Arithmetical Structures on Paths and Cycles

Let G be a finite, connected graph. An arithmetical structure on G is a pair of positive integer vectors d, r such that (diag (d) - A) r=0 , where A is the adjacency matrix of G. We investigate the combinatorics of arithmetical structures on path and cycle graphs, as well as the associated critical groups (the torsion part of the cokernels of the matrices (diag (d) - A)). For paths, we prove that arithmetical structures are enumerated by the Catalan numbers, and we obtain refined enumeration results related to ballot sequences. For cycles, we prove that arithmetical structures are enumerated by the binomial coefficients ((2n-1)/(n-1)) , and we obtain refined enumeration results related to multisets. In addition, we determine the critical groups for all arithmetical structures on paths and cycles

Plant proteostasis-a proven and promising target for crop improvement - Editorial

The Green Revolution of the 1960s accomplished dramatic increases in crop yields through genetic improvement, chemical fertilisers, irrigation, and mechanisation. However, the current trajectory of population growth, against a backdrop of climate change and geopolitical unrest, predicts that agricultural production will be insufficient to ensure global food security in the next three decades. Improvements to crops that go beyond incremental gains are urgently needed. Plant biology has also undergone a revolution in recent years, through the development and application of powerful technologies including genome sequencing, a pantheon of ‘omics techniques, precise genome editing, and step changes in structural biology and microscopy. Proteostasis- the collective processes that control the protein complement of the cell, comprising synthesis, modification, localisation, and degradation- is a field that has benefitted from these advances. This special issue presents a selection of the latest research in this vibrant field, with a particular focus on protein degradation. In the current article, we highlight the diverse and widespread contributions of plant proteostasis to agronomic traits, suggest opportunities and strategies to manipulate different elements of proteostatic mechanisms for crop improvement, and discuss the challenges involved in bringing these ideas into practice

Neutron scattering at high temperature and levitation techniques

Studies of the liquid state present an obvious fundamental interest and are also important for technological applications since the molten state is an essential stage in various industrial processes (e.g. glass making, single crystal growing, iron and steel making). Most of the physical properties of a high-temperature liquid are related to its atomic structure. Thus it is important to develop devices to probe the local environment of the atoms in the sample. At very high temperature, it is difficult to use conventional furnaces, which present several problems. In particular, physical contact with the container can contaminate the sample and/or modify its structural properties. Such problems encouraged the development of containerless techniques, which are powerful tools to study high-temperature melts. By eliminating completely any contact between sample and container, it is possible to study the sample with a very high degree of control and to access very high temperatures. An additional advantage of levitation methods is that it is possible to supercool hot liquids down to several hundred of degrees below their equilibrium freezing point, since heterogeneous nucleation processes are suppressed