Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.Comment: 9 page, 4 ps figures are include

Highly Designable Protein Structures and Inter Monomer Interactions

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include

Experimental realization of high-fidelity teleportation via a non-Markovian open quantum system

Open quantum systems and study of decoherence are important for our fundamental understanding of quantum physical phenomena. For practical purposes, a large number of quantum protocols exist that exploit quantum resources, e.g., entanglement, which allows us to go beyond what is possible to achieve by classical means. We combine concepts from open quantum systems and quantum information science and give a proof-of-principle experimental demonstration—with teleportation—that it is possible to implement efficiently a quantum protocol via a non-Markovian open system. The results show that, at the time of implementation of the protocol, it is not necessary to have the quantum resource in the degree of freedom used for the basic protocol—as long as there exists some other degree of freedom or the environment of an open system, which contains useful resources. The experiment is based on a pair of photons, where their polarizations act as open system qubits and frequencies as their environments, while the path degree of freedom of one of the photons represents the state of Alice's qubit to be teleported to Bob's polarization qubit.</p

Energy metabolites as biomarkers in ischemic and dilated cardiomyopathy

With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and non-ischemic HF by using a multi-OMICS approach. Serum metabolites and mRNAseq and epigenetic DNA methylation profiles were analyzed from blood and left ventricular heart biopsy specimens of the same individuals. In total we collected serum from n = 82 patients with Dilated Cardiomyopathy (DCM) and n = 51 controls in the screening stage. We identified several metabolites involved in glycolysis and citric acid cycle to be elevated up to 5.7-fold in DCM (p = 1.7 × 10(-6)). Interestingly, cardiac mRNA and epigenetic changes of genes encoding rate-limiting enzymes of these pathways could also be found and validated in our second stage of metabolite assessment in n = 52 DCM, n = 39 ischemic HF and n = 57 controls. In conclusion, we identified a new set of metabolomic biomarkers for HF. We were able to identify underlying biological cascades that potentially represent suitable intervention targets

Differential profiling of lacrimal cytokines in patients suffering from thyroid-associated orbitopathy.

The aim was to investigate the levels of cytokines and soluble IL-6R in the tears of patients with thyroid-associated orbitopathy (TAO) disease. Schirmer's test was adopted to collect tears from TAO patients (N = 20, 17 women, mean age (±SD): 46.0 years (±13.4)) and healthy subjects (N = 18, 10 women, 45.4 years (±18.7)). Lacrimal cytokines and soluble IL-6R (sIL-6R) were measured using a 10-plex panel (Meso Scale Discovery Company) and Invitrogen Human sIL-6R Elisa kit, respectively. Tear levels of IL-10, IL-12p70, IL-13, IL-6 and TNF-α appeared significantly higher in TAO patients than in healthy subjects. Interestingly, IL-10, IL-12p70 and IL-8 levels increased in tears whatever the form of TAO whereas IL-13, IL-6 and TNF-α levels were significantly elevated in inflammatory TAO patients, meaning with a clinical score activity (CAS) ≥ 3, compared to controls. Furthermore, only 3 cytokines were strongly positively correlated with CAS (IL-13 Spearman coeff. r: 0.703, p = 0.0005; IL-6 r: 0.553, p = 0.011; IL-8 r: 0.618, p = 0.004, respectively). Finally, tobacco use disturbed the levels of several cytokines, especially in patient suffering of TAO. The differential profile of lacrimal cytokines could be useful for the diagnosis of TAO patients. Nevertheless, the tobacco use of these patients should be taken into account in the interpretation of the cytokine levels

Evaluation of safety of Hammada salicornica in cell culture

Background and objectives: A pharmaceutical products that is planned to be used in clinic, should not only have beneficial effects but also be safe too. Preclinical studies in animals are costly and need considering ethical issues. Cell culture can be used before animal tests. Considering useful effects of these methods, we have evaluated safety of total methanol extract of Hammada salicornica and its aqueous and petroleum ether fractions in cell culture.Methods: Total methanol extract was prepared with the standard method of maceration. Different fractions were prepared by liquid-liquid fractionation and the extracts were then dried with rotary evaporator. After determination of bactericidal concentration of the extracts, 400 ug/mL, the cytotoxicity was tested at various concentrations regarding the minimum antibacterial concentration by MTT test. Hep-2c and VERO cell lines were used in MTT test. A range of concentrations (10-500 ug/mL) of the extracts were prepared and were added to about 70% confluent 96 well plates. After exposure for 48 h, MTT solution was added to the wells, and 4 h later formazan crystals were solubilized and optical densities were read at 570 nm. Results: Cytotoxicity Index was calculated and significance test was performed using t-test comparing the Index of the test and control group at each concentration. No significant difference was observed. Conclusion: Various fractions of H. salicornica were not cytotoxic at concentrations above bactericidal concentrations (up to 500 ug/mL). The results need to be confirmed in animal studies before using in human subjects