Roles of Predicted Glycosyltransferases in the Biosynthesis of the Rhizobium etli CE3 O Antigen

The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer. The genetic regions required for its synthesis have been identified, and the nucleotide sequences are known. The structure of the O antigen has been determined, but the roles of specific genes in synthesizing this structure are relatively unclear. Within the known O-antigen genetic clusters of this strain, nine open reading frames (ORFs) were found to contain a conserved glycosyltransferase domain. Each ORF was mutated, and the resulting mutant lipopolysaccharide (LPS) was analyzed. Tricine SDS-PAGE revealed stepwise truncations of the O antigen that were consistent with differences in mutant LPS sugar compositions and reactivity with O-antigen-specific monoclonal antibodies. Based on these results and current theories of O-antigen synthesis, specific roles were deduced for each of the nine glycosyltransferases, and a model for biosynthesis of the R. etli CE3 O antigen was proposed. In this model, O-antigen biosynthesis is initiated with the addition of N-acetyl-quinovosamine-phosphate (QuiNAc-P) to bactoprenol-phosphate by glycosyltransferase WreU. Glycosyltransferases WreG, WreE, WreS, and WreT would each act once to attach mannose, fucose, a second fucose, and 3-O-methyl-6-deoxytalose (3OMe6dTal), respectively. WreH would then catalyze the addition of methyl glucuronate (MeGlcA) to complete the first instance of the O-antigen repeat unit. Four subsequent repeats of this unit composed of fucose, 3OMe6dTal, and MeGlcA would be assembled by a cycle of reactions catalyzed by two additional glycosyltransferases, WreM and WreL, along with WreH. Finally, the O antigen would be capped by attachment of di- or tri-O-methylated fucose as catalyzed by glycosyltransferase WreB

Genetic Basis for \u3cem\u3eRhizobium etli\u3c/em\u3e CE3 O-Antigen O-Methylated Residues That Vary According to Growth Conditions

The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer with O methylation being the predominant type of sugar modification. There are two O-methylated residues that occur, on average, once per complete O antigen: a multiply O-methylated terminal fucose and 2-O methylation of a fucose residue within a repeating unit. The amount of the methylated terminal fucose decreases and the amount of 2-O-methylfucose increases when bacteria are grown in the presence of the host plant, Phaseolus vulgaris, or its seed exudates. Insertion mutagenesis was used to identify open reading frames required for the presence of these O-methylated residues. The presence of the methylated terminal fucose required genes wreA, wreB, wreC, wreD, and wreF, whereas 2-O methylation of internal fucoses required the methyltransferase domain of bifunctional gene wreM. Mutants lacking only the methylated terminal fucose, lacking only 2-O methylation, or lacking both the methylated terminal fucose and 2-O methylation exhibited no other lipopolysaccharide structural defects. Thus, neither of these decorations is required for normal O-antigen length, transport, or assembly into the final lipopolysaccharide. This is in contrast to certain enteric bacteria in which the absence of a terminal decoration severely affects O-antigen length and transport. R. etli mutants lacking only the methylated terminal fucose were not altered in symbiosis with host Phaseolus vulgaris, whereas mutants lacking only 2-O-methylfucose exhibited a delay in nodule development during symbiosis. These results support previous conclusions that the methylated terminal fucose is dispensable for symbiosis, whereas 2-O methylation of internal fucoses somehow facilitates early events in symbiosis

Selecting fast folding proteins by their rate of convergence

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using only the very initial parts of the dynamical trajectories. It does not require any preliminary knowledge of the native state and can be applied to different kinds of models, including atomistic descriptions. We tested the method within both the lattice and off-lattice model frameworks and obtained several so far unknown good folders. The unbiased algorithm also allows to determine the optimal folding temperature and takes at least 3--4 orders of magnitude less time steps than those needed to compute folding times

Triple-Star Candidates Among the Kepler Binaries

We present the results of a search through the photometric database of eclipsing Kepler binaries (Prsa et al. 2011; Slawson et al. 2011) looking for evidence of hierarchical triple star systems. The presence of a third star orbiting the binary can be inferred from eclipse timing variations. We apply a simple algorithm in an automated determination of the eclipse times for all 2157 binaries. The "calculated" eclipse times, based on a constant period model, are subtracted from those observed. The resulting O-C (observed minus calculated times) curves are then visually inspected for periodicities in order to find triple-star candidates. After eliminating false positives due to the beat frequency between the ~1/2-hour Kepler cadence and the binary period, 39 candidate triple systems were identified. The periodic O-C curves for these candidates were then fit for contributions from both the classical Roemer delay and so-called "physical" delay, in an attempt to extract a number of the system parameters of the triple. We discuss the limitations of the information that can be inferred from these O-C curves without further supplemental input, e.g., ground-based spectroscopy. Based on the limited range of orbital periods for the triple star systems to which this search is sensitive, we can extrapolate to estimate that at least 20% of all close binaries have tertiary companions.Comment: 19 pages, 13 figures, 3 tables; ApJ, 2013, 768, 33; corrected Fig. 7, updated references, minor fixes to tex

Modeling and Optimization of Quality Variability for Decision Support Systems in Biofuel Production

Biofuels are a promising alternative to fossil fuel depletion, due to their sustainable production from living or recently living organic matter (i.e., biomass). Biofuel production offers benefits that are not present in non-sustainable resources, like the reduction of air pollution. According to government agencies, biofuel production is expected to increase in the U.S. within the next few years because of government initiatives. In order to become a feasible alternative to satisfy market demand, biofuels require strategic improvements in areas such as supply chain management to deal with the variability within the biomass. Advanced analysis tools might be utilized to integrate biomass physical and chemical properties into the decision processes. This chapter introduces a principal component analysis (PCA) to determine significant factors that affect the operations within the supply chain and, later on, incorporates those factors in an optimization model for the decision analysis. The results show that incorporating quality-related properties has a significant impact in the solution of the optimization program

M-Dwarf Fast Rotators and the Detection of Relatively Young Multiple M-Star Systems

We have searched the Kepler light curves of ~3900 M-star targets for evidence of periodicities that indicate, by means of the effects of starspots, rapid stellar rotation. Several analysis techniques, including Fourier transforms, inspection of folded light curves, 'sonograms', and phase tracking of individual modulation cycles, were applied in order to distinguish the periodicities due to rapid rotation from those due to stellar pulsations, eclipsing binaries, or transiting planets. We find 178 Kepler M-star targets with rotation periods, P_rot, of < 2 days, and 110 with P_rot < 1 day. Some 30 of the 178 systems exhibit two or more independent short periods within the same Kepler photometric aperture, while several have three or more short periods. Adaptive optics imaging and modeling of the Kepler pixel response function for a subset of our sample support the conclusion that the targets with multiple periods are highly likely to be relatively young physical binary, triple, and even quadruple M star systems. We explore in detail the one object with four incommensurate periods all less than 1.2 days, and show that two of the periods arise from one of a close pair of stars, while the other two arise from the second star, which itself is probably a visual binary. If most of these M-star systems with multiple periods turn out to be bound M stars, this could prove a valuable way of discovering young hierarchical M-star systems; the same approach may also be applicable to G and K stars. The ~5% occurrence rate of rapid rotation among the ~3900 M star targets is consistent with spin evolution models that include an initial contraction phase followed by magnetic braking, wherein a typical M star can spend several hundred Myr before spinning down to periods longer than 2 days.Comment: 17 pages, 12 figures, 2 tables; accepted for publication in The Astrophysical Journa

Experimental approval of the extended flat bands and gapped subbands in rhombohedral multilayer graphene

Graphene layers are known to stack in two stable configurations, namely ABA or ABC stacking, with drastically distinct electronic properties. Unlike the ABA stacking, little has been done to experimentally investigate the electronic properties of ABC graphene multilayers. Here, we report the first magneto optical study of a large ABC domain in a graphene multilayers flake, with ABC sequences exceeding 17 graphene sheets. The ABC-stacked multilayers can be fingerprinted with a characteristic electronic Raman scattering response, which persists even at room temperatures. Tracing the magnetic field evolution of the inter Landau level excitations from this domain gives strong evidence to the existence of a dispersionless electronic band near the Fermi level, characteristic of such stacking. Our findings present a simple yet powerful approach to probe ABC stacking in graphene multilayer flakes, where this highly degenerated band appears as an appealing candidate to host strongly correlated states.Comment: 8 pages, 4 figure

Inhalación de esporas de Aspergillus fumigatus induce en ratones una inflamación de las vías aéreas similar a la observada en equinos con Obstrucción Recurrente de las Vías Aéreas

The aim of this study was to determine if mice exposed to Aspergillus (A.) fumigatus spores develop airway inflammation in a similar manner to Recurrent Airway Obstruction (RAO) in horses. Different groups of 2-, 5-, 6- and 8-month-old Rockefeller (RK) mice were used throughout the experiment. The mice were maintained in the animal house for 16 days and kept in cages containing hay contaminated with A. fumigatus. After 16 days of mold exposure, the mice were bled and sacrificed to obtain bronchoalveolar lavage fluid (BALF) or lung tissues for histological analysis. In addition, we measured the levels of A. fumigatus-specific antibodies by ELISA. The results demonstrated that inhalation of A. fumigatus spores in mice induced an inflammatory response in the lungs that was characterized by peribronchiolar and perivascular mononuclear infiltration and bronchiolar luminal exudates. Moreover, there was extensive folding of the airway epithelia, which is a sign of airway smooth muscle contraction and smooth muscle hypertrophy. In addition, we observed a high number of neutrophils and an increase in IgE, IgG1 and IgG2a antibodies in the BALF from mice that were older than 5 months and were exposed to A. fumigatus. These animals recovered from their respiratory distress when they were placed in a remission environment. We conclude that simple exposure of mice to moldy hay induces a condition that is similar to RAO in horses. Therefore, using this mouse model for the study of equine RAO offers the opportunity to approximate the immunologic response to airborne irritants and allergens as well as to evaluate pharmacological therapies.El objetivo de este estudio fue determinar si ratones expuestos a esporas de Aspergillus fumigatus desarrollan una inflamación alérgica de las vías respiratorias similar a la observada en equinos con Obstrucción Recurrente de las Vías Aéreas (ORVA). Para esto se utilizaron ratones Rockefeller (RK) de 2, 5, 6 y 8 meses respectivamente, los cuales se mantuvieron por 16 días en jaulas que contenían heno contaminado con A. fumigatus. Posterior a la exposición, los animales fueron sangrados y sacrificados para la obtención de suero sanguíneo, lavado broncoalveolar (LBA) y muestras de tejido pulmonar. Además, se midieron los niveles de anticuerpos específicos para A. fumigatus a través de un ELISA indirecto. Los resultados mostraron que la inhalación de esporas de A. fumigatus en ratones induce una respuesta alérgica inflamatoria en pulmones similar a lo observado en ORVA equino, con un aumento del porcentaje de neutrófilos en el LBA y cambios histológicos pulmonares característicos de una hipersensibilidad bronquial. Asimismo, se observó un aumento de los niveles de inmunoglubulinas IgE, IgG1 e IgG2a específicas para este hongo en fluidos bronquiales. Además, los animales remitieron el estrés respiratorio cuando fueron expuestos en un ambiente de remisión. Se puede concluir que la simple exposición de esporas de A. fumugatus produce una condición alérgica similar al ORVA en equinos. Por lo tanto, este modelo experimental puede ser de utilidad para el estudio de los mecanismos inmunológicos, y probar nuevas opciones terapéuticas para esta enfermedad respiratoria de los caballos

Analytical calculation of the excess current in the OTBK theory

We present an analytical derivation of the excess current in Josephson junctions within the Octavio-Tinkham-Blonder-Klapwijk theory for both symmetric and asymmetric barrier strengths. We confirm the result found numerically by Flensberg et al. for equal barriers [Phys. Rev. B 38, 8707 (1988)], including the prediction of negative excess current for low transparencies, and we generalize it for differing barriers. Our analytical formulae provide for convenient fitting of experimental data, also in the less studied, but practically relevant case of the barrier asymmetry.Comment: 13 pages, 3 figures, submitted to Superconductor Science and Technolog