Ammonia assimilation in Bacillus polymyxa. 15N NMR and enzymatic studies

Pathways of ammonia assimilation into glutamic acid and alanine in Bacillus polymyxa were investigated by 15N NMR spectroscopy in combination with measurements of the specific activities of glutamate dehydrogenase, glutamine synthetase, glutamate synthetase, alanine dehydrogenase, and glutamic-alanine transaminase. Ammonia was found to be assimilated into glutamic acid predominantly by NADPH-dependent glutamate dehydrogenase with a Km of 2.9 mM for NH4+ not only in ammonia-grown cells but also in nitrate-grown and nitrogen-fixing cells in which the intracellular NH4+ concentrations were 11.2, 1.04, and 1.5 mM, respectively. In ammonia-grown cells, the specific activity of alanine dehydrogenase was higher than that of glutamic-alanine transaminase, but the glutamate dehydrogenase/glutamic-alanine transaminase pathway was found to be the major pathway of 15NH4+ assimilation into [15N]alanine. The in vitro specific activities of glutamate dehydrogenase and glutamine synthetase, which represent the rates of synthesis of glutamic acid and glutamine, respectively, in the presence of enzyme-saturating concentrations of substrates and coenzymes are compared with the in vivo rates of biosynthesis of [15N]glutamic acid and [alpha,gamma-15N]glutamine observed by NMR, and implications of the results for factors limiting the rates of their biosynthesis in ammonia- and nitrate-grown cells are discussed

Glutamate biosynthesis in Bacillus azotofixans. 15N NMR and enzymatic studies

Pathways of ammonia assimilation into glutamic acid in Bacillus azotofixans, a recently characterized nitrogen-fixing species of Bacillus, were investigated through observation by NMR spectroscopy of in vivo incorporation of 15N into glutamine and glutamic acid in the absence and presence of inhibitors of ammonia-assimilating enzymes, in combination with measurements of the specific activities of glutamate dehydrogenase, glutamine synthetase, glutamate synthase, and alanine dehydrogenase. In ammonia-grown cells, both the glutamine synthetase/glutamate synthase and the glutamate dehydrogenase pathways contribute to the assimilation of ammonia into glutamic acid. In nitrate-grown and nitrogen-fixing cells, the glutamine synthetase/glutamate synthase pathway was found to be predominant. NADPH-dependent glutamate dehydrogenase activity was detectable at low levels only in ammonia-grown and glutamate-grown cells. Thus, B. azotofixans differs from Bacillus polymyxa and Bacillus macerans, but resembles other N2-fixing prokaryotes studied previously, as to the pathway of ammonia assimilation during ammonia limitation. Implications of the results for an emerging pattern of ammonia assimilation by alternative pathways among nitrogen-fixing prokaryotes are discussed, as well as the utility of 15N NMR for measuring in vivo glutamate synthase activity in the cell

Fundamental studies in geodynamics

Research in fundamental studies in geodynamics continued in a number of fields including seismic observations and analysis, synthesis of geochemical data, theoretical investigation of geoid anomalies, extensive numerical experiments in a number of geodynamical contexts, and a new field seismic volcanology. Summaries of work in progress or completed during this report period are given. Abstracts of publications submitted from work in progress during this report period are attached as an appendix

Effect of the nitrogen source on glutamine and alanine biosynthesis in Neurospora crassa. An in vivo 15N nuclear magnetic resonance study

The influences of different nitrogen sources on the relative rates of biosynthesis of glutamine and alanine have been studied by 15N nuclear magnetic resonance spectroscopy of intact Neurospora crassa mycelia suspensions. The rate of glutamine synthesis was fastest after growth in media deficient in free ammonium ion, whereas it was slowest following growth in media containing both glutamic acid and glutamine. The reverse trend was observed for the biosynthesis of alanine. A competition between the two biosynthetic pathways for the same substrate, glutamic acid, was found to limit the rate of alanine synthesis when glutamine synthesis was rapid. The observed in vivo rates of these reactions are compared to the reported specific activities of the enzymes catalyzing the reactions, and implications of these results for nitrogen regulation of these pathways under various physiological conditions are discussed

Orbital effects in manganites

In this paper I give a short review of some properties of the colossal magnetoresistance manganites, connected with the orbital degrees of freedom. Ions Mn{3+}, present in most of these compounds, have double orbital degeneracy and are strong Jahn-Teller ions, causing structural distortions and orbital ordering. Mechanisms leading to such ordering are shortly discussed, and the role of orbital degrees of freedom in different parts of the phase diagram of manganites is described. Special attention is paid to the properties of low-doped systems (doping 0.1 - 0.25), to overdoped systems (x > 0.5), and to the possibility of a novel type of orbital ordering in optimally doped ferromagnetic metallic manganites.Comment: 28 pages, 7 figures, to be published in J. Mod. Phys.

Independent response modulation of visual cortical neurons by attentional and behavioral states

Sensory processing is influenced by cognitive and behavioral states, but how these states interact to modulate responses of individual neurons is unknown. We trained mice in a visual discrimination task wherein they attended to different locations within a hemifield while running or sitting still, enabling us to examine how visual responses are modulated by spatial attention and running behavior. We found that spatial attention improved discrimination performance and strengthened visual responses of excitatory neurons in the primary visual cortex whose receptive fields overlapped with the attended location. Although individual neurons were modulated by both spatial attention and running, the magnitudes of these influences were not correlated. While running-dependent modulation was stable across days, attentional modulation was dynamic, influencing individual neurons to different degrees after repeated changes in attentional states. Thus, despite similar effects on neural responses, spatial attention and running act independently with different dynamics, implying separable mechanisms for their implementation

The chiral and flavour projection of Dirac-Kahler fermions in the geometric discretization

It is shown that an exact chiral symmetry can be described for Dirac-Kahler fermions using the two complexes of the geometric discretization. This principle is extended to describe exact flavour projection and it is shown that this necessitates the introduction of a new operator and two new structures of complex. To describe simultaneous chiral and flavour projection, eight complexes are needed in all and it is shown that projection leaves a single flavour of chiral field on each.Comment: v2: 17 pages, Latex. 5 images eps. Added references, reformatted and clarification of some point

Rank-Ordering Statistics of Extreme Events: Application to the Distribution of Large Earthquakes

Rank-ordering statistics provides a perspective on the rare, largest elements of a population, whereas the statistics of cumulative distributions are dominated by the more numerous small events. The exponent of a power law distribution can be determined with good accuracy by rank-ordering statistics from the observation of only a few tens of the largest events. Using analytical results and synthetic tests, we quantify the systematic and the random errors. We also study the case of a distribution defined by two branches, each having a power law distribution, one defined for the largest events and the other for smaller events, with application to the World-Wide (Harvard) and Southern California earthquake catalogs. In the case of the Harvard moment catalog, we make more precise earlier claims of the existence of a transition of the earthquake magnitude distribution between small and large earthquakes; the $b$-values are $b_2 = 2.3 \pm 0.3$ for large shallow earthquakes and $b_1 = 1.00 \pm 0.02$ for smaller shallow earthquakes. However, the cross-over magnitude between the two distributions is ill-defined. The data available at present do not provide a strong constraint on the cross-over which has a $50\%$ probability of being between magnitudes $7.1$ and $7.6$ for shallow earthquakes; this interval may be too conservatively estimated. Thus, any influence of a universal geometry of rupture on the distribution of earthquakes world-wide is ill-defined at best. We caution that there is no direct evidence to confirm the hypothesis that the large-moment branch is indeed a power law. In fact, a gamma distribution fits the entire suite of earthquake moments from the smallest to the largest satisfactorily. There is no evidence that the earthquakes of the Southern California catalog have a distribution with tw

Absence of sign problem in two-dimensional N=(2,2) super Yang-Mills on lattice

We show that N=(2,2) SU(N) super Yang-Mills theory on lattice does not have sign problem in the continuum limit, that is, under the phase-quenched simulation phase of the determinant localizes to 1 and hence the phase-quench approximation becomes exact. Among several formulations, we study models by Cohen-Kaplan-Katz-Unsal (CKKU) and by Sugino. We confirm that the sign problem is absent in both models and that they converge to the identical continuum limit without fine tuning. We provide a simple explanation why previous works by other authors, which claim an existence of the sign problem, do not capture the continuum physics.Comment: 27 pages, 24 figures; v2: comments and references added; v3: figures on U(1) mass independence and references added, to appear in JHE