Phenogenetic Characterization of a Group of Giant φKZ-like Bacteriophages of Pseudomonas aeruginosa

A comparative study was made of a group ofPseudomonas aeruginosa virulent giant DNA bacteriophages similar to phage KZ in several genetic and phenotypic properties (particle size, particle morphology, genome size, appearance of negative colonies, high productivity, broad spectrum of lytic activity, ability to overcome the suppressing effect of plasmids, absence of several DNA restriction sites, capability of general transduction, pseudolysogeny). We have recently sequenced the phage KZ genome (288 334 bp) [J. Mol. Biol., 2002, vol. 317, pp. 1–19]. By DNA homology, the phages were assigned to three species (represented by phages KZ, Lin68, and EL, respectively) and two new genera (KZ and EL). Restriction enzyme analysis revealed the mosaic genome structure in four phages of the KZ species (KZ, Lin21, NN, and PTB80) and two phages of the EL species (EL and RU). Comparisons with respect to phage particle size, number of structural proteins, and the N-terminal sequences of the major capsid protein confirmed the phylogenetic relatedness of the phages belonging to the KZ genus. The origin and evolution of the KZ-like phages are discussed. Analysis of protein sequences encoded by the phage KZ genome made it possible to assume wide migration of the KZ-like phages (wandering phages) among various prokaryotes and possibly eukaryotes. Since the phage KZ genome codes for potentially toxic proteins, caution must be exercised in the employment of large bacteriophages in phage therapy.     

Isolation and characterization of lytic phages fromBacterioides ruminicola ssbrevis

Two bacteriophages (Brb01 and Brb02), lytic toBacteroides ruminicola ssbrevis AR20, were isolated from sewage water. Both phages possessed polyhedral heads and long noncontractile tails, and were classified as Siphoviridae of morphotype B1. Bacteria resistant to phages Brb01 and Brb02 arose following lysis of broth cultures. Survivors of Brb01 infection were capsulated but remained susceptible to Brb02 infection. Survivors of Brb02 infection were noncapsulated and were resistant to attack by both Brb01 and Brb02. Neither phage lysogenized the host. Both phages contained double-stranded DNA, and their restriction endonuclease digestion patterns indicated that the phage genomes were circularly permuted and terminally redundant. Phage Brb01 genome was examined in greater detail and confirmed to be circularly permuted, of size 33 kb, with a terminal redundancy of 2 kb, or 6% of the length of the genome. Circularly permuted genomes in phages of rumen bacteria do not appear to have been reported previously.At present, there is considerable interest in the genetic manipulation of rumen bacteria. The characterization of the phages described herein provides the basic information required for their use in the construction of vectors for the transfer of genetic material.     

DNA homology and adsorption specificity of Pseudomonas aeruginosa virulent bacteriophages

Summary The DNA homology and adsorption specificity of newly isolated virulent bacteriophages of P. aeruginosa have been studied. On the basis of this analysis all phages were divided into four groups: k, m, mnP78-like and mnF82-like bacteriophages. DNA's of k as well as m phages were shown to possess different restriction patterns although they have an extensive homology. Unlike other groups, k phages were characterized by the presence of T4 DNA ligase-repaired, single-chain breaks.Abbreviations kbp kilobase pairs - EM electron microscopy     

Average phase difference theory and 1∶1 phase entrainment in interlimb coordination

The dynamics of coupled biological oscillators can be modeled by averaging the effects of coupling over each oscillatory cycle so that the coupling depends on the phase difference between the two oscillators and not on their specific states. Average phase difference theory claims that mode locking phenomena can be predicted by the average effects of the coupling influences. As a starting point for both empirical and theoretical investigations, Rand et al. (1988) have proposed d/dt= — K sin ), with phase-locked solutions =arcsin( /K), where is the difference between the uncoupled frequencies and K is the coupling strength. Phase-locking was evaluated in three experiments using an interlimb coordination paradigm in which a person oscillates hand-held pendulums. was controlled through length differences in the left and right pendulums. The coupled frequency _c was varied by a metronome, and scaled to the eigenfrequency _v of the coupled system K was assumed to vary inversely with _c. The results indicate that: (1) and K contribute multiplicatively to (2) =0 or = regardless of K when =0; (3) 0 or regardless of when K is large (relative to ); (4) results (1) to (3) hold identically for both in phase and antiphase coordination. The results also indicate that the relevant frequency is _c/_v rather than _c. Discussion high-lighted the significance of confirming =arcsin(/K) for more general treatments of phase-locking, such as circle map dynamics, and for the 11 phase-entrainment which characterizes biological movement systems.     

The low-light reduction in the quantum yield of photosynthesis: potential errors and biases when calculating the maximum quantum yield

Photosynthesis-irradiance (P-E) curves are widely used to describe photosynthetic efficiency and potential. Contemporary models assume maximal photosynthetic quantum yield () at low irradiances. But P-E observations made with both oxygen evolution and carbon uptake techniques show that this is not always the case. Using new and published data in conjunction with modeling exercises, we demonstrate that regardless of the mechanism there can be reductions in at low irradiances that are not readily observable using conventional P-E analyses. We also show that analytical errors, such as inaccurate estimation of dark oxygen consumption or carbon uptake, can markedly affect the structure of -E curves with negligible effect on P-E curve structure. Whether from respiration `corrections' or other mechanisms, these deviations in at low light levels from the maximum quantum yield of photosynthesis (_max) can lead to significant errors (> 50%) in the estimation of the linear portion of the P-E curve and ultimately _max. Non-linear models of P-E, such as the rectangular hyperbola, quadratic, exponential and hyperbolic tangent that are commonly used to estimate the initial slope () of the P-E curve assume that is maximal at low light levels and therefore can err in the estimation of _max when is reduced at low light levels. Using a diverse data set of 622 P-E curves with a total of 7623 points, we show that although model skills are high (r ² = 0.96 ± 0.05, 0.97 ± 0.04, 0.97 ± 0.04 and 0.97 ± 0.04, respectively), a large fraction of the model-predicted _max differ by greater than 10% from true _max values (91%, 50%, 82% and 46%, respectively). Data from these observations and modeling exercises lead us to suggest that _max be determined by directly estimating the true maximum of a -E curve rather than using the more conventional methodology employing the initial slope of the P-E curve.This revised version was published online in October 2005 with corrections to the Cover Date.     

A use of Ramachandran potentials in protein solution structure determinations

A strategy is developed to use database-derived - constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived - constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the - values for each residue are examined. In the second and final run, the database-derived - constraints are enforced only for those residues which in the first run have ended in one and the same favored - region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.     

Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles

The concept of self-consistent J coupling evaluation exploits redundant structure information inherent in large sets of 3J coupling constants. Application to the protein Desulfovibrio vulgaris flavodoxin demonstrates the simultaneous refinement of torsion-angle values and related Karplus coefficients. The experimental basis includes quantitative coupling constants related to the polypeptide backbone torsion originating from a variety of heteronuclear 2D and 3D NMR correlation experiments, totalling 124 3J(HN,H), 129 3J(HN,C), 121 3J(HN,C), 128 3J(Ci–1,Hi), 121 3J(Ci–1,Ci), and 122 3J(Ci–1,Ci). Without prior knowledge from either X-ray crystallography or NMR data, such as NOE distance constraints, accurate dihedral angles are specified for 122 non-glycine and non-proline residues out of a total of 147 amino acids. Different models of molecular internal mobility are considered. The Karplus coefficients obtained are applicable to the conformational analysis of torsions in other polypeptides.     

Measurement of Three-bond, 13C′-13Cβ J Couplings in Human Ubiquitin by a Triple Resonance, E. COSY-type NMR Technique

A [CO]HN(CA)CB-E.COSY pulse scheme is described for measurement of three-bond couplings, 3JCC, between carbonyl and aliphatic C carbons in ubiquitin, uniformly enriched with 13C and 15N. A Karplus relation, 3JCC = 1.28 cos2( - 120°) -1.02 cos( - 120°) +0.30 Hz, is obtained by correlating the 3JCC values measured for human ubiquitin with backbone angles from its crystal structure. As predicted, the new Karplus parametrization yields 3JCC values slightly larger than previously obtained by quantitative J correlation [Hu, J.-S. and Bax, A. (1997) J. Am. Chem. Soc., 119, 6360-6368], but considerably smaller than what has been reported on the basis of other E.COSY-type measurements carried out on flavodoxin.     

Activation of peritoneal macrophages in patients with gynecological malignancies by sizofiran and recombinant interferon-γ

We investigated the influence of the combined use of sizofiran, a-1,3-glucan and a recombinant interferon- (rIFN-) upon biological activities of peritoneal macrophages (M). The number of peritoneal M and the production of cytokines (interleukin-1, interferon- and tumor necrosis factor) was increased by the combined treatment. Fully activated peritoneal M based on the increased number of elongated pseudopods were observed by electromicroscope. Sizofiran seems to assure a sufficient supply of M to kill tumor cells in the peritoneal cavity and co-administered rIFN- seems to directly stimulate the accumulated M in addition to its direct cytotoxicity against tumor cells. This combination therapy may be a step to the prevention of the recurrence of gynecological malignancies including ovarian cancer, after a negative second-look laparotomy.Abbreviations rIFN- recombinant interferon- - IL-1 interleukin-1 - TNF tumor necrosis factor - SLL second look laparotomy     

Ordered distribution of α-putrescinylthymine in the DNA of bacteriophage φW-14

In the DNA of bacteriophage W-14, half the thymine is replaced by a -putrescinylthymine (putThy). Analysis of monopyrimidine tracts shows that putThy and thymine are distributed nonrandomly in W-14 DNA: The sequence purine-putThy-purine occurs more than twice as frequently as the sequence purine-thymine-purine, which means that the post-replicative modification of W-14 DNA is sequence-specific.     

The relationship between CO2 assimilation and electron transport in leaves

The inter-relationships between the quantum efficiencies of photosystems I (_I) and II (_II) and the quantum yield of CO₂ fixation % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGak0dh9WrFfpC0xh9vqqj-hEeeu0xXdbba9frFj0-OqFf% ea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs0dXdbPYxe9vr0-vr% 0-vqpWqaaeaabaGaciaacaqabeaadaqaaqaaaOqaaiabeA8aMnaaBa% aaleaacaWGdbGaam4tamaaBaaameaacaaIYaaaleqaaaqabaaaaa!3BD3!\[\phi _{CO_2 } \] were investigated in pea (Pisum sativum (L)) leaves with differing rates of photosynthesis using both photorespiratory and non-photorespiratory conditions, and in a leaf of Hedera helix (L) under photorespiratory conditions. The results indicate that under photorespiratory conditions the relationship between % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGak0dh9WrFfpC0xh9vqqj-hEeeu0xXdbba9frFj0-OqFf% ea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs0dXdbPYxe9vr0-vr% 0-vqpWqaaeaabaGaciaacaqabeaadaqaaqaaaOqaaiabeA8aMnaaBa% aaleaacaWGdbGaam4tamaaBaaameaacaaIYaaaleqaaaqabaaaaa!3BD3!\[\phi _{CO_2 } \] and both _I and _II is non-linear and variable. The relationship between _I and _II under these circumstances remains predominantly linear. Under non-photorespiratory conditions, leaves with a low rate of photosynthesis due to sink limitation exhibit a non-linear relationship between _I and _II, though the relationship between _I and _II remains linear suggesting a close relationship between linear electron flow and CO₂ fixation. Leaves irradiated at the CO₂ compensation point also exhibit a non-linear relationship between _I and _II. These results suggest that for leaves in air linear electron flow is the predominant source of energy for metabolism. The role of cyclic electron transport is considered when the requirement for the products of linear electron transport is depressed.Abbreviations q_p the coefficient for photochemical quenching of chlorophyll fluorescence - _exe the quantum efficiency of excitation energy capture by open PS II traps - _II the quantum efficiency for electron transport by PS II - _I the quantum efficiency (for electron transport) by PS I - % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGak0dh9WrFfpC0xh9vqqj-hEeeu0xXdbba9frFj0-OqFf% ea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs0dXdbPYxe9vr0-vr% 0-vqpWqaaeaabaGaciaacaqabeaadaqaaqaaaOqaaiabeA8aMnaaBa% aaleaacaWGdbGaam4tamaaBaaameaacaaIYaaaleqaaaqabaaaaa!3BD3!\[\phi _{CO_2 } \] the quantum yield for CO₂ fixation (obtained as the gross rate of CO₂ fixation divided by the irradiance) - % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGak0dh9WrFfpC0xh9vqqj-hEeeu0xXdbba9frFj0-OqFf% ea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs0dXdbPYxe9vr0-vr% 0-vqpWqaaeaabaGaciaacaqabeaadaqaaqaaaOqaaiabgs5aenaaBa% aaleaacqaH8oqBdaWgaaadbaGaamisamaaCaaabeqaaiabgUcaRaaa% aeqaaaWcbeaaaaa!3CB0!\[\Delta _{\mu _{H^ + } } \] trans-thylakoid proton potential difference - PAQF photosynthetically active quantum flux     

The use of 1JCαHα coupling constants as a probe for protein backbone conformation

Summary Simple pseudo-3D modifications to the constant-time HSQC and HCACO experiments are described that allow accurate (±0.5 Hz) measurement of one bond J_CH coupling constants in proteins that are uniformly enriched with ¹³C. An empirical ,-surface is calculated which describes the deviation of ¹J_CH from its random coil value, using 203 ¹J_CH values measured for residues in the proteins calmodulin, staphylococcal nuclease, and basic pancreatic trypsin inhibitor, for which and are know with good precision from previous X-ray crystallographic studies. Residues in -helical conformation exhibit positive deviations of 4–5 Hz, whereas deviations in -sheet are small and, on average, slightly negative. Data indicate that ¹J_CH depends primarily on , and that ¹J_CH may be useful as a qualitative probe for secondary structure. Comparison of ¹J_CH coupling constants measured in free calmodulin and in its complex with a 26-aminoacid peptide fragment of myosin light-chain kinase confirm that the calmodulin secondary structure is retained upon complexation but that disruption of the middle part of the central helix is even more extensive than in free calmodulin. Supplementary material available from the authors: One table listing 352 ¹J_CH and ¹J-values, together with ,-values for 203 residues of known conformation. Two figures showing (a) a Ramachandran plot of the ,-values of 203 residues used in deriving ¹J(,), and (b) the r.m.s.d. ¹J(,) distribution.     

Derivation of 13C chemical shift surfaces for the anomeric carbons of oligosaccharides and glycopeptides using ab initio methodology

The dependence between the anomeric carbon chemical shift and the glycosidic bond , dihedral angles in oligosaccharide and glycopeptide model compounds was studied by Gauge-Including Atomic Orbital (GIAO) ab initio calculations. Complete chemical shift surfaces versus and for d-Glcp-d-Glcp disaccharides with (11), (12), (13), and (14) linkages in both - and -configurations were computed using a 3-21G basis set, and scaled to reference results from calculations at the 6-311G^** level of theory. Similar surfaces were obtained for GlcNAcThr and GlcNAcSer model glycopeptides in - and -configurations, using in this case different conformations for the peptide moiety. The results obtained for both families of model compounds are discussed. We also present the determination of empirical formulas of the form ¹³C=f(,) obtained by fitting the raw ab initio data to trigonometric series expansions suitable for use in molecular mechanics and dynamics simulations. Our investigations are consistent with experimental observations and earlier calculations performed on smaller glycosidic bond models, and show the applicability of chemical shift surfaces in the study of the conformational behavior of oligosaccharides and glycopeptides.     

Holling's “hungry mantid” model for the invertebrate functional response considered as a Markov process. Part II: Negligible handling time

In this paper we analyse a stochastic model for invertebrate predation taking account of the predator's satiation. This model approximates Holling's hungry mantid model when handling time is negligible (see Part I). For this model we derive equations from which we can calculate the functional response and the variance of the total catch. Moreover we study a number of approximations which can be used to calculate these quantities in practical cases in a relatively simple manner.List of Notation a rate constant of digestion - b maximum of rate constant of prey encounter in the mantid - c satiation threshold for search - c satiation threshold for pursuit in the mantid - c _i (w^1/2(N- N)ⁱ) - expectation operator - f rate of change of satiation during search - F functional response: mean number of prey eaten per unit of time - g rate constant of prey capture - h probability generating function of N conditional on S = s times p - H probability generating function of N - m_i ¹ - n, N number of prey caught - p probability density of S - p_n simultaneous probability (density) of N and S - q probability of strike success - r dummy variable in generating function - s, S satiation - T _s search time - T _d digestion time - v asymptotic rate of increase of var v - V asymptotic rate of increase of var N - w weight of edible part of prey - W standard Wiener process - x prey density - z (N{S = s}-N)p - rate constant of prey escape time maximum pursuit time - (v{S = + w ^1/2}-v) - present time as a fraction of the time from the start to the end of the experiment - hazard rate of T _s - mean time between (downward) passages of S through c - v w_–1/2(N-) - edible prey biomass density - probability density of , number pi - parameter of Weibull distribution of T _s = (1/2acx(-g(c)))_1/2 - w_–1/2(S -) - satiation in the guzzler approximation: solution to d/dt = f() + g(), (0)=S(0). - biomass functional response: wF - total biomass catch in the guzzler approximation: solution to d/dt = g(), (0) = 0     

Modeling Virus Adsorption in Batch and Column Experiments

Experiments with batch suspensions, recirculating columns and flow-through columns have been carried out involving a sandy soil and five bacteriophages: MS2, PRD1, X174, Q and PM2. In batch and recirculating column experiments, attachment and detachment rate coefficients were determined by fitting a two-parameter (attachment and detachment) model. In general, attachment and detachment rate coefficients were not found to be significantly different between the two kinds of experiments. There was one exception, however: MS2 appeared to detach faster in the presence of strong advective flow. In the case of flow-through column experiments, it is shown that a two-site model, with adsorption to equilibrium and kinetic sites, fits the breakthrough curves of all the phages, except PM2, satisfactorily. A one-site kinetic model was found to be appropriate for phage PM2. A small proportion of bacteriophages MS2, PRD1, and Q adsorbed to equilibrium sites, whereas a large proportion of X174 adsorbed to equilibrium sites. Such a distinction between adsorption to equilibrium and kinetic sites cannot be made in the case of batch or recirculating column experiments. Kinetic attachment rate coefficients were found to be significantly higher for the bacteriophages with presumably stronger negative charge. This may be ascribed to the presence of multivalent cations. Under these conditions, bacteriophage X174 appears to behave more conservatively than more negatively charged viruses, and may then be a better choice as a relatively conservative tracer for virus transport through the subsurface.     

The growth of Saccharomyces cerevisiae CBS 426 on mixtures of glucose and ethanol: a model

Saccharomyces cerevisiae CBS 426 was grown in continuous culture in a defined medium with a mixture of glucose and ethanol as carbon source. Growth on ethanol as the sole carbon source was only possible after the addition of a small amount of glutamic acid. The flows of glucose, ethanol, oxygen, carbon dioxide and biomass to and from the system were measured and a model for the growth of the yeast on the carbon sources constructed. The model is shown to allow independent estimation of Y_ATP and P/O. Y_ATP is not independent of the substrate used, but the amount of ATP used in the production of biomass from the monomers is approximately the same for growth on ethanol and on glucose.Nomenclature C chemical state vector - C_i component of the chemical state vector (C-mol) - C_x biomass present in the system (C-mol biomass) - H₂ reduction equivalents (NAD(P)H + H⁺ and FADH₂) - k the amount of ATP required in the production of 1 C-mol of biomass from the monomers (mol ATP/C-mol biomass) - m_ATP maintenance requirement for ATP (mol ATP/C-mol biomass·h) - P/O (=), efficiency of the oxidative phosphorylation (mol ATP/atom O) - r vector of reaction rates - r_i component of the vector of reaction rates (C-mol/h) - r_ATP rate of ATP production (mol ATP/h) - r_x rate of biomass production (C-mol biomass/h) - Y_ATP Y_ATP growth yield on ATP (C-mol biomass/mol ATP) - (Y_ATP)_max maximum growth yield on ATP - stoichiometry matrix - P/O - vector of the flows to the system - _s flow of glucose to the system (C-mol glucose/h) - _o flow of oxygen to the system (mol O₂/h) - _c flow of carbon dioxide to the system (mol CO₂/h) - _x flow of biomass to the system (C-mol biomass/h) - _e flow of ethanol to the system (C-mol ethanol/h) - _w flow of water produced during metabolism (mol H₂O/h)     

The occurrence of HT-2 toxin and other trichothecenes in Norwegian cereals

A total of 449 grain samples, 102 barley, 169 wheat and 178 oat samples were collected from different regions of Norway from 1996–1998 crops, mainly from grain loads and silos. The samples were analysed for type A and B trichothecenes, the largest groups of mycotoxins produced by the Fusarium species, by gas chromatography with mass spectrometric detection (GC-MS). Factors affecting the presence of the different trichothecenes are discussed. Deoxynivalenol (DON) and HT-2 toxin were the trichothecenes most frequently detected, followed by T-2 toxin, nivalenol, and scirpentriol, scirpentriol being detected only in seven samples (>20 g/kg).Oats were the grain species most heavily contaminated with an incidence(% >20 g/kg) and mean concentration of positive samples of 70%(115 g/kg) for HT-2 toxin, 30% (60 g/kg) for T-2 toxin, 57%(104 g/kg) for DON, and 10% (56 g/kg) for nivalenol. The corresponding values for barley were 22% (73 g/kg), 5% (85 g/kg),17% (155 g/kg) and 6% (30 g/kg), and for wheat 1.2% (20 g/kg),0.6% (20 g/kg), 14% (53 g/kg) and 0% for HT-2, T-2, DON and nivalenol, respectively. Norwegian oats were found to contain HT-2 and T-2 toxin in concentrations that might be at threat to human health for high consumers of oats. The amount of DON was significantly lower than in the crop from previous years.This revised version was published online in October 2005 with corrections to the Cover Date.     

Exact solutions for chemical bond orientations from residual dipolar couplings

New methods for determining chemical structures from residual dipolar couplings are presented. The fundamental dipolar coupling equation is converted to an elliptical equation in the principal alignment frame. This elliptical equation is then combined with other angular or dipolar coupling constraints to form simple polynomial equations that define discrete solutions for the unit vector(s). The methods are illustrated with residual dipolar coupling data on ubiquitin taken in a single anisotropic medium. The protein backbone is divided into its rigid groups (namely, its peptide planes and C frames), which may be solved for independently. A simple procedure for recombining these independent solutions results in backbone dihedral angles and that resemble those of the known native structure. Subsequent refinement of these - angles by the ROSETTA program produces a structure of ubiquitin that agrees with the known native structure to 1.1 Å C rmsd.     

Correlation between 15N NMR chemical shifts in proteins and secondary structure

Summary An empirical correlation between the peptide ¹⁵N chemical shift, ¹⁵N_i, and the backbone torsion angles _i, _i–1 is reported. By using two-dimensional shielding surfaces (_i1–1), it is possible in many cases to make reasonably accurate predictions of ¹⁵N chemical shifts for a given structure. On average, the rms error between experiment and prediction is about 3.5 ppm. Results for threonine, valine and isoleucine are worse (4.8 ppm), due presumably to ₁-distribution/-gauche effects. The rms errors for the other amino acids are 3 ppm, for a typical maximal chemical shift range of 15–20 ppm. Thus, there is a significant correlation between ¹⁵N chemical shift and secondary structure.     

Comparison of laboratory- and field-derived soil water retention curves for a fine sand soil using tensiometric,resistance and capacitance methods

The approximate range from 100 to 50% of plant-available water in Apopka fine sand (loamy, siliceous, hyperthermic Grossarenic Paleudult) is 0.08–0.04 cm³ cm^–3 soil water content () or –5 to –15 kPa of soil water matric potential (). This narrow range of plant-available soil water is extremely dry for most soil water sensors. Knowledge of the soil water retention curves for these soils is important for effective irrigation of crops in fine sand soils of subtropical and tropical regions of the world. The primary objective of this study was to compare sandy soil water retention curves in the field as measured by tensiometer and resistance block values and capacitance sensor . The second objective was to compare these curves to one developed on a Florida fine sand soil using a pressure plate apparatus. Tensiometer and resistance block values were compared to values from capacitance sensors calibrated gravimetrically. The effective range of both tensiometers and resistance sensors in fine sand soils is between –5 and –20 kPa . Soil water potential values for both sensors were within 2 kPa of the mean for each sensor. Change in was similar over the range of 0.04–0.08 cm³ cm^–3 . Curves for the two sensors were different by 4 kPa at 0.04 cm³ cm^–3. The relationship between and were similar at 10–20, 20–30 and 40–50 cm depths. This was not true for a laboratory determined soil water retention curve for the same soil type. These differences are significant in soils with very low water holding capacities. Differences between laboratory- and field-determined retention curves could be due to a combination of entrapped air in the field soil and/or alteration in bulk density in the laboratory samples.