Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

Background  

The Ambiguous Restraints for Iterative Assignment (ARIA) approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list.     

Relationship between nuclear magnetic resonance chemical shift and protein secondary structure

An analysis of the 1H nuclear magnetic resonance chemical shift assignments and secondary structure designations for over 70 proteins has revealed some very strong and unexpected relationships. Similar studies, performed on smaller databases, for 13C and 15N chemical shifts reveal equally strong correlations to protein secondary structure. Among the more interesting results to emerge from this work is the finding that all 20 naturally occurring amino acids experience a mean alpha-1H upfield shift of 0.39 parts per million (from the random coil value) when placed in a helical configuration. In a like manner, the alpha-1H chemical shift is found to move downfield by an average of 0.37 parts per million when the residue is placed in a beta-strand or extended configuration. Similar changes are also found for amide 1H, carbonyl 13C, alpha-13C and amide 15N chemical shifts. Other relationships between chemical shift and protein conformation are also uncovered; in particular, a correlation between helix dipole effects and amide proton chemical shifts as well as a relationship between alpha-proton chemical shifts and main-chain flexibility. Additionally, useful relationships between alpha-proton chemical shifts and backbone dihedral angles as well as correlations between amide proton chemical shifts and hydrogen bond effects are demonstrated.     

A novel protocol based on HN(C)N for rapid resonance assignment in ((15)N, (13)C) labeled proteins: implications to structural genomics

A novel protocol, based on the HN(C)N experiment, has been developed for rapid assignment of backbone H(N) and (15)N resonances in ((15)N, (13)C) labeled proteins. The protocol exploits the directly observable (15)N and H(N) sequential correlations and the distinctive peak patterns in the different planes of the HN(C)N spectrum, depending upon the nature of the residues displaying the correlations. Glycines and prolines, which are responsible for the distinctive features, provide many check/start points for the sequential walks. These features enhance the speed of data analysis and render side chain assignments less crucial for the success of the assignments. The application of the protocol has been demonstrated with FK506 binding protein (FKBP, molecular mass 12 kDa).     

Differentiation in sex investment by clones and populations of Daphnia

Dormancy is an ecological strategy by which organisms avoid stressful environments, but it also can have genetic consequences. Many facultative parthenogens shift from asexual to sexual reproduction to enter dormancy. Hence, conditions that favour dormancy are predicted to select for more sex, which should increase clonal diversity. We examined lake populations of Daphnia that face different ecological risks to remaining active year‐round, and quantified the extent to which they have differentiated in their investment in dormancy and sex. There was substantial genetic variation among populations and clones for sex induction and production of dormant eggs, and striking evidence of gender specialization. We also observed a positive association between the magnitudes of population‐level investment in dormancy and of variance among clones in sex induction. These results document an ecological gradient in dormancy that is manifest as a genetic gradient in clonal variation for the propensity to engage in sex.     

Offspring sex ratio variation in relation to brood size and mortality in a promiscuous species: the Aquatic Warbler Acrocephalus paludicola

We analyse nestling sex ratio variation in the Aquatic Warbler Acrocephalus paludicola to test for predictions from sex allocation theory that the brood sex ratio is close to parity. We also tested Fiala's (1980) prediction that there is no difference in sex ratio between broods affected and not affected by mortality, and whether a shift in primary sex ratios or simple differential mortality by sex underlies that difference. Furthermore, we explore additional analytical possibilities for inferring proximate mechanisms through simulation modelling. In the Aquatic Warbler, which is promiscuous, the overall sex ratio determined by molecular sexing of nestlings at 8–11 days of age did not deviate significantly from parity (proportion of females 0.509), nor did we find any predictive effect of brood size, maternal body mass, fat condition, wing and bill length, laying date, mean daily temperature, and multiple-male mating. However, extensive simulation suggested that the whole pattern of sex ratio variation is unlikely to arise purely by chance: (1) there is a diverging sex ratio between complete and partial broods, (2) large broods tended to be female-biased and small broods male-biased, and (3) low ambient temperature prior to the laying period seemed to increase the proportion of female offspring in complete broods. We conclude that most variation in nestling sex ratio is non-adaptive in nature, and results from variation in female nestlings mortality dependent on brood size and sex ratio.     

Prospects for resonance assignments in multidimensional solid-state NMR spectra of uniformly labeled proteins

Summary The feasibility of assigning the backbone ¹⁵N and ¹³C NMR chemical shifts in multidimensional magic angle spinning NMR spectra of uniformly isotopically labeled proteins and peptides in unoriented solid samples is assessed by means of numerical simulations. The goal of these simulations is to examine how the upper limit on the size of a peptide for which unique assignments can be made depends on the spectral resolution, i.e., the NMR line widths. Sets of simulated three-dimensional chemical shift correlation spectra for artificial peptides of varying length are constructed from published liquid-state NMR chemical shift data for ubiquitin, a well-characterized soluble protein. Resonance assignments consistent with these spectra to within the assumed spectral resolution are found by a numerical search algorithm. The dependence of the number of consistent assignments on the assumed spectral resolution and on the length of the peptide is reported. If only three-dimensional chemical shift correlation data for backbone ¹⁵N and ¹³C nuclei are used, and no residue-specific chemical shift information, information from amino acid side-chain signals, and proton chemical shift information are available, a spectral resolution of 1 ppm or less is generally required for a unique assignment of backbone chemical shifts for a peptide of 30 amino acid residues.     

The effects of temperature, body mass and feeding on metabolic rate in the tsetse fly Glossina morsitans centralis

Abstract.  Metabolic rate variation with temperature, body mass, gender and feeding status is documented for Glossina morsitans centralis . Metabolic rate [mean ± SE; VCO₂= 19.78 ± 3.11 μL CO₂ h⁻¹ in males (mean mass = 22.72 ± 1.41 mg) and 27.34 ± 3.86 μL CO₂ h⁻¹ in females (mean mass = 29.28 ± 1.96 mg) at 24 °C in fasted individuals] is strongly influenced by temperature, body mass and feeding status, but not by gender once the effects of body mass have been accounted for. A significant interaction between gender and feeding status is seen, similar to patterns of metabolic rate variation documented in Glossina morsitans morsitans . Synthesis of metabolic rate-temperature relationships in G. m. centralis , G. m. morsitans and Glossina pallidipes indicate that biting frequency as well as mortality risks associated with foraging will probably increase with temperature as a consequence of increasing metabolic demands, although there is little evidence for variation among species at present. Furthermore, metabolic rate–body mass relationships appear to be similarly invariant among these species. These data provide important physiological information for bottom-up modelling of tsetse fly population dynamics.     

Measures for the assessment of fuzzy predictions of protein secondary structure

Many of the recent secondary structure prediction methods incorporate the idea of fuzzy set theory, where instead of assigning a definite secondary structure to a query residue, probability for the residue being in each of the conformational states is estimated. Moreover, continuous assignment of conformational states to the experimentally observed protein structures can be performed in order to reflect inherent flexibility. Although various measures have been developed for evaluating performances of secondary structure prediction methods, they depend only on the most probable secondary structures. They do not assess the accuracy of the probabilities produced by fuzzy prediction methods, and they cannot incorporate information contained in continuous assignments of conformational states to observed structures. Three important measures for evaluating performance of a secondary structure prediction algorithm, Q score, Segment OVerlap (SOV) measure, and the k-state correlation coefficient (Corr), are deformed into fuzzy measures F score, Fuzzy OVerlap (FOV) measure, and the fuzzy correlation coefficient (Forr), so that the new measures not only assess probabilistic outputs of fuzzy prediction methods, but also incorporate information from continuous assignments of secondary structure. As an example of application, prediction results of four fuzzy secondary structure prediction methods, PSIPRED, PROFking, SABLE, and PREDICT, are assessed using the new fuzzy measures.     

Sex-specific differences in body condition indices and seasonal mass loss in Tufted Puffins

ABSTRACT.   Reduced prey availability can affect the growth and survival of nestling seabirds. However, few studies have demonstrated similar effects on indices of adult body condition. We examined body condition and seasonal mass loss of breeding adult male and female Tufted Puffins ( Fratercula cirrhata ) at Chiniak Bay, Kodiak Island, Alaska, in 2004–2005. We determined sex using genetic analysis, developed a discriminant function to determine sex using morphometric measurements, and examined the body condition of adult males and females relative to the growth rates of their offspring. We found that morphological measurements were only moderately useful for sexing Tufted Puffins, with 74% of adults ( N = 176) correctly classified. We also found that the relationship between adult body mass and size differed between sexes and conclude that body condition indices must be calculated separately for each sex to avoid inter- and intrasexual bias. Body condition of male and female Tufted Puffins declined during the chick-rearing period. However, body condition of females did not differ between years, whereas male condition declined to a greater degree during 2004 when the mass of young at fledging was significantly lower. Although these results suggest that adult male Tufted Puffins sacrifice their own body condition in years of diminished nestling growth and females do not, reasons for this apparent intersexual difference in reproductive strategies remain unclear.     

NMR: prediction of protein flexibility

We present a protocol for predicting protein flexibility from NMR chemical shifts. The protocol consists of (i) ensuring that the chemical shift assignments are correctly referenced or, if not, performing a reference correction using information derived from the chemical shift index, (ii) calculating the random coil index (RCI), and (iii) predicting the expected root mean square fluctuations (RMSFs) and order parameters (S2) of the protein from the RCI. The key advantages of this protocol over existing methods for studying protein dynamics are that (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone assignments. When chemical shift assignments are available, protein flexibility parameters, such as S2 and RMSF, can be calculated within 1-2 h using a spreadsheet program.     

Patterns of Carbon, Nitrogen and Phosphorus Dynamics in Decomposing Foliar Litter in Canadian Forests

We examined the patterns of nitrogen (N) and phosphorus (P) gain, retention or loss in ten foliar tissues in a litterbag experiment over 6 years at 18 upland forest sites in Canada, ranging from subarctic to cool temperate. N was usually retained in the decomposing litter until about 50% of the original C remained. The peak N content in the litter was observed at between 72 and 99% of the original C remaining, with C:N mass quotients between 37 and 71 (mean 55). The rate of N release from the litters was not related to the original N concentration, which may be associated with the generally narrow range (0.59–1.28% N) in the litters. P was immediately lost from all litters, except beech leaves, with critical litter C:P mass quotients for P release being in the range 700–900. The rate of P loss was inversely correlated with the original litter P concentration, which ranged from 0.02 to 0.13%. The soil underlying the litterbags influenced the pattern of N and P dynamics in the litters; there were weak correlations between the N and P remaining at 60% C remaining in the litters and the C:N and C:P quotients of the surface layer of the soil. There was a trend for higher N and P retention in the litter at sites with lower soil C:N and N:P quotients, respectively. Although there was a large variation in C:N, C:P and N:P quotients in the original litters (29–83, 369–2122 and 5–26, respectively), and some variation in the retention or loss of N and P in the early stages of decomposition, litters converged on C:N, C:P and N:P quotients of 30, 450 and 16, when the C remaining fell below 30%. These quotients are similar to that found in the surface organic matter of these ecosystems.     

Determinants of fat oxidation during exercise in healthy men and women: a cross-sectional study.

The aim of the present study was to establish fat oxidation rates over a range of exercise intensities in a large group of healthy men and women. It was hypothesised that exercise intensity is of primary importance to the regulation of fat oxidation and that gender, body composition, physical activity level, and training status are secondary and can explain part of the observed interindividual variation. For this purpose, 300 healthy men and women (157 men and 143 women) performed an incremental exercise test to exhaustion on a treadmill [adapted from a previous protocol (Achten J, Venables MC, and Jeukendrup AE. Metabolism 52: 747-752, 2003)]. Substrate oxidation was determined using indirect calorimetry. For each individual, maximal fat oxidation (MFO) and the intensity at which MFO occurred (Fat(max)) were determined. On average, MFO was 7.8 +/- 0.13 mg.kg fat-free mass (FFM)(-1).min(-1) and occurred at 48.3 +/- 0.9% maximal oxygen uptake (Vo(2 max)), equivalent to 61.5 +/- 0.6% maximal heart rate. MFO (7.4 +/- 0.2 vs. 8.3 +/- 0.2 mg.kg.FFM(-1).min(-1); P < 0.01) and Fat(max) (45 +/- 1 vs. 52 +/- 1% Vo(2 max); P < 0.01) were significantly lower in men compared with women. When corrected for FFM, MFO was predicted by physical activity (self-reported physical activity level), Vo(2 max), and gender (R(2) = 0.12) but not with fat mass. Men compared with women had lower rates of fat oxidation and an earlier shift to using carbohydrate as the dominant fuel. Physical activity, Vo(2 max), and gender explained only 12% of the interindividual variation in MFO during exercise, whereas body fatness was not a predictor. The interindividual variation in fat oxidation remains largely unexplained.     

TEDOR with adiabatic inversion pulses: Resonance assignments of <Superscript>13</Superscript>C/<Superscript>15</Superscript>N labelled RNAs

We have examined via numerical simulations the performance characteristics of different 15N RF pulse schemes employed in the transferred echo double resonance (TEDOR) experimental protocol for generating 13C-15N dipolar chemical shift correlation spectra of isotopically labelled biological systems at moderate MAS frequencies (omega(r) approximately 10 kHz). With an 15N field strength of approximately 30-35 kHz that is typically available in 5 mm triple resonance MAS NMR probes, it is shown that a robust TEDOR sequence with significant tolerance to experimental imperfections sa as H1 inhomogeneity and resonance offsets can be effectively implemented using adiabatic heteronuclear dipolar recoupling pulse schemes. TEDOR-based 15N-13C and 15N-13C-13C chemical shift correlation experiments were carried out for obtaining 13C and 15N resonance assignments of an RNA composed of 97 (CUG) repeats which has been implicated in the neuromuscular disease myotonic dystrophy.     

Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala

The genus Abies has a complex history in southern México and Guatemala. In this region, four closely related species, Abies flinckii , A. guatemalensis , A. hickelii , and A. religiosa , are distributed in fragmented and isolated montane populations. Range-wide genetic variation was investigated across species using cytoplasmic DNA markers with contrasted inheritance. Variation at two maternally inherited mitochondrial DNA markers was low. All species shared two of the nine mitotypes detected, while the remaining seven mitochondrial DNA types were restricted to a few isolated stands. Mitochondrial genetic differentiation across taxa was high ( G _ST = 0.933), it was not related to the taxonomic identity ( amova ; P  > 0.05) of the populations, and it was not phylogeographically structured ( G _ST ≈  N _ST). In contrast, variation at three paternally inherited chloroplast DNA microsatellites was high. Chloroplast genetic differentiation was lower ( G _ST = 0.402; R _ST = 0.547) than for mitochondrial DNA, but it was significantly related to taxonomy ( amova ; P  < 0.001), and exhibited a significant phylogeographical structure ( G _ST <  R _ST). Different analyses of population structure indicated that A. flinckii was the most divergent taxon, while the remaining three species formed a relatively homogeneous group. However, a small number of the populations of these three taxa, all located at the limits of their respective ranges or in the Transverse Volcanic Belt, diverged from this main cluster. These trends suggest that the Mesoamerican Abies share a recent common ancestor and that their divergence and speciation is mainly driven by genetic drift and isolation during the warm interglacial periods.     

Relationships between bird morphology and prey selection in two sympatric Great Cormorant Phalacrocorax carbo subspecies during winter

Variation in bird morphology (notably sex size dimorphism) has been suggested to contribute to differences in food use between individuals. We explore the hypothesis of food partitioning (diet overlap and prey size selection) in two sympatric subspecies of the Great Cormorant Phalacrocorax carbo with respect to bird morphology (subspecies and sex) in inland French waters. These areas represent a recent and increasing contact zone used as a common non-territorial winter feeding area by the continental P. c. sinensis and the marine P. c. carbo subspecies. A high dietary overlap between subspecies and sexes was found at the major sites studied. Prey size selection was found to be site-specific and generally related to a gradient of structural size and body mass (male P. c. carbo  > male P. c. sinensis  > female P. c. carbo  > female P. c. sinensis ). With respect to bird morphology, differences in prey size consumed by Great Cormorants were more pronounced between sexes in freshwater habitats than between subspecies. This was reinforced by the fact that P. c. carbo birds entering inland areas were smaller than birds on the coast. These results also suggest that bird morphology is an important determinant of dietary differences. Our study demonstrated that P. c. carbo is an efficient generalist forager in continental areas, and food partitioning in type and size of prey between the two subspecies is low.     

A RAPID ASSESSMENT APPROACH FOR EVALUATING SILVER CARP GENDER

Silver carp Hypophthalmichthys molitrix were introduced into the U.S. to control water quality in aquaculture ponds. From this point of origin, silver carp escaped into nearby rivers through multiple flood events. Because of their documented negative effects on native biota, silver carp have been labeled as problematic. Therefore, evaluating the biology and ecology of these non-indigenous species is critical. Multiple parameters are needed to evaluate silver carp populations(length, weight, age, and sex). Furthermore, developing methods for rapidly acquiring these data are needed. In relation to sex determination, sexual dimorphism was observed where males exhibit distinct pectoral fin ray features. Specifically, males have pronounced ridges or a "rough patch" on the dorsal surface of pectoral fins. Therefore, to test if this was an applicable way of determining silver carp gender; silver carp were collected from Midwestern U.S. rivers(N=2015) in the fall of 2011(N=870), spring of 2012(N=645), winter of 2013—2014(N=202) and summer2015(N=323) via electrofishing. For each silver carp collected, presence(e.g., rough patch) or absence(e.g.,smooth) of pronounced ridges on the top side of the pectoral fins was recorded, and an incision was made in the body cavity to identify gender. Based on the results of our evaluation, gender was correctly identified over99% of the time(2006 out of 2015) based on the pectoral fin dimorphism. In the samples taken in the winter of 2013—2014 and summer of 2015, accuracy for silver carp shorter than 300 mm and longer than 800 mm was 53.7%(19 out of 41) while accuracy for silver carp between 300 mm and 800 mm total length was 98.9%(289 out of 292). This study provides a rapid assessment approach for evaluating silver carp gender.     

Communication of gender from human breath odors: Relationship to perceived intensity and pleasantness

During five consecutive daily test sessions, 10 men and women rated the relative intensity and pleasantness of breath odors from 14 males and 19 females on a no-oral-hygiene regimen. In addition, the likely gender of the donor of each odor was also estimated. The breath odors of males were rated, on the average, as more intense and less pleasant than the breath odors of females. Women consistently gave lower pleasantness ratings to the odors than did men. Both the male and female judges assigned the breath odors to the correct gender classes at a frequency unlikely due to chance, although the females were more accurate in this regard. An inverse relation between breath odor intensity and pleasantness was noted. Systematic changes in the rated intensity and pleasantness of the odors were present across the 5 days of the study period. These data suggest that differences exist between the breath odors of men and women, and that humans, like many other mammals, may be capable of assessing gender from oral odors. However, such assignments conceivably reflect the strategy of assigning stronger and less pleasant odors to the male category, and weaker and less unpleasant odors to the female category, regardless of the true sex of the odor donor.     

The Roles of Sex,Mass and Individual Specialisation in Partitioning Foraging-Depth Niches of a Pursuit-Diving Predator

Intra-specific foraging niche partitioning can arise due to gender differences or individual specialisation in behaviour or prey selection. These may in turn be related to sexual size dimorphism or individual variation in body size through allometry. These variables are often inter-related and challenging to separate statistically. We present a case study in which the effects of sex, body mass and individual specialisation on the dive depths of the South Georgia shag on Bird Island, South Georgia are investigated simultaneously using a linear mixed model. The nested random effects of trip within individual explained a highly significant amount of the variance. The effects of sex and body mass were both significant independently but could not be separated statistically owing to them being strongly interrelated. Variance components analysis revealed that 45.5% of the variation occurred among individuals, 22.6% among trips and 31.8% among Dives, while R² approximations showed gender explained 31.4% and body mass 55.9% of the variation among individuals. Male dive depths were more variable than those of females at the levels of individual, trip and dive. The effect of body mass on individual dive depths was only marginally significant within sexes. The percentage of individual variation in dive depths explained by mass was trivial in males (0.8%) but substantial in females (24.1%), suggesting that differences in dive depths among males was largely due to them adopting different behavioural strategies whereas in females allometry played an additional role. Niche partitioning in the study population therefore appears to be achieved through the interactive effects of individual specialisation and gender upon vertical foraging patch selection, and has the potential to interact in complex ways with other axes of the niche hypervolume such as foraging locations, timing of foraging and diet.     

Seed fitness of hermaphrodites in areas with females and anther smut disease: Silene acaulis and Microbotryum violaceum

Sex-dependent infection rates could change the effective sex ratio of a population. Here, I tested whether females and hermaphrodites of Silene acaulis were equally likely to be infected by Microbotryum violaceum, a fungus that sterilizes the host, and whether sex allocation in hermaphrodites differed between low and high disease plots. Sex ratios of healthy and diseased plants were estimated in five natural plots. Fitness gained through seed production was estimated by measuring seed quantity and quality for each sex morph in eight plots for 2 yr; four plots had 1-5% disease frequency and four plots had 18-25% disease frequency. Sex ratios of healthy and diseased plants did not differ in five plots. The proportion of fitness hermaphrodites gained through ovules varied from 25 to 48%, indicating that this population is near the cosexual end of gynodioecy. Variation in functional gender of hermaphrodites was not explained by sex-dependent infection rates. Spatial heterogeneity in resources and microclimate seems to be important in explaining both disease frequency and variation in seed production by females and hermaphrodites.     

De novo protein structure generation from incomplete chemical shift assignments

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.