Estimation of uncertainties in X-ray refinement results by use of perturbed structures

The uncertainties in the refined parameters for a 1.5-A X-ray structure of carbon-monoxy (FeII) myoglobin are estimated by combining energy minimization with least-squares refinement against the X-ray data. The energy minimizations, done without reference to the X-ray data, provide perturbed structures which are used to restart conventional X-ray refinement. The resulting refined structures have the same, or better, R-factor and stereochemical parameters as the original X-ray structure, but deviate from it by 0.13 A rms for the backbone atoms and 0.31 A rms for the sidechain atoms. Atoms interacting with a disordered sidechain, Arg 45 CD3, are observed to have larger positional uncertainties. The uncertainty in the B-factors, within the isotropic harmonic motion approximation, is estimated to be 15%. The resulting X-ray structures are more consistent with the energy parameters used in simulations.     

Phylogenetic systematics of the nymphaeales

A cladistic analysis was applied to reveal the phylogenetic relationships among the Nymphaeales. Seventeen out of twenty three characters in gross morphology, anatomy and palynology were analyzed, for their evolutionary polarities. From the results of the present analysis, the phylogenetic status of each genus and their relationships were clarified: 1)Nelumbo is a distinct taxon and is presumed to have originated from an ancestral stock of the Nymphaeales; 2)Ceratophyllum has a close phylogenetic relationship withCabomba; and 3) in the Nymphaeaceaesensu stricto, Nuphar and the remaining genral constitute a monophyletic group. A conclusion obtained from the present analysis was that the following three families should be recognized in the Nymphaeales; Nelumbonaceae Nymphaeaceae, and Ceratophyllaceae. The generaBrasenia andCabomba are traditionally classified in the Nymphaeaceae or in the independent family Cabombaceae. However, they should be included in the family Ceratophyllaceae.     

Rhodobacter capsulatus MT113: A single mutation results in the absence of c-type cytochromes and in the absence of the cytochrome bc1 complex

MT113, a nonphotosynthetic mutant of Rhodobacter capsulatus previously characterized as lacking cytochrome c₂ is shown to lack also cytochrome c₁, the Rieske iron-sulfur cluster and the antimycin sensitive semiquinone Q_c, all components of the cytochrome bc₁ complex. Although MT113 contained b-type cytochromes and other iron-sulfur clusters at nearly wild-type level, it lacks c-type cytochromes. Based on antibody detection, c₂ apoprotein was absent in MT113, however the apoproteins corresponding to the cytochromes b and c₁ and the Rieske iron-sulfur cluster were present in reduced amounts. Genetic analysis indicated that the lesion appears to be due to a single mutation which is not localized in the structural genes of cytochrome c₂ or the bc₁ complex. These data taken together suggest that the pleiotropic mutation in MT113 might be related to the biosynthesis of c-type cytochromes.     

Variation in length and age at sexual maturity of Atlantic groundfish: a reply

Synopsis The assertion has been made by Halliday (1987) that trends in size and age at maturity of Atlantic groundfish published by Beacham (1983a, b, c, d, e, f) are artifacts induced by errors in determining the sex of an individual, distinguishing between immature and mature fish, sampling fish outside of the regular spawning season, and by nonrandom sampling of the population. In particular, Halliday asserts that for the Atlantic argentine,Argentina silus analysis, the conclusions of Beacham (1983a) that: (1) median length at sexual maturity declined over time; and (2) males matured at older ages than did females are invalid owing to biases in both sampling and analysis. In fact, if some of the biases indicated by Halliday were significant, then the decline in median length at sexual maturity is enhanced and the conclusions of Beacham (1983a) reinforced. Size and age at sexual maturity are dynamic characters in many vertebrate populations, and the fact that they should change for Atlantic groundfish should not be surprising given variable exploitation patterns in the fisheries since 1960.     

水翁花蕾和水翁叶精油的化学成分研究

水翁的花营和鲜叶经水蒸汽蒸馏得到一种淡黄色的精油,前者出油率为0.18％。后者为0.08％。我们应用毛细管气相色谱,气相色谱/质谱联用,红外光谱和紫外光谱等方法,对两种精油进行化学分成分析,分别鉴定出35个和27个已知化学成分。两者相同的化学成分有:β-罗勒烯(Z)、β-罗勒烯(E)、α-蒎烯、β-蒎烯、月桂烯、小茴香烯、香叶醇、顺式-丁香烯、橙花叔醇等23个化学成分,分别占花营精油全油的90％和叶精油95％以上。     

Linkage analysis of the myosin heavy chain gene in Dictyostelium discoideum using a mutation generated by homologous recombination

Summary A mutation (mhcA1 in strain HMM) created by insertional gene inactivation was used to map the Dictyostelium discoideum myosin heavy chain gene (mhcA) to linkage group IV. Three phenotypic traits associated with this mutation (slow colony growth, inability of the mutant to develop past aggregation, and the presence of five to ten integrated vector copies) cosegregated as expected for the consequences of a single insertional event. This linkage was confirmed using a restriction fragment length polymorphism. The mhcA1 mutation was recessive to wild type and was nonallelic with mutations at the following loci on linkage group IV: aggJ, aggL, couH, minA, phgB and tsgB. This work demonstrates the ability to apply standard techniques developed for D. discoideum parasexual genetic analyses to mutants generated by transformation, which is of particular relevance to analysis of genes for which no classical mutations or restriction fragment length polymorphisms are available.     

Restriction analysis of lambda EMBL3 background recombinants: occurrence of lambda phages carrying a head to tail oriented left arm DNA sequence

Summary Eight representative recombinant background clones of λEMBL3 were analysed usingKpnI,BamHI,SalI,EcoRI andHindIII digestion. We found that λEMBL3 carries its own left arm in theBamHI cloning site. In this way, recombinant molecules were found to be generated which can grow onEscherichia coli strain NM539. In all cases analysed, the left arm DNA was inserted in a head to tail orientation. Seven clones carried a restoredBamHI site at thecos site-BamHI site connection. In the region where the inserted left arm and the right arm were ligated,BamHI cloning produces a large palindromic sequence consisting of two polylinkers. ThisBamHI site was incompletely cleaved in all cases analysed. We assume that a part of the λ DNA molecule in this region shows a cruciform structure prohibiting recognition or cleavage of this site by restriction endonucleaseBamHI.     

Comparison of population dynamics between slow- and fast-growing strains of the rotifer Brachionus calyciflorus pallas in continuous culture

Summary The population dynamics of a slow- and a fast-growing strain of the rotifer Brachionus calyciflorus are compared. Rotifers were grown in steady-states, at various specific growth rates (), in both two-stage chemostat and turbidostat cultures on the green alga Chlorella pyrenoidosa. Population variables, including specific ingestion (I), loss (L) and filtration (F) rates, yield (Y), production (P) and half-saturation coefficient of growth (K _g), were calculated using a growth model based on saturation kinetics. I, L, F and K _g were shown to be higher and Y and P lower for the fast-growing strain. Differences between the two strains with regard to these variables may represent tradeoffs associated with the faster potential growth rate. Steady-state relationships between these values and for the fast-growing strain, however, deviated from model predictions which suggest a possible shift from carbon to non-carbon growth limitation.     

How important is seed predation to recruitment in stable populations of long-lived perennials?

Summary The many evolutionary modifications to seed biology in response to seed predation do not necessarily imply that seed predators have an important impact on population recruitment. This is because competition between individual plants for rare safe sites can cause an oversupply of seeds so far as a population is concerned. The importance of seed losses to population recruitment at any point in time is related to the abundance of safe sites (Fig. 1): it is zero when safe sites are absent, negligible when safe sites are rare, and greatest when safe sites are numerous enough for recruitment to be limited by seed supply. Here I interpret the impact of severe seed losses on population recruitment in four species of long-lived perennials (Eucalyptus baxteri, Leptospermum juniperinum, Casuarina pusilla and L. myrsinoides) by considering these losses in terms of the overall seed dynamics of the populations. I focus on seed supply and seedling survival, as a measure of the current abundance of safe sites, and the maintenance of seed banks, as a measure of the ability of populations to exploit any future changes in safe site abundance. Insect seed predators destroyed about 95% of total seeds in each case. However, these losses do not necessarily have an important impact on population recruitment, because: (i) in most years recruitment appears to be limited by a rarity of safe sites, and not by seed supply (which was as high as 43 germinable seeds/m²/yr); and (ii) the losses did not prevent the establishment of large seed banks (ranging from >30 to >1000 viable seeds/m²) potentially capable of exploiting temporary conditions favourable for recruitment. In contrast to the situation with many annual plants, patterns of recruitment in stable populations of long-lived perennials are often extremely complex, and the significance of seed losses therefore difficult to determine.     

Using growth analysis to interpret competition between a C3 and a C4 annual under ambient and elevated CO2

Summary Detailed growth analysis in conjunction with information on leaf display and nitrogen uptake was used to interpret competition between Abutilon theophrasti, a C₃ annual, and Amaranthus retroflexus, a C₄ annual, under ambient (350 l l^-1) and two levels of elevated (500 and 700 l l^-1) CO₂. Plants were grown both individually and in competition with each other. Competition caused a reduction in growth in both species, but for different reasons. In Abutilon, decreases in leaf area ratio (LAR) were responsible, whereas decreased unit leaf rate (ULR) was involved in the case of Amaranthus. Mean canopy height was lower in Amaranthus than Abutilon which may explain the low ULR of Amaranthus in competition. The decrease in LAR of Abutilon was associated with an increase in root/shoot ratio implying that Abutilon was limited by competition for below ground resources. The root/shoot ratio of Amaranthus actually decreased with competition, and Amaranthus had a much higher rate of nitrogen uptake per unit of root than did Abutilon. These latter results suggest that Amaranthus was better able to compete for below ground resources than Abutilon. Although the growth of both species was reduced by competition, generally speaking, the growth of Amaranthus was reduced to a greater extent than that of Abutilon. Regression analysis suggests that the success of Abutilon in competition was due to its larger starting capital (seed size) which gave it an early advantage over Amaranthus. Elevated CO₂ had a positive effect upon biomass in Amaranthus, and to a lesser extent, Abutilon. These effects were limited to the early part of the experiment in the case of the individually grown plants, however. Only Amaranthus exhibited a significant increase in relative growth rate (RGR). In spite of the transitory effect of CO₂ upon size in individually grown plants, level of CO₂ did effect final biomass of competitively grown plants. Abutilon grown in competition with Amaranthus had a greater final biomass than Amaranthus at ambient CO₂ levels, but this difference disappeared to a large extent at elevated CO₂. The high RGR of Amaranthus at elevated CO₂ levels allowed it to overcome the difference in initial size between the two species.This study was supported by a grant from the US Department of Energy