Refined crystal structure of Streptomyces griseus trypsin at 1.7 A resolution

Streptomyces griseus trypsin (SGT) is a bacterial serine proteinase that is more homologous to mammalian than to other bacterial enzymes. The structure of SGT has been solved primarily by molecular replacement, though some low-resolution phase information was supplied by heavy-atom derivatives. The mammalian pancreatic serine proteinases bovine trypsin (BT) and alpha-chymotrypsin (CHT) were used as molecular replacement models. Because these proteins have low homology with SGT compared to the majority of other successful replacement models, new strategies were required for molecular replacement to succeed. The model of SGT has been refined at 1.7 A resolution to a final R-factor of 0.161 (1 A = 0.1 nm); the correlation coefficient between all observed and calculated structure factor amplitudes is 0.908. Solvent molecules located in the crystal structure play an important role in stabilizing buried charged and polar groups. An additional contribution to stability can be seen in the fact that the majority of the charged side-chains are involved in ionic interactions, sometimes linking the two domains of SGT. A comparison of SGT with BT shows that the greatest similarities are in the active-site and substrate-binding regions, consistent with their similar substrate specificities. The modeling of complexes of SGT with two inhibitors of BT, pancreatic trypsin inhibitor (PTI) and the third domain of Japanese quail ovomucoid (OMJPQ3), helps to explain why PTI inhibits SGT but OMJPQ3 does not. Like BT, but unlike other bacterial serine proteinases of known structure, SGT has a buried N terminus. SGT has also a well-defined Ca2+-binding site, but this site differs in location from that of BT.     

Composition,export, and import of drift vegetation on a tropical,plant-dominated,fringing-reef platform (Caribbean Panama)

For 15 months, the composition and abundance of drift vegetation were determined from a plantdominated fringing reef at Galeta Point, Caribbean Panama. Five nets located downstream of the reef platform continuously sampled 1.0–1.3 ha of reef flat which included 137–202 m of fore reef. Time series and multiple correlation analysis were done to evaluate the dependence of drift biomass on selected physical and biological factors. Export and import rates and turnover times were derived and compared between the dominant species. Floating leaves, branches, and seeds of higher plants were the major components of imported drift with 52% of the dry weight mass, followed by algae and seagrass each with 19%, the water hyacinth Eichhornia with 2%, and floating tar with 8%. Exported biomass from the reef platform was higher in the dry-season (late November–March) than in the wet-season (April-early November). Within the 1.0–1.3 ha sampling area, export estimates ranged from 37–294 kg mo^-1 for the seagrass Thalassia, 3–171 kg mo^-1 for the alga Laurencia, and 3–74 kg mo^-1 for the alga Acanthophora. Multiple correlation models indicated that meteorological and hydrographic conditions explained between 31 to 65% of the variance in the drift biomass and that the best predictors of exported biomass were tidal elevation and wind speed (3 week lag). Export rates increased with high tides and strong winds and decreased with elevated water temperatures. Autocorrelations of drift biomass were generally highest at 2 week intervals, suggesting that the quantity of drift removed from the platform was, in part, related to spring and neap tide cycles. Export rates were also affected by the morphology of the vegetation, development of uprights, and location on the reef platform. Import rates of terrestrial-plant debris, the hyacinth Eichhornia, the seagrass Syringodium, and the brown alga Sargassum did not exhibit pronounced seasonal patterns in abundance and averaged 60.2, 1.9, 1.1, and 2.7 g d^-1m^-1, respectively. Wind speed was negatively correlated with Sargassum abundance, suggesting that strong winds depleted it from nearshore waters. Floating tar averaged about 10 g d^-1m^-1, the highest reported in the Caribbean. The plant-dominated fringing reef at Galeta Point is shown to be a major source, as well as a recipient, of drift vegetation.     

Callus formation and plantlet regeneration from protoplasts derived from suspension cultures of wheat (Triticum aestivum L.)

Protoplasts were isolated from anther-derived suspension cultures of commercial wheat (Triticum aestivum L. cv. Chris). The protoplasts were released enzymatically and isolated by centrifugation on a sucrose cushion. The isolated protoplasts were initially cultured in a liquid medium in the dark. Numerous microcalli were produced under these conditions, some of which differentiated into globular embryos. Upon transfer to a solid medium and exposure to 16h/8h light/dark cycle, the protocalli proliferated and many of the somatic embryos matured. Complete plantlets were obtained and maintained in sterile culture.Abbreviations 2,4-D 2,4-Dichlorophenoxyacetic acid - MES 2-[N-morpholino] ethanesulfonic acid     

Bias in leaf area — sapwood area ratios and its impact on growth analysis in Pinus contorta

Summary Two alternative estimators of individual tree leaf area (A₁) area are used to derive estimates of leaf-area index (L) for 40 plots in Pinus contorta Dougl. stands. One estimator of A₁ is based on the common assumption of a constant ratio between A₁ and sapwood cross-sectional area at breast height (A_s). The second estimator of A₁ accounts for tree-to-tree variation in the relation between A₁ and A_s. The apparent relationship between stand growth and leaf-area index is strongly dependent on the way leaf area is estimated. When L is derived from a constant A₁A_s ratio, stand growth appears to be strongly correlated with L. However, when L is based on estmates of A₁ that account for tree-to-tree variation in the A₁ — A_s relation, stand growth is seen to be only weakly related to L. Stand structure, quantified as percent live-crown, accounts for a great deal of the observed variation in leaf-area efficiency. These contrasting relationships illustrate the importance of unbiased estimates of L in interpreting the link between stand-level processes and leaf area.Utah Aggriculural Experiment Station Journal Paper No. 3333     

Some mathematical aspects of mapping DNA cosmids

A number of experimental and mathematical problems must be solved before high resolution physical maps of mammalian chromosomes can be reliably determined. Such a map might consist of an ordered set of nonsequenced, overlapping DNA fragments 20,000-40,000 bases long, produced by digestion of a chromosome, using two restriction enzymes. Map construction requires assigning a signature to each fragment that differentiates it unambiguously from every other fragment, and then devising a computationally efficient algorithm that will provide a unique ordering of the fragments. In the first part of this paper we present a polynomial time algorithm that yields a unique map, and is largely independent of the method for assigning signatures. In the next section we analyze the distribution of lengths of restriction digest fragments and discuss the implications for the algorithm, including the expected number of map gaps. Finally, we discuss a specific method for assigning signatures proposed by Hans Lehrach, based on which of a panel of probes binds to a given fragment. In particular we examine the effects of fragment length heterogeneity on the theoretical optimum length and number of probes, and the extent to which false signatures might be obtained by nonspecific binding. We conclude that the Lehrach strategy is effective provided the number of probes is >-150, but that each fragment will need testing with at most 25 probes.     

On a simplified model for pattern formation in honey bee colonies

We present a simplified version of a previously presented model (Camazine et al. (1990)) that generates the characteristic pattern of honey, pollen and brood which develops on combs in honey bee colonies. We demonstrate that the formation of a band of pollen surrounding the brood area is dependent on the assumed form of the honey and pollen removal terms, and that a significant pollen band arises as the parameter controlling the rate of pollen input passes through a bifurcation value. The persistence of the pollen band after a temporary increase in pollen input can be predicted from the model. We also determine conditions on the parameters which ensure the accumulation of honey in the periphery and demonstrate that, although there is an important qualitative difference between the simplified and complete models, an analysis of the simplified version helps us understand many biological aspects of the more complex complete model. Corresponding author     

Peptidergic regulation of the Limulus midgut

1. The morphology and innervation of the midgut (intestine) in the horseshoe crab, Limulus polyphemus was investigated. The organization of this tissue was examined with routine histology. Radioimmunoassay, immunohistochemistry and high performance liquid chromatography were employed to detect, localize and identify peptidergic innervation of the midgut. The actions of synthetic and native proctolin-like and FMRFamide-like peptides were compared on the isolated midgut preparation. 2. Levels of proctolin and FMRFamide were determined in extracts of Limulus midgut tissue using radioimmunoassay. High levels of proctolin-like immunoreactivity (69.5 +/- 11.3 ng/g) were detected, while levels of FMRFamide-like immunoreactivity (0.8 +/- 0.2 ng/g) were less. Proctolin levels were equally distributed, while the levels of FMRFamide-like immunoreactivity exhibited an anterior bias. 3. Proctolin- and FMRFamide-like immunoreactivities in the Limulus midgut were localized with immunohistochemistry. Proctolin- and FMRFamide-immunoreactive elements were detected in intestinal nerve branches and individual fibers running along the surface of the midgut in whole-mount preparations. In sectioned tissue, staining for these peptides was observed throughout the midgut, typically associated with muscle bands and fibers. Only a few immunoreactive cell bodies were observed. 4. Proctolin, and several FMRFamide-like peptides produced distinct and opposing actions on the isolated Limulus midgut preparation. Proctolin elicited contracture and rhythmic contractions of this tissue, while FMRFamide and N-terminally extended analogs of FLRFamide relaxed gut tension. FMRFamide-like peptides partially reversed the excitatory actions of proctolin. 5. Proctolin- and FMRFamide-like peptides in Limulus midgut extracts were partially characterized with high performance liquid chromatography. One peak of proctolin-like activity was detected on a linear gradient of 18 to 31.5% acetonitrile. The native proctolin-like peptide produced excitatory actions on the isolated midgut preparation which were indistinguishable from those produced by synthetic proctolin. Several peaks of FMRFamide-like bioactivity (Busycon radula protractor muscle assay) were detected with a linear gradient of 5 to 30% acetonitrile. Fractions from two distinct peaks produced FMRFamide-like inhibitory effects on the isolated Limulus midgut preparation. These findings suggest a role for proctolin-like and FMRFamide-like peptides as regulators of intestinal motility in Limulus.