Structural and functional domains of cellobiohydrolase I from trichoderma reesei

Limited proteolysis (papain) of the cellobiohydrolase I (CBH I, 65 kDa) from Trichoderma reesei led to the seperation of two functional domains: a core protein (55 kDa) containing the active site, and a C-terminal glycopeptide (10 kDa) implicated in binding to the insoluble matrix (cellulose). The quaternary structures of the intact CBH I and its core in solution are now compared by small angle X-ray scattering (SAXS) measurements. The molecular parameters derived for the core (Rg=2.09 nm, D_max=6.5 nm) and for the intact enzyme (Rg=4.27 nm, D_max=18 nm) indicate very different shapes. The resulting models show a tadpole-like structure for the intact enzyme where the isotropic part coincides with the core protein and the flexible tail part should be identified with the C-terminal glycopeptide. Thus in this enzyme, functional differentiation is reflected in structural peculiarities.Abbreviations SAXS small angle X-ray scattering - SDS-PAGE SDS-polyacrylamide gel electrophoresis - IEF-PAG polyacrylamide gel isoelectric focusing; cellobiohydrolase (CBH, 1,4--glucan cellobio hydrolase (E.C.3.2.1.91)) - D_max maximum diameter - Rg radius of gyration     

The vectoring of cactophilic yeasts by Drosophila

Summary At two locations in the Sonoran Desert, yeasts were sampled from species of Drosophila, the flies' cactus hosts, and other neighboring sources of cactophilic yeasts to determine the relation between the yeasts vectored by the fly and the yeasts found in their breeding sites. D. mojavensis, D. nigrospiracula, and D. mettleri vectored yeast assemblages significantly more similar to the yeast species found on the rot from which the flies were collected than to the yeasts found on other rots from the flies host cactus or other rotting cactus at the same site. Rots with Drosophila had fewer yeast species than those without flies, suggesting that flies were associated with younger rots. Rots with flies and the Drosophila also had more yeast species with the capability to produce ethyl acetate than rots without flies. The results support the contention that cactophilic Drosophila feed on a subset of the yeasts available in an area, and may act to maintain differences among the yeast communities found on different species of cactus.     

Establishment of Plantago lanceolata L. and Plantago major L. among grass

Summary Establishment of Plantago lanceolata and P. major ssp major among grass was studied in a field experiment in which survival and selection on date of seedling emergence and plant size was investigated in relation to the vegetation structure. P. major — in contrast to P. lanceolata — was not able to establish itself in grass because of its lower competitive ability caused by later germination, smaller seedling size, and shorter leaves. In both species there was selection for early germination. For P. lanceolata a significant correlation was found between the strength of selection and the light climate, determined by the structure of the grass sward. Plants that germinated early were at an advantage because they were larger, especially the leaves, when compared with plants that germinated late. It seems likely that selection was mainly by competition for light. Contrary to expectation P. major-seedlings had a higher shade tolerance than those of P. lanceolata. The performance of both species is discussed in relation to their different life strategies.Grassland species research group publication no 142     

Refined structure of human carbonic anhydrase II at 2.0 Å resolution

The structure of human erythrocytic carbonic anhydrase II has been refined by constrained and restrained structure–factor least-squares refinement at 2.0 Å resolution. The conventional crystallographic R value is 17.3%. Of 167 solvent molecules associated with the protein, four are buried and stabilize secondary structure elements. The zinc ion is ligated to three histidyl residues and one water molecule in a nearly tetrahedral geometry. In addition to the zinc-bound water, seven more water molecules are identified in the active site. Assuming that Glu-106 is deprotonated at pH 8.5, some of the hydrogen bond donor–acceptor relations in the active site can be assigned and are described here in detail. The Oγ1 atom of Thr-199 donates its proton to the Oε1 atom of Glu-106 and can function as a hydrogen bond acceptor only in additional hydrogen bonds.     

Structure and floristic composition of the lowland rain forest of Los Tuxtlas,Mexico

Physiognomy, structure and floristic composition of one hectare of lowland tropical rain forest was studied in detail at Los Tuxtlas, Mexico. Physiognomically, the Los Tuxtlas forest should be classified as lowland tropical high evergreen rain forest. The forest showed a closed canopy at 30–35 m. Of all woody, non-climbing species with a DBH1.0 cm 89.4% (94.5% of all individuals) were evergreen, 25.4% (59.5% of the individuals) had compound leaves, and over 80% of species (and individuals) had leaves in the notophyll and mesophyll size classes. The forest structure was characterized by a low density (2976 individuals with a DBH1.0 cm, 346 individuals with a DBH10.0 cm, per ha, excluding vines) with an average basal area (38.1 m², DBH1.0 cm, 34.9 m², DBH10.0 cm, per ha, excluding vines). This was attributed to the relative maturity of the forest on the study plot. The study plot contained 234 species (11 208 individuals with a height 0.5 m), of which 55.1% (34.8% of individuals) were trees, 9.4% (6.8%) shrubs, 3.4% (44.3%) palms, 20.1% (5.2%) vines, 6.8% (8.7%) herbs and 5.1% (0.3%) of unknown lifeform. Furthermore, 58 species of epiphytes and hemi-epiphytes were found. Diversity of trees, shrubs and palms with a DBH1.0 cm was calculated as Shannon-Wiener index (4.65), Equitability index (0.65), and Simpson index (0.10). The dominance-diversity curve showed a lognormal form, characteristic for tropical rain forest. The community structure was characterized by a relative dominance of Astrocaryum mexicanum in the understorey, Pseudolmedia oxyphyllaria in the middle storeys, and Nectandra ambigens in the canopy. Species population structures of 31 species showed three characteristic patterns, differentiated by recruitment: continuously high, discontinuously high, and continuously low recruitment. Height/diameter and crown cover/diameter diagrams suggested a very gradual shift from height growth to crown growth during tree development. Forest turnover was calculated as 138 years. Compared to other tropical rain forests the Los Tuxtlas forest had 1. similar leaf physiognomical characteristics, 2. a lower diversity, 3. a lower density, 4. an average basal area, and 5. a slow canopy turnover.     

Morphological dispersion of introduced Hawaiian finches: evidence for competition and a Narcissus effect

Summary Morphological analyses were conducted on finch species introduced to Oahu, Hawaii. As many as 25 species of finches representing four families (Emberizidae, Fringillidae, Ploecidae, Estrildidae) have been introduced to Oahu. Of these, 15 species currently have established wild populations. When compared with pools of 25 and 23 species introduced to Oahu, the 15 surviving species are morphologically overdispersed. This result is consistent with the hypothesis that competition has influenced the outcome of these introductions. We also tested the hypothesis that surviving introduced finches in one habitat (sugarcane fields) were morphologically overdispersed. When the seven surviving finch species found in sugarcane were compared with the pools of 25 and 23 species, they too were morphologically overdispersed. However, when the seven sugarcane species were compared with a species pool consisting of only the surviving 15 species found across Oahu, they were not morphologically overdispersed. This result suggests that morphological analyses of community structure based only on comparisons of assemblages of surviving species may be biased by a Narcissus effect.     

Structure of the sugar-phosphate moiety of lipid A from lipooligosaccharide of Neisseria meningitidis group B,strain BC5S No. 125

On the basis of chemical and NMR data the partial structure of lipid A from lipooligosaccharide (LOS) of Neisseria meningitidis group B, strain BC₅S No 125 was established. Lipid A consisted of disaccharide 2-deoxy-6-O-[2-deoxy-2-(3-hydroxytetradecanoylamino)--gluco-pyranosyl]-2-(3-hydroxytetradecanoylamino)--glucopyranose carrying the -(2-aminoethyl)pyrophosphate residue at 0–4 and the pyrophosphate or phosphate residue at 0–1. On hydrolysis of the acidic form of LOS with 1% acetic acid the substituent at 0–1 was practically completely removed whereas that at 0–4 was stable. The analogous hydrolysis of the Mg-salt of LOS was accompanied by splitting off the pyrophosphate linkage in the substituent at 0–4. Hydrolysis of LOS at pH 4.5 in the presence of SDS led mainly to a lipid A preparation retaining both pyrophosphate residues.Abbreviations KDO 2-keto-3-deoxyoctulosonic acid - LA-I, LA-II preparations of lipid A - LOS lipooligosaccharide - LOS-H⁺ the acidic form of LOS - OS oligosaccharide - TLC thin-layer chromatography - GLC-MS gas-liquid chromatography/mass spectrometry     

Application of a directed conformational search for generating 3-D coordinates for protein structures from alpha-carbon coordinates.

A directed conformational search algorithm using the program CONGEN (ref. 3), which samples backbone conformers, is described. The search technique uses information from the partially built structures to direct the search process and is tested on the problem of generating a full set of backbone Cartesian coordinates given only alpha-carbon coordinates. The method has been tested on six proteins of known structure, varying in size and classification, and was able to generate the original backbone coordinates with RMSs ranging from 0.30-0.87A for the alpha-carbons and 0.5-0.99A RMSs for the backbone atoms. Cis peptide linkages were also correctly identified. The procedure was also applied to two proteins available with only alpha-carbon coordinates in the Brookhaven Protein Data Bank; thioredoxin (SRX) and triacylglycerol acylhydrolase (TGL). All-atom models are proposed for the backbone of both these proteins. In addition, the technique was applied to randomized coordinates of flavodoxin to assess the effects of irregularities in the data on the final RMS. This study represents the first time a deterministic conformational search was used on such a large scale.     

The gap theory in forest dynamics

Since the late 1970s, ecologists interested in forest dynamics have focused their attention to the responses of individuals, populations and communities to “gaps” which are openings created in the forest canopy. This review intended to introduce some collective knowledge on major subjects of the gap theory in forest dynamics, in relation to gap-disturbance regimes, tree regeneration behaviour and community structure.     

Fish size and habitat depth relationships in headwater streams

Summary Surveys of 262 pools in 3 small streams in eastern Tennessee demonstrated a strong positive relationship between pool depth and the size of the largest fish within a pool (P<0.001). Similarly, the largest colonizers of newly-created deep pools were larger than the colonizers of shallow pools. We explored the role of predation risk in contributing to the bigger fish — deeper habitat pattern, which has been noted by others, by conducting five manipulative field experiments in two streams. Three experiments used stoneroller minnows (Campostoma anomalum); one used creek chubs (Semotilus atromaculatus); and one used striped shiners (Notropis chrysocephalus). The stoneroller experiments showed that survival of fish approximately 100 mm in total length (TL) was much lower in shallow pools (10 cm deep) than in deep (40 cm maximum) pools (19% versus 80% survival over 12 d in one experiment) and added cover markedly increased stoneroller survival in shallow pools (from 49% to 96% in an 11-d experiment). The creek chub experiment showed that, as for stonerollers, pool depth markedly influenced survival: the chubs survived an average of 4.9 d in shallow pools and >10.8 d in deep pools. In the striped shiner experiment in shallow artificial streamside troughs, no individuals 75–100 mm TL survived as long as 13 d, where-as smaller (20–25 mm) fish had 100% survival over 13 d. The results of the experiments show that predation risk from wading/diving animals (e.g., herons and raccoons) is much higher for larger fishes in shallow water than for these fishes in deeper water or for smaller fish in shallow water. We discuss the role of predation risk from two sources (piscivorous fish, which are more effective in deeper habitats, and diving/wading predators, which are more effective in shallow habitats) in contributing to the bigger fish — deeper habitat pattern in streams.