Non-intertwined binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better markers of regular secondary structures than nonconstrained patterns

Patterns of hydrophobic and hydrophilic residues (binary patterns) play an important role in protein architecture and can be roughly categorized into two classes regarding their preferential participation in α‐helices or β‐strands. However, a single binary pattern can be embedded into different longer patterns carrying opposite structural information and thus cannot be as much informative as expected. Here, we consider conditional binary patterns, or hydrophobic clusters, whose existence is conditioned by the presence of a minimum number of nonhydrophobic residues, called the connectivity distance, that separate two hydrophobic amino acids assumed to belong to two distinct patterns. Conditional binary patterns are distinct from simple ones in that they are not intertwined, i.e., they can not include or be included in other conditional patterns and therefore carry a much more differentiated information, in particular being dramatically better correlated with regular secondary structures (especially β ones). The distribution of these nonintertwined binary patterns in natural proteins was assessed relative to randomness, evidencing the structural bricks that are favored and disfavored by evolutionary selection. Several connectivity distances as well as several hydrophobic alphabets were tested, evidencing the clear superiority of a connectivity distance of 4, which mimics the minimum current length of loops in globular domains, and of the VILFMYW alphabet, selected from structural data (secondary structure propension and Voronoï tesselation), in highlighting fundamental properties of protein folds. Proteins 2003;51:236–244. © 2003 Wiley‐Liss, Inc.     

Insectivory by Gorilla gorilla gorilla in Southeast Cameroon

Our study extends quantitative analyses of insect-eating by gorillas (Gorilla gorilla gorilla) to Cameroon. During a 2-mo period (May–June 2001), we recorded and analyzed feeding traces on plants and insects and in gorilla feces. We found 180 feeding traces, 17% of which involved insectivory. Seventy-eight percent of the fecal samples (n = 36) contained insects. Ants were found in 61% of the samples, termites in 39%, while 56% of the samples contained remains of other insects. We added 14 new species to the known insect diet of western lowland gorillas. Overall, social insects are predominant. The choice of prey by the Ntonga gorillas gives new clues for the existence of cross-cultural differences among gorilla populations. A comparison of the overall frequency of insectivory with those at other sites in Central Africa indicate a possible effect of forest disturbance on the insectivorous behavior of gorillas. The study suggests the existence of temporal variation in ant- and termite-eating by gorillas.     

Influence of the culture medium constituents and inoculum size on the accumulation of blue pigment and cell growth of Lavandula spica

The effects of the concentration of PO₄ ^3-, NO₃ ^–, Fe ²⁺, sucrose and inoculum size on the accumulation of blue pigment and growth of suspension cultures of Lavandula spica D.C. ( L. latifolia Vill.), were studied. The combination of 2.5 mM PO₄ ^3-, 14.1 mM NO₃ ^–, 1 mM Fe ²⁺, 30 g l^–1 sucrose and 10 g l^–1fresh weight of inoculum, promoted a 7-fold enhancement on the productivity of blue pigment in comparison to the control medium. Among all the culture medium constituents tested, phosphate exerted the highest beneficial effect and Fe²⁺ showed to be essential for the accumulation of the pigment. High levels of sucrose (60 or 90 g l^–1) did not stimulate the accumulation of blue pigment. In these conditions, cell growth and cell viability were drastically affected.     

Plantlet regeneration from subculturable nodular callus of Pinus radiata

An efficient planlet regeneration system via nodular callus formation is described for Pinus radiata. Subculturable nodular callus was induced at its highest frequency (93%) on embryonic explants excised from seeds at an early stage of germination (radicle length 2–5 mm). The optimal medium for nodular callus tissue proliferation was LP basal medium that was modified by reducing the concentration of potassium nitrate to 500 mg l^–1 and supplemented with 22.2 M 6-benzyladenine (BAP) and 2.85 M indole-3-butyric acid (IBA). Bud differentiation from the nodules was achieved by reducing BAP and sucrose concentrations in the culture medium. The maximum frequency of adventitious bud formation occurred on LP basal medium containing 2% sucrose and 0.44 M BAP on which about 61% of the transferred nodules formed buds. During the next 6 weeks of culture on the same cytokinin-free medium multiple shoots elongated from the buds. These shoots were excised and transferred to root initiation medium (RIM2.1), consisting of full-stregth SH macro- and micro-salts, 1000 mg l^–1 myo-inositol, 0.4 mg l^–1 thiamine-HCl, 2% sucrose and a combination of naphthaleneacetic acid (NAA), IBA and BAP at concentrations of 2.69, 4.93 and 0.11 M, respectively. After 5–15 days, root meristems were initiated on the stem bases. The highest rooting frequency was achieved when shoots were treated for 10 days on RIM2.1 medium, before being transferred to half-strength Schenk and Hildebrandt medium with 1% sucrose and without growth regulators for root growth.     

Spatio-temporal growth dynamics of a subAlpine Pinus uncinata stand in the French Alps

Natural forests are characterised by a high level of both spatial and temporal heterogeneity. The major processes involved in the creation and maintenance of forest heterogeneity in temperate climates are small-sized canopy disturbances. The resulting openings also modify the growth conditions for the remaining trees. The analysis of tree growth responses using dendrochronological techniques allows the reconstruction of the time sequence of the disturbances. The radial growth analysis is coupled here with both a spatial analysis and a demographic analysis of the forest structure. The age classes are temporally organised in cohorts and spatially distributed in spatial aggregates. The analysis of the most documented disturbance event allowed us to determine the size of the disturbance response patch (between 0.036 and 0.073 ha) and the duration of the disturbance (six years). We considered that this small-scale disturbance event may have been caused by the fall of a single tree and has freed the surrounding trees of its competition.     

Systemic induction of the biosynthesis of terpenic compounds in Digitalis lanata

A bacterial screening was carried out in the rhizosphere of two Digitalis species, D. thapsi and D. parviflora, both at the vegetative stage and at flowering. A total of 480 isolates were characterised at genus level, Bacillus being the dominant genera in all cases. Fifty percent of the Bacillus strains isolated from each species were analysed by PCR-RAPDs. At 85% similarity, 12 groups separated for D. thapsi and 18 for D. parviflora. One strain of each group was selected for biological assay on D. lanata, evaluating growth promotion and cardenolide content in leaves after inoculation performed in the root system. The plant parameters evaluated were leaf surface area, shoot and root dry weight and leaf number. Lanatoside C content was evaluated by HPLC. Only 17 strains caused significant increases in at least one of the parameters evaluated. The most striking result was that some strains promoted growth and increased cardenolide content at the same time. This effect was detected on leaves while inoculation was carried out on roots. Interestingly, these two parameters are not enhanced simultaneously under regular conditions in pot or in tissue cultures.     

LmbJ and LmbIH protein levels correlate with lincomycin production in Streptomyces lincolnensis

AIMS: To demonstrate the expression of two overlapping genes lmbJ and lmbIH in Streptomyces lincolnensis and to document LmbJ and LmbIH protein levels during the lincomycin production phase. To analyse presumable function of the LmbIH protein. METHODS AND RESULTS: Lincomycin production was monitored by thin-layer chromatography, proteins LmbJ and LmbIH were assayed in the cell-free extracts of S. lincolnensis by immunodetection. LmbJ occurred at stable level (2-4 mg x g(-1) of total proteins) for a long time period (36-96 h of cultivation) covering the whole production phase. This fairly corresponds to the catalytic function of the protein in the antibiotic biosynthesis (N-demethyllincomycin methyltransferase). On the contrary, LmbIH reached the detectable level (0.1 and 0.7 mg x g(-1)) just for a short period at 60-72 h. CONCLUSIONS: The absence of LmbIH protein at a detectable level during the major part of the antibiotic production phase casts doubt on its possible catalytic function. Rather a different connection with the final biosynthetic steps, e.g. regulatory, can be envisaged. SIGNIFICANCE AND IMPACT OF THE STUDY: Expression of a newly found putative regulatory gene was demonstrated during production of industrial antibiotic, lincomycin.     

Community-level flowering phenology and fruit set: Comparative study of 25 woody species in a secondary forest in Japan

We investigated the flowering phenology, pollinator visitation, and fruit set of 25 animal-pollinated woody species in a warm temperate secondary forest in Japan. Various species flowered sequentially from February to October. The principal pollinators were bumblebees, honey-bees, flies and/or beetles and birds; bumblebees and flies/beetles pollinated most trees. The duration of flowering was shorter for species that bloomed in the middle of the season than it was for species that bloomed earlier or later in the season. The timing of flowering was more synchronous within species that had a shorter flowering duration; this was also detected when phylogenetically independent contrasts were calculated. This could be important for the effective pollination of species with a short flowering duration because such species bloom sequentially over a short period of less than 1month around May. Fruit set was related not to pollinator type, sex expression, flowering sequence (in order of the date of peak flowering) or flowering duration, but to the relative abundance of the species in the forest. This correlation was detected for fly- and beetle-pollinated species but not for bumblebee-pollinated species. Thus, relatively rare plant species with opportunistic pollinators might experience limited fruit set because of insufficient pollinator services. Bagging experiments conducted on eight hermaphrodite species revealed that the fruit set of bagged flowers was nearly zero, lower than that of control flowers. These results indicate the importance of pollinators for successful reproduction and thus for the coexistence of plants in this secondary forest.     

Convenient method for determining the absolute configuration of chiral alcohols with racemic 1H NMR anisotropy reagent,M(alpha)NP acid: use of HPLC-CD detector

A convenient method for determining the absolute configuration of chiral secondary alcohols using the racemic NMR anisotropy reagent, (+/-)-2-methoxy-2-(1-naphthyl)propionic acid [(+/-)-M(alpha)NP acid], and an HPLC-CD detector was developed. The method was successfully applied to some chiral alcohols derived from (-)-alpha-santonin.     

Pigment dynamics and autumn leaf senescence in a New England deciduous forest,eastern USA

The leaves of woody plants at Harvard Forest in Central Massachusetts, USA, changed color during senescence; 70% (62/89) of the woody species examined anatomically contained anthocyanins during senescence. Anthocyanins were not present in summer green leaves, and appeared primarily in the vacuoles of palisade parenchyma cells. Yellow coloration was a result of the unmasking of xanthophyll pigments in senescing chloroplasts. In nine red-senescing species, anthocyanins were not detectable in mature leaves, and were synthesized de novo in senescence, with less than 20µg cm^–2 of chlorophyll remaining. Xanthophyll concentrations declined in relation to chlorophyll to the same extent in both yellow- and red-leaved taxa. Declines in the maximum photosystemII quantum yield of leaves collected prior to dawn were only slightly less in the red-senescing species, indicating no long-term protective activity. Red-leaved species had significantly greater mass/area and lower chlorophylla/b ratios during senescence. Nitrogen tissue concentrations in mature and senescent leaves negatively correlated to anthocyanin concentrations in senescent leaves, weak evidence for more efficient nitrogen resorption in anthocyanic species. Shading retarded both chlorophyll loss and anthocyanin production in Cornus alternifolia, Acer rubrum, Acer saccharum, Quercus rubra and Viburnum alnifolium. It promoted chlorophyll loss in yellow-senescing Fagus grandifolia. A reduced red:far-red ratio did not affect this process. Anthocyanins did not increase leaf temperatures in Q.rubra and Vaccinium corymbosum on cold and sunny days. The timing of leaf-fall was remarkably constant from year to year, and the order of senescence of individual species was consistent.