Responses of crown development to canopy openings by saplings of eight tropical submontane forest tree species in Indonesia: a comparison with cool-temperate trees

BACKGROUND AND AIMS: Growth in trunk height in canopy openings is important for saplings. How saplings increase height growth in canopy openings may relate to crown architectural constraints. Responses of crown development to canopy openings in relation to trunk height growth were studied for saplings (0.2-2.5 m tall) of eight tropical submontane forest tree species in Indonesia. The results of this study were also compared with those of temperate trees in northern Japan. METHODS: The crown architecture differed among the eight tropical species, i.e. they had sparsely to highly developed branching structures. Crown allometry was compared among the eight species in each canopy condition (closed canopy or canopy openings), and between closed canopy and canopy openings within a species. A general linear regression model was used to analyse how each species increases height growth rate in canopy openings. Crown allometry and its plasticity were compared between tropical and temperate trees by a nested analysis of covariance. KEY RESULTS: Tropical submontane trees had responses similar to cool-temperate trees, showing an increase in height in canopy openings, i.e. taller saplings of sparsely branched species increase height growth rates by increasing the sapling leaf area. Cool-temperate trees have a wider crown projection area and a smaller leaf area per crown projection area to avoid self-shading within a crown compared with tropical submontane trees. Plasticity of the crown projection area is greater in cool-temperate trees than in tropical submontane trees, probably because of the difference in leaf longevity. CONCLUSIONS: This study concluded that interspecific variation in the responses of crown development to canopy openings in regard to increasing height related to the species' branching structure, and that different life-forms, such as evergreen and deciduous trees, had different crown allometry and plasticity.     

A limited survey of aflatoxin B1 contamination in Indonesian palm kernel cake and copra meal sampled from batches

Samples from large (100–200 tons) batches of palm kernel cake (PKC, n?=?20) and copra meal (CM, n?=?13) were collected at production facilities of four Indonesian feed mill manufacturers and analysed for aflatoxin B₁ (AFB₁) by ELISA. Recoveries using spiked samples ranged from 86 to 113 %, with relative standard deviations of <9 % (PKC) and <6 % (CM). All batches were positive for AFB₁: in PKC, at levels of 5.8–93.1 μg/kg (mean 49 μg/kg), and in CM, at levels of 1.1–147 μg/kg (mean 38.1 μg/kg). AFB₁ levels were, in most batches, below the maximum level (100 μg/kg) recommended by the National Standardisation Agency, Republic of Indonesia. However, about half of the batches exceeded both the European Union and USA regulations for AFB₁ in animal feed. In conclusion, serious efforts are necessary to control production, storage and shipment of palm kernel cake and copra meal for feed purposes, and clearly not only for products intended for export but also to reduce AFB₁ levels in domestic Indonesian feed.     

Resistance factors in pepper inhibit larval development of thrips (Frankliniella occidentalis)

The western flower thrips [Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)] is a major pest in pepper cultivation. Therefore, host plant resistance to thrips is a desirable trait. The objectives of this study were to determine the effect of resistance on the development of thrips and to identify metabolite compounds related to the resistance. Three highly resistant, three medium resistant, and three susceptible pepper accessions were used in this study. Adult and pre‐adult survival, developmental time, and oviposition rate were assessed. Gas chromatography‐mass spectrometry was used to identify compounds that correlate with the level of resistance to thrips. Our results show that resistance of pepper accessions has a significant effect on oviposition rate and larval mortality. Seven compounds were identified that correlate with resistance to thrips and six compounds were identified that correlate with susceptibility to thrips. Some of these compounds, such as tocopherols, were previously shown to have an effect on insects in general. Also, some specific secondary metabolites (alkanes) seem to be more abundant in susceptible accessions and were induced by thrips infestation.     

Benzodiazepines stimulate sodium ion transport in frog skin epithelium

Benzodiazepine binding sites are present in a variety of non-neuronal tissues including the kidney where they are localized to distal nephron segments. It is postulated that renal binding sites are involved in modulating ion transport. This study examined the effects of two benzodiazepines on sodium transport in frog skin epithelium, a model system for sodium transport in renal collecting duct. Treatment of short-circuited frog skin with diazepam (a non-selective benzodiazepine agonist) stimulated amiloride-sensitive short-circuit current, reflecting stimulation of active sodium transport. The diazepam response was equally effective with either serosal or mucosal application of the drug. Maximal stimulation of the current (42 +/- 8%) was achieved with 10 microM diazepam (serosal). Short-circuit current was similarly augmented by serosal or mucosal addition of Ro5-4864, a benzodiazepine agonist with selective activity at peripheral (non-neuronal) receptors. The natriferic response to diazepam was additive to that of vasopressin or cyclic AMP suggesting that the mode of action of benzodiazepines is probably distinct from the cyclic AMP pathway. Thus, frog skin appears to be a useful model to examine the epithelial effects of benzodiazepines. Whether stimulation of sodium transport, however, involves peripheral-type benzodiazepine receptors in this tissue requires further studies.     

Molecular weight change of polyhydroxyalkanoate (PHA) caused by the PhaC subunit of PHA synthase from Bacillus cereus YB-4 in recombinant Escherichia coli

Polyhydroxyalkanoate (PHA)-producing Bacillus strains possess class IV PHA synthases composed of two subunit types, namely, PhaR and PhaC. In the present study, PHA synthases from Bacillus megaterium NBRC15308(T) (PhaRC(Bm)), B. cereus YB-4 (PhaRC(YB4)), and hybrids (PhaR(Bm)C(YB4) and PhaR(YB4)C(Bm)) were expressed in Escherichia coli JM109 to characterize the molecular weight of the synthesized poly(3-hydroxybutyrate) [P(3HB)]. PhaRC(Bm) synthesized P(3HB) with a relatively high molecular weight (M(n) = 890 × 10(3)) during 72 h of cultivation, whereas PhaRC(YB4) synthesized low-molecular-weight P(3HB) (M(n) = 20 × 10(3)). The molecular weight of P(3HB) synthesized by PhaRC(YB4) decreased with increasing culture time and temperature. This time-dependent behavior was observed for hybrid synthase PhaR(Bm)C(YB4), but not for PhaR(YB4)C(Bm). These results suggest that the molecular weight change is caused by the PhaC(YB4) subunit. The homology between PhaCs from B. megaterium and B. cereus YB-4 is 71% (amino acid identity); however, PhaC(YB4) was found to have a previously unknown effect on the molecular weight of the P(3HB) synthesized in E. coli.     

FunRich: An open access standalone functional enrichment and interaction network analysis tool

As high‐throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user‐friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich ( http://www.funrich.org ) is user‐friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).     

Biochemical and molecular characterisation of the 2,3-dichloro-1-propanol dehalogenase and stereospecific haloalkanoic dehalogenases from a versatile <Emphasis Type="Italic">Agrobacterium</Emphasis> sp.

We previously reported the presence of both haloalcohol and haloalkanoate dehalogenase activity in the Agrobacterium sp. strain NHG3. The versatile nature of the organism led us to further characterise the genetic basis of these dehalogenation activities. Cloning and sequencing of the haloalcohol dehalogenase and subsequent analysis suggested that it was part of a highly conserved catabolic gene cluster. Characterisation of the haloalkanoate dehalogenase enzyme revealed the presence of two stereospecific enzymes with a narrow substrate range which acted on d -2-chloropropionic and I-2-chloropropionoic acid, respectively. Cloning and sequencing indicated that the two genes were separated by 87 bp of non-coding DNA and were preceded by a putative transporter gene 66 bp upstream of the d-specific enzyme.