T-RMSD: A Fine-grained, Structure-based Classification Method and its Application to the Functional Characterization of TNF Receptors

This study addresses the relation between structural and functional similarity in proteins. We introduce a novel method named tree based on root mean square deviation (T-RMSD), which uses distance RMSD (dRMSD) variations to build fine-grained structure-based classifications of proteins. The main improvement of the T-RMSD over similar methods, such as Dali, is its capacity to produce the equivalent of a bootstrap value for each cluster node. We validated our approach on two domain families studied extensively for their role in many biological and pathological pathways: the small GTPase RAS superfamily and the cysteine-rich domains (CRDs) associated with the tumor necrosis factor receptors (TNFRs) family. Our analysis showed that T-RMSD is able to automatically recover and refine existing classifications. In the case of the small GTPase ARF subfamily, T-RMSD can distinguish GTP- from GDP-bound states, while in the case of CRDs it can identify two new subgroups associated with well defined functional features (ligand binding and formation of ligand pre-assembly complex). We show how hidden Markov models (HMMs) can be built on these new groups and propose a methodology to use these models simultaneously in order to do fine-grained functional genomic annotation without known 3D structures. T-RMSD, an open source freeware incorporated in the T-Coffee package, is available online.     

Micropropagation of Curry Leaf Tree [Murraya koenigii (L.) Spreng.] by axillary proliferation using intact seedlings

An efficient and reproducible procedure for the large scale propagation of Murraya koenigii (L.) Spreng. (Curry Leaf Tree) is described. High-frequency direct shoot proliferation was induced in intact seedlings of M. koenigii on modified Murashige and Skoog (1962) (MS) medium supplemented with 5.0 mg/l benzyladenine. Shoot buds originated from the region adjacent to the apex of the primary shoot and the epicotyledonary node of the intact seedling. Shoots elongated following transfer to MS medium without plant growth regulators. The shoot-forming capacity of intact seedlings was influenced by explant orientation. Maximum shoot proliferation was obtained when the shoot-forming region was in direct contact with the medium surface or slightly embedded into the medium. Proliferating shoot cultures were established by repeatedly subculturing mother seedlings on fresh medium of the same composition after excising all newly formed shoots. Roots were formed on excised shoots when they were transfered to half-strength MS containing 1.0 mg/l indole-3-butyric acid. Plantlets were acclimatized and established in soil where they exhibited normal growth. Received: 25 September 1996 / Revised version received: 5 May 1997 / Accepted: 22 May 1997     

The effect of human disturbance on tree species composition and demographic structure in Kalinzu Forest Reserve,Uganda

Tree abundance and species composition in the mechanically logged, intensively pitsawn and minimally disturbed areas of Kalinzu Forest Reserve were determined. The spatial and diameter size‐class distribution of ten selected tree species representing pioneer, secondary colonizer, understorey, canopy, dominant and endangered species were also assessed. The species were: Musanga leo‐errerae, Trema orientalis, Funtumia africana, Strombosia scheffleri, Oxyansus speciosus, Parinari excelsa, Tabernaemontana holstii, Newtonia buchananii, Lovoa swynnertonii and Entandrophragma angolense. The mean stem density of all trees ≥0.5 m in height was 2809.1 per hectare and 150 species were enumerated in the three forest areas. Most individuals (47.73%) and species (75.0%) were recorded in the minimally disturbed and least in the mechanically logged areas. Of the selected species, F. africana was the most abundant (n = 789) and widely distributed in each of the areas. Entandrophragma angolense was the least abundant (n = 63) and most of its individuals (74.6%) were recorded in the minimally disturbed area. Funtumia africana and S. scheffleri (subcanopy), O. speciosus and T. holstii (understorey), N. buchananii (canopy) and P. excelsa (an upper canopy and a climax species of this forest reserve) had an inverse J‐shaped diameter size‐class structure while pioneer species (M. leo‐errerae and T. orientalis) had a bell‐shaped size‐class structure.     

Nesting biology of Black-shouldered Kite (Elanus caeruleus) in oil palm landscape in Carey Island,Peninsular Malaysia

Black-shouldered Kite (Elanus caeruleus) is a well-known raptor that inhabits open areas such as oil palm plantation or paddy field. To determine preferable habitat and nesting site of Black-shouldered Kite in oil palm landscape, we conducted a study on Black-shouldered Kite’s nesting biology in Carey Island, Selangor, Malaysia. We divided the island into six types of habitat and conducted road-side count of Black-shouldered Kite from April 2009 to February 2011. Whenever the Black-shouldered Kite was detected, we thoroughly searched the surrounding area for their nest. In total, we have recorded forty nests. The nests were built on 15 species of trees but most of the trees shared common physical characteristics. Some novice breeders also used oil palm tree as their nesting site. Structure and building materials of nests constructed on oil palm trees were different from nests built on other trees. Of all breeding attempts, only four nests which were located in residential area adjacent to young oil palm habitat were successful. Among important characteristics of successful nesting site include taller trees with strong branches and good leaf coverage. These trees not only protect nests from predator detection (except from other predatory birds) and physical environment but also facilitate Black-shouldered Kite’s foraging activities by providing good vantage point.     

Proteinase inhibitors from lonchocarpus capassa (appleleaf) seed

Four proteinase inhibitors (DE-1 to DE-4) were purified from L. capassa seed by chromatographic procedures involving Sephadex G-50 and DEAE-cellulose. They comprise each 80 amino acids (MW ca 10 000) including fourteen half-cystine residues. The partial amino acid sequence of inhibitor DE-4 was determined; 60 of the 80 residues have been sequenced. The MW, cystine content and partial sequence of DE-4 resemble those of the Bowman-Birk-type proteinase inhibitors. The properties of inhibitors DE-1 and DE-4 are very similar. Each contains a potent inhibitor for porcine trypsin but they inhibit bovine α-chymotrypsin only weakly.     

Plant regeneration through somatic embryogenesis in protoplast cultures of sandalwood (Santalum album L.)

Summary Protoplasts were isolated from embryogenic cell suspension cultures derived from proliferating shoot segments of a 20-year-old sandalwood tree (Santalum album Linn.). Under appropriate conditions, isolated protoplasts divided in liquid culture medium and produced embryogenic cell aggregates and globular embryos. Plating of cell aggregates on a fresh medium facilitated the differentiation of somatic emryos which further developed into plantlets.Abbreviations BAP 6-benzylaminopurine - 2,4-D 2,4-dichlorophenoxyacetic acid - GA₃ Gibberellic acid - IAA indoleacetic acid - IBA indolebutrytic acid - MES 2-(N-morpholino)ethane sulfonic acid - MS Murashige and Skoog's medium as modified in the text     

Performance of two Picea abies (L.) Karst. stands at different stages of decline

Summary The water relations of Picea abies in a healthy stand with green trees only and a declining stand with trees showing different stages of needle yellowing were investigated in northern Bavaria. The present study is based on observations of trees differing in their nutritional status but apparently green on both sites in order to identify changes in the response pattern which might be caused by atmospheric concentrations of air pollutants and could lead to the phenomenon of decline. Transpiration was measured as water flow through the hydroactive xylem using an equilibrium mass-flow measurement system. Total tree transpiration was monitored diurnally, from July 1985 until October 1985 at both sites. The relationship between transpiration and meteorological measurements indicated that transpiration was a linear function of the vapor pressure deficit. No differences in transpiration of green trees were observed between the two sites. Canopy transpiration was 57%–68% of total throughfall and 41%–54% of total rainfall. Due to this positive water balance, soil water potential at 10 and 20 cm depths remained close to-0.02 MPa (max.-0.09 MPa) for most of the summer. Soil water potential was correlated with the difference between the weekly precipitation and transpiration. No differences in the water relations of apparently healthy trees in the two P. abies stands were observed. It is concluded that differences between green trees at the two sites in terms of nutrient relations or growth rate cannot be explained by changes in whole-tree transpiration or soil water status.     

Assessment of the competitiveness of fast-growing rhizobia infectingAcacia senegal using antibiotic resistance and melanin production as identification markers

The competitiveness of fourRhizobium sp. strains infectingAcacia senegal and originating in the Sudan was assessed in a growth chamber experiment using Sudanese soil, WhenAcacia senegal was inoculated with pure cultures of the strains, there were statistically significant differences among the strains with respect to the numbers of nodules formed, the amount of dry matter produced and acetylene reduction activity. However, the best strain when applied as a pure culture, was only the second best as a competitor. Two strains with inferior symbiotic capabilities were also bad competitors but nevertheless reduced the yields of the plants when they were applied as inocula mixed with the better strains. The bacterial markers used to assess nodule occupancy were resistance to streptomycin or spectinomycin. Two of the strains formed the dark-brown pigment melanin. Melanin production was a stable characeristic, well suited to serve as an intrinsic identification marker when assessing the competitiveness of melanin-producing versus non-producing strains in controlled conditions.     

Mariculture development in Kenya: alternatives to siting ponds in the mangrove ecosystem

Pond culture of brackishwater prawns and shrimps has recently generated much interest in Kenya. The mangrove areas are the target zones for the construction of these ponds. With the increasing awareness of the unique ecological role played by the mangroves, there is an urgent need to stop the conversion of mangrove swamps into aquaculture ponds. To develop pond aquaculture without destroying the mangroves, a shift from tide-fed to pump-fed pond systems is recommended in order to divert the farming from the mangroves to higher grounds. Mangrove-friendly mariculture practices like pen, cage and raft culture are discussed. Methods of efficiently utilising the already destroyed mangrove areas are considered.