GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.     

Evidence for naturally acquired T cell-mediated mucosal immunity to Neisseria meningitidis

Naturally acquired protective immunity against Neisseria meningitidis is thought to partially explain the disparity between the high levels of carriage in the human nasopharynx and the rare incidence of disease. To investigate this immunity to Neisseria meningitidis at the mucosal level, in vitro cellular responses to outer membrane vesicle preparations derived from this pathogen were examined using mononuclear cells from the palatine tonsils of adults and children. Characterization of these responses was achieved by depletion of CD45RA(+), CD45RO(+), and CD19(+) populations and outer membrane vesicles derived from isogenic mutants expressing different serosubtypes of the major outer membrane protein, porin A (PorA), no PorA and membrane preparations from a mutant with no LPS (LpxA(-)). The magnitude of cellular proliferative responses against the outer membrane vesicles were strongly associated with age and were largely T cell mediated, involving both CD45RO(+) and CD45RA(+) T cell phenotypes. Responses were not dependent on LPS but consisted of both PorA cross-specific and non-PorA-dependent responses. Cellular immunity against Neisseria meningitidis was found to be frequently associated with systemic IgG Abs but was not associated with serum bactericidal Abs. For the first time our results demonstrate an age-associated acquisition of mucosal T effector/memory cell responses to Neisseria meningitidis. This mucosal cellular immunity can be present in the absence of serum bactericidal Abs, a classical marker of protective immunity.     

Serum pigmentation in Cyclopterus lumpus L

Female lumpsuckers, Cyclopterus lumpus L., have blue-green blood serum and subcutaneous gelatinous tissue; the male's are red/magenta in colour. The female serum contains a chromoprotein with biliverdin as the prosthetic group; the male serum contains the same biliverdin pigment but this is normally masked by a red pigment, probably phycoerythrin. The female serum also contains the red pigment but at a much lower concentration than in the male. These bile pigments are probably formed by the breakdown of haem in the liver. Lumpsucker gall bladders are relatively small and do not enlarge during starvation. Storage of bile pigments in the serum and subcutaneous jelly may have arisen in response to the problems of regular long-term starvation. The pigments now appear to have an additional sexual signalling function.     

Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection

Several primate models indicate that cytotoxic T lymphocyte-inducing vaccines may be unable to prevent human immunodeficiency virus infection but may have a long-term benefit in controlling viral replication and delaying disease progression. Here we show that analysis of the kinetics of antigen-specific CD8+ T-cell expansion suggests a delay in activation following infection that allows unimpeded early viral replication. Viral kinetics do not differ between controls and vaccinees during this delay phase. An increase in virus-specific CD8+ T-cell numbers around day 10 postinfection coincides with a slowing in viral replication in vaccinees and reduces peak viral loads by around 1 log. However, this response is too little too late to prevent establishment of persistent infection.     

Discovery of novel, orally active dual NK1/NK2 antagonists

Exploration of the SAR around selective NK2 antagonists, SR48968 and ZD7944, led to the discovery that naphth-1-amide analogues provide potent dual NK1 and NK2 antagonists. ZD6021 inhibited binding of [3H]-NKA or [3H]-SP to human NK1 and NK2 receptors, with high-affinity (K(i)=0.12 and 0.62nM, respectively). In functional assays ZD6021 had, at 10(-7)M, in human pulmonary artery pK(B)=8.9 and in human bronchus pK(B)=7.3, for NK1 and NK2, respectively. Oral administration of ZD6021 to guinea pigs dose-dependently attenuated ASMSP induced extravasation of plasma proteins, ED(50)=0.5mg/kg, and NK2 mediated bronchoconstriction, ED(50)=13mg/kg.     

Progesterone treatment abolishes exogenously expressed ionic currents in Xenopus oocytes

Fully grown oocytes of Xenopus laevis undergo resumption of the meiotic cycle when treated with the steroid hormone progesterone. Previous studies have shown that meiotic maturation results in profound downregulation of specific endogenous membrane proteins in oocytes. To determine whether the maturation impacts the functional properties of exogenously expressed membrane proteins, we used cut-open recordings from Xenopus oocytes expressing several types of Na(+) and K(+) channels. Treatment of oocytes with progesterone resulted in a downregulation of heterologously expressed Na(+) and K(+) channels without a change in the kinetics of the currents. The time course of progesterone-induced ion channel inhibition was concentration dependent. Complete elimination of Na(+) currents temporally coincided with development of germinal vesicle breakdown, while elimination of K(+) currents was delayed by approximately 2 h. Coexpression of human beta(1)-subunit with rat skeletal muscle alpha-subunit in Xenopus oocytes did not prevent progesterone-induced downregulation of Na(+) channels. Addition of 8-bromo-cAMP to oocytes or injection of heparin before progesterone treatment prevented the loss of expressed currents. Pharmacological studies suggest that the inhibitory effects of progesterone on expressed Na(+) and K(+) channels occur downstream of the activation of cdc2 kinase. The loss of channels is correlated with a reduction in Na(+) channel immunofluorescence, pointing to a disappearance of the ion channel-forming proteins from the surface membrane.     

Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants

The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P < 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m(3) completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 x 10(6) cells ml(-1) or 4 x 10(12) cells m(-2). We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge.     

A weakly voltage-dependent, nonselective cation channel mediates toxic sodium influx in wheat

To determine the transporters responsible for toxic Na(+) influx in wheat (Triticum aestivum), root plasma membrane preparations were screened using the planar lipid bilayer technique as an assay for Na(+)-permeable ion channel activity. The predominant channel in the bilayer was a 44-pS channel that we called the nonselective cation (NSC) channel, which was nonselective for monovalent cations and weakly voltage dependent. Single channel characteristics of the NSC channel were compared with (22)Na(+) influx into excised root segments. Na(+) influx through the NSC channel resembled (22)Na(+) influx in its partial sensitivity to inhibition by Ca(2+), Mg(2+), and Gd(3+), and its insensitivity to all other inhibitors tested (tetraethylammonium, quinine, Cs(+), tetrodotoxin, verapamil, amiloride, and flufenamate). Na(+) influx through the NSC channel also closely resembled an instantaneous current in wheat root protoplasts (S.D. Tyerman, M. Skerrett, A. Garill, G.P. Findlay, R. Leigh [1997] J Exp Bot 48: 459-480) in its permeability sequence, selectivity for K(+) over Na(+) (approximately 1.25), insensitivity to tetraethylammonium, voltage independence, and partial sensitivity to Ca(2+). Comparison of tissue, protoplast (S.D. Tyerman, M. Skerrett, A. Garill, G.P. Findlay, R. Leigh [1997] J Exp Bot 48: 459-480), and single- channel data indicate that toxic Na(+) influx is catalyzed by a single transporter, and this is likely to be the NSC channel identified in planar lipid bilayers.     

Butterfly species richness and abundance in the Katavi ecosystem of western Tanzania

We sampled butterflies in six different habitat types in and around Katavi National Park, a remote reserve consisting primarily of miombo woodland and seasonal lakes in western Tanzania. Blendon traps set for 531 trap days and 143 h of butterfly netting at 35 sites yielded 186 species from five families over a 4‐month period during the wet season. Eight of these species constituted possible range extensions. Butterfly abundance and species richness were low in cultivated habitats but high in open riverine habitats; many butterfly species were found only in seasonally flooded grassland. This study constitutes the first butterfly species inventory from this poorly‐known national park, shows that protection of dry season water sources provides an important conservation service for invertebrates as well as large mammals, and that increased cultivation outside miombo parks can reduce local butterfly diversity.     

Foraging impacts of Asian megafauna on tropical rain forest structure and biodiversity

Megaherbivores are known to influence the structure, composition, and diversity of vegetation. In Central Africa, forest elephants act as ecological filters by breaking tree saplings and stripping them of foliage. Much less is known about impacts of megafauna on Southeast Asian rain forests. Here, we ask whether herbivory by Asian megafauna has impacts analogous to those of African forest elephants. To answer this, we studied forest (1) structure, (2) composition, (3) diversity, and (4) tree scars in Belum and Krau, two protected areas of Peninsular Malaysia, and compared the results with those obtained in African forests. Elephants are abundant in Belum but have been absent in Krau since 1993. We found that stem density and diversity, especially of tree saplings, were higher in Krau than in Belum. Palms and other monocots were also more abundant in Krau. In Belum, however, small monocots (<1 m tall) were very abundant but larger ones (>1 m tall) were virtually absent, suggesting size‐selective removal. The frequency of stem‐break scars was equal at Belum and Krau but less than in Central Africa and greater than in the Peruvian Amazon where tapirs are the only megafauna. Pigs and tapirs could also contribute to the high frequency of tree scars recorded in Malaysian forests. Forest‐dwelling elephants in Asia seem to have a reduced impact on tree saplings compared to African forest elephants, but a very strong impact on monocots.