Multi-gene region phylogenetic analyses suggest reticulate evolution and a clade of Australian origin among paleotropical woody bamboos (Poaceae: Bambusoideae: Bambuseae)

The paleotropical woody bamboo subtribe Bambusinae has not been satisfactorily circumscribed and remains a major taxonomic problem. Genera such as Holttumochloa, Mullerochloa and Temburongia have not been confidently assigned to this subtribe. The phylogenetic relationships among genera hitherto placed in or near the Bambusinae, together with the related subtribes Racemobambosinae and Melocanninae, were investigated using three chloroplast DNA markers (rps16-trnQ, trnC-rpoB and trnD-T intergenic spacers) and a nuclear DNA marker (granule-bound starch synthase I, GBSSI) for a sample of 51 ingroup species and 2 outgroup species. Phylogenetic analyses revealed four distinct lineages among the members of the currently recognized Bambusinae: (1) the Bambusa-Dendrocalamus-Gigantochloa (BDG) complex, (2) the Holttumochloa-Kinabaluchloa clade, (3) the Dinochloa-Mullerochloa-Neololeba-Sphaerobambos (DMNS) clade and (4) Temburongia simplex. The BDG complex, which comprises the core of the Bambusinae, appears to have a complex evolutionary history as indicated by incongruence between the cpDNA and the nuclear gene topologies. Introgressive hybridization and incomplete lineage sorting are possible underlying causes for this complexity. The distinction of the climbing-scrambling bamboo lineages from the core Bambusinae and Racemobambosinae suggests directions for investigating the possible existence of further subtribes with increased taxon and geographical sampling. Possible biogeographic scenarios associated with the Holttumochloa-Kinabaluchloa clade and the DMNS clade are discussed.     

Identification of pathogenic Helicobacter species by chaperonin-60 differentiation on plastic DNA arrays

A microarray method for bacterial species identification based on cpn60 and 16S rDNA hybridization was developed. Specific cpn60 or 16S rDNA oligonucleotides from various Helicobacter or Campylobacter species were printed and immobilized onto a proprietary plastic solid support. Using universal primers, fragments derived from either cpn60 or 16S rDNA genes from single isolates or from a complex human waste sludge DNA sample spiked with Helicobacter pylori were biotinylated and hybridized to the plastic slide. Subsequent querying with a streptavidin-horseradish peroxidase conjugate followed by color development using tetramethylbenzidine resulted in accurate Helicobacter species identification with no cross-hybridization to either the 16S rDNA or the cpn60 sequence of a closely related strain of Campylobacter jejuni. The combination of a nonfluorescence visual detection system with a polymer-based DNA microarray slide has resulted in a molecular tool that should prove useful in numerous applications requiring rapid, low-cost bacterial species identification.     

Nucleotide sequence of the cryptic plasmid pTT8 from Thermus thermophilus HB8 and isolation and characterization of its high-copy-number mutant

The complete nucleotide sequence of pTT8, a cryptic plasmid from Thermus thermophilus HB8, was determined. pTT8 was 9328bp long and its G+C content was 69%. pTT8 contained eight putative open reading frames, three of which showed extensive similarities to the plasmid addiction proteins PasA and PasB of pTC-F14 and pAM10.6, and the RepA protein of the ColE2-related plasmids, respectively. During the analysis of pTT8-based plasmid pPP442, which had been obtained during a promoter-screening experiment, we occasionally isolated a plasmid with a relatively high-copy-number. This plasmid, pPP442m, contained a 1025 bp fragment derived from the genome of the HB27 host strain immediately upstream of the putative repA gene. Using the ori region of pPP442m, we constructed an expression vector, pTEV131m, with an estimated high-copy-number of 30-40. This plasmid was stably maintained in T. thermophilus HB27 under nonselective conditions for at least 100 generations. Cloning of the alpha-amylase gene of Bacillus stearothermophilus DY-5 into pTEV131m gave more than twofold production of the enzyme compared with pTEV131, the parental plasmid.     

PREDATION BY THE TOXIC DINOFLAGELLATE DINOPHYSIS FORTII ON THE CILIATE MYRIONECTA RUBRA AND OBSERVATION OF SEQUESTRATION OF CILIATE CHLOROPLASTS1

This is the first report of the propagation of the toxic dinoflagellate Dinophysis fortii Pavill. under laboratory conditions when fed on the marine ciliate Myrionecta rubra grown with the cryptophyte Teleaulax amphioxeia (W. Conrad) D. R. A. Hill. In contrast, reduced growth of D. fortii (max. of 3–4 divisions) and formation of small cells were observed in the absence of the ciliate or when provided with T. amphioxeia only as prey, showing that D. fortii cannot utilize T. amphioxeia as prey. In the TEM observation of D. fortii cells, which had fully fed on the ciliate prey, well‐developed chloroplasts (5–12 μm in length) were seen and three thylakoids were usually arranged in most of the chloroplasts observed, but chloroplasts having two thylakoids were sometimes confirmed. In cells starved for 4 weeks, decrease of chloroplast numbers and disappearance of large chloroplasts were observed, and only a few small chloroplasts (0.5–2 μm in length) remained in the marginal regions. In the observation of the sequestration process of the chloroplasts ingested from M. rubra by D. fortii, within 15 min after D. fortii captured M. rubra, incorporation of almost all of the chloroplasts was observed, while most of the other cell contents still remained in the M. rubra cell. After that, dispersion of the ingested chloroplasts toward the marginal regions was confirmed, suggesting that chloroplasts of M. rubra are ingested and dispersed in D. fortii cells in advance of the ingestion of the other cell contents to prevent them from being digested in food vacuoles. The ingested chloroplasts can also function as kleptoplastids.     

Effects of coastal reclamation on riverine macrobenthic infauna (Sungei Punggol) in Singapore

A three-year annual survey (1998–2000) wascarried out at Sungei (= River) Punggol ofSingapore to investigate the effects of coastalreclamation on macrobenthic community. Familynumber and abundance of macrobenthossignificantly decreased close to the reclaimedarea but significantly increased away from itduring the survey period. Community structureof macrobenthic infauna also changedsignificantly over time. Very few benthicanimals were found near the reclaimed area, andfamily number and abundance of macrobenthosincreased with distance from the reclaimedarea. These results suggest that reclamationhas a damaging effect on macrobenthic communityand significantly changes the community structure of macrobenthos, but may be beneficial to benthic infauna beyond the reclaimed area.     

Global stability in a class of prey-predator models

Global stability is established in a class of prey-predator models. This includes a prey-predator model in which the predator has Type 2 functional response and no intraspecific interactions. Two simple examples demonstrate that Kolmogoroff’s theorem does not apply to some members of this class of models.     

Structural and functional domains in human tumour necrosis factors.

Human tumour necrosis factors (hTNFs) alpha and beta are related pleiotropic cytokines which share many activities and compete with each other for binding to two receptor components on many cell types. Although structural and biological data indicate that the active form of hTNF-alpha may be a symmetrical trimer, the manner in which hTNFs interact with their receptors to trigger a myriad of cell type-dependent responses is not clear. A combination of chemical modification, epitope mapping and site-directed mutagenesis approaches suggest that at least four distinct peptide sequences are important for the biological activity of hTNF-alpha. In particular, certain peptide sequences between amino acid positions 11 and 35 in hTNF-alpha appear to be critical for receptor binding and triggering biological responses. The recent cloning of the two hTNF-alpha/beta receptors opens the way for precise mapping of the functional domains in hTNFs.