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PubMed2004

RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.

Two, apparently functional, paralogues of the RPB2 gene, which encodes the second largest subunit of RNA polymerase II, are shown to be present in two major groups of asterid plants. Although all other land plants surveyed so far have been found to have only one of these two copies, the RPB2 gene phylogeny inferred from the 3' half of the gene for 35 angiosperm taxa and six other land plants indicates that the duplication of the RPB2 gene occurred earlier than the time for origin of the asterid group, probably near the origin of "core eudicots." The d copy is present in all plants which are unambiguously assigned to the core eudicots, whereas the I copy is retained only in the lamiid clade, Ericales, and Escallonia, all belonging to the asterid group of plants. Both parsimony and likelihood analyses of sequences from the 3' half of the gene give strong bootstrap support for these conclusions. There is no support for monophyly of the taxa having both copies. Thus, numerous losses of one of the copies must be inferred. Structurally, both paralogues appear functional, and transcription is demonstrated for both copies. In the lamiid group, the d copy has lost introns 18-23. The well supported phylogenetic relationships implied by the RPB2 gene phylogeny are largely congruent with well supported phylogenetic hypotheses based on other sequence data. However, Ilex, usually assigned to the campanuliid clade, is instead supported as being a member of the lamiid clade, both from sequence data and the presence of an I copy as well as the loss of introns 18-23 in the d copy. Escallonia, supported as a member of the campanuliid clade both by RPB2-d-sequences and previously published DNA sequence data, has all the introns 18-23 in its d copy, as do all other members studied from the campanuliid group. We used the Markov Chain Monte Carlo (MCMC) approach of the MrBayes program to implement Maximum Likelihood bootstrapping. Under the same model of evolution, bootstrapping frequencies are significantly lower than the Bayesian posterior probabilities inferred from the MCMC chain.

Gene Dosage↗
PubMed2001

Lateglacial and Early Holocene vegetation history of the northern Wetterau and the Amöneburger Basin (Hessen), central-west Germany.

The Lateglacial and Early Holocene vegetation history of the northern Wetterau and Amöneburger Basin, two intra-montane basins in Hessen, central-west Germany, is reconstructed by means of pollen and macrofossil analyses. Regional pollen assemblage zones are defined for the Lateglacial and Early Holocene. After calibration of the radiocarbon dates and establishment of age/depth relationships, the ages of the pollen zone boundaries are calculated. The regional vegetation changes correlate closely with the major fluctuations in the delta18O curve of the Greenland ice cores spanning the same time period. During the early Lateglacial, the open herbaceous vegetation with dwarf shrubs in the northern Wetterau was replaced by woodlands. Initially these woodlands consisted of birch, but after the immigration of pine, mixed forests of pine and birch developed. Soon after its immigration pine became dominant and pine woodlands largely replaced the birch forests. Only on the locally wetter substrates of the river floodplain did Betula stands persist. Gradually the importance of herbaceous communities declined and the pine woodlands lost their open character. During the Lateglacial two regressive phases in the vegetation succession are reflected in the data which are equated with the Older- and Younger Dryas biozones. At the beginning of the Younger Dryas, the forest-limit was lowered and the importance of herbaceous communities increased. Later, pine woodlands thinned and Ericales became part of the vegetation, indicating the development of more acid, nutrient-poor soils. A subdivision of the Younger Dryas biozone into a wetter, colder first part and a drier, warmer second part is suggested. At the beginning of the Early Holocene, pine woodlands became more closed and soils more stabilised. The transition between the Younger Dryas and Preboreal biozones is indicated by a lithological change to organic (-rich) deposits. Betula stands persisted on the locally wetter substrates of the fluvial plains. At the end of the early Preboreal, there was an extension of Betula stands on the river floodplains. This is interpreted as a phase in which climate was temporarily wetter, perhaps a reflection of a short-term climatic oscillation, the so-called Preboreal oscillation. During the Preboreal biozone, ferns became more important in the local vegetation of the mires, and later during the Boreal they formed the undergrowth of swamp forests. During the Boreal biozone, a major expansion of hazel took place in both areas. On the hills and slopes of the northern Wetterau and the Amöneburger Basin, open pine forests and hazel scrub developed with grasses and Pteridium in the field layer. In the river valleys, pine forests were replaced by deciduous mixed forests with oak, elm and later also with lime.

Journal Article↗
PubMed2004

Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world's largest flower.

All parasites are thought to have evolved from free-living ancestors. However, the ancestral conditions facilitating the shift to parasitism are unclear, particularly in plants because the phylogenetic position of many parasites is unknown. This is especially true for Rafflesia, an endophytic holoparasite that produces the largest flowers in the world and has defied confident phylogenetic placement since its discovery >180 years ago. Here we present results of a phylogenetic analysis of 95 species of seed plants designed to infer the position of Rafflesia in an evolutionary context using the mitochondrial gene matR (1,806 aligned base pairs). Overall, the estimated phylogenetic tree is highly congruent with independent analyses and provides a strongly supported placement of Rafflesia with the order Malpighiales, which includes poinsettias, violets, and passionflowers. Furthermore, the phylogenetic placement of Mitrastema, another enigmatic, holoparasitic angiosperm with the order Ericales (which includes blueberries and persimmons), was obtained with these data. Although traditionally classified together, Rafflesia and Mitrastema are only distantly related, implying that their endoparasitic habits result from convergent evolution. Our results indicate that the previous significant difficulties associated with phylogenetic placement of holoparasitic plants may be overcome by using mitochondrial DNA so that a broader understanding of the origins and evolution of parasitism may emerge.

DNA, Mitochondrial↗
PubMed1986

Zeatin biosynthesis from N-(Delta-isopentenyl)adenine in Actinidia and other woody plants.

Tissue cultures of Actinidia kolomikta can be maintained as callus through repeated passages on a nutrient medium devoid of cytokinin but containing inorganic nutrients, sucrose, and other basal organics plus auxin. Under these conditions, actively growing callus contained 2 and 0.5 nmol of the cytokinins zeatin [io(6)Ade; 6-(4-hydroxy-3-methylbut-2-enylamino)purine] and N(6)-(Delta(2)-isopentenyl)adenine (i(6)Ade), respectively, per gram (fresh weight). When tissues were transferred from cytokininless medium to 30 muM i(6)Ade, endogenous io(6)Ade increased linearly to 160 nmol/g (fresh weight) during 8 hr, and i(6)Ade increased to 5 nmol/g (fresh weight) in 2 hr and then declined. The apparent K(m) for i(6)Ade in A. kolomikta and Actinidia chinensis x Actinidia arguta callus and in tissue slices of A. arguta stems was 12 muM. In addition, the reaction(s) converting i(6)Ade to io(6)Ade was O(2)-requiring and specific for i(6)Ade versus N(6)-(Delta(2)-isopentenyl)adenosine (i(6)A). When A. kolomikta callus was fed 30 muM i(6)A, io(6)Ade increased and reached a concentration corresponding to 6 nmol/g (fresh weight) in 8 hr. Ribosylzeatin (io(6)A) did not increase. Under N(2) during i(6)A feeds, i(6)A accumulated rather than being metabolized to i(6)Ade, suggesting that i(6)A normally may be metabolized via i(6)AMP and i(6)Ade to io(6)Ade. A survey of 30 species of woody plants in 20 families of dicotyledonous angiosperms indicated that the ability to accumulate io(6)Ade (>/=10 nmol/g) in 24-hr feeds with 30 muM i(6)Ade was restricted to certain systematic groups-e.g., order Ericales, families Oleaceae and Rubiaceae. This suggests that plants may differ in their pathways for io(6)Ade biosynthesis and that cytokinin biochemistry has potential as a taxonomic character above the species and genus levels.

Journal Article↗
PubMed2004

Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification.

We present a phylogenetic dating of asterids, based on a 111-taxon tree representing all major groups and orders and 83 of the 102 families of asterids, with an underlying data set comprising six chloroplast DNA markers totaling 9914 positions. Phylogenetic dating was done with semiparametric rate smoothing by penalized likelihood. Confidence intervals were calculated by bootstrapping. Six reference fossils were used for calibration. To explore the effects of various sources of error, we repeated the analyses with alternative dating methods (nonparametric rate smoothing and the Langley-Fitch clock-based method), alternative tree topologies, reduced taxon sampling (22 of the 111 taxa deleted), partitioning the data into three genes and three noncoding regions, and calibrating with single reference fossils. The analyses with alternative topologies, reduced taxon sampling, and coding versus noncoding sequences all yielded small or in some cases no deviations. The choice of method influenced the age estimates of a few nodes considerably. Calibration with reference fossils is a critical issue, and use of single reference fossils yielded different results depending on the fossil. The bootstrap confidence intervals were generally small. Our results show that asterids and their major subgroups euasterids, campanulids, and lamiids diversified during the Early Cretaceous. Cornales, Ericales, and Aquifoliales also have crown node ages from the Early Cretaceous. Dipsacales and Solanales are from the Mid-Cretaceous, the other orders of core campanulids and core lamiids from the Late Cretaceous. The considerable diversity exhibited by asterids almost from their first appearance in the fossil record also supports an origin and first phase of diversification in the Early Cretaceous.

DNA, Chloroplast↗
PubMed2000

A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes.

Ericoid mycorrhizal fungi form symbioses with the roots of members of the Ericales. Although only two genera have been identified in culture, the taxonomic diversity of ericoid symbionts is certainly wider. Genetic variation among 40 ericoid fungal isolates was investigated in this study. PCR amplification of the nuclear small-subunit ribosomal DNA (SSU rDNA) and of the internal transcribed spacer (ITS), followed by sequencing, led to the discovery of DNA insertions of various sizes in the SSU rDNA of most isolates. They reached sizes of almost 1,800 bp and occurred in up to five different insertion sites. Their positions and sizes were generally correlated with morphological and ITS-RFLP grouping of the isolates, although some insertions were found to be optional among isolates of the same species, and insertions were not always present in all SSU rDNA repeats within an isolate. Most insertions were identified as typical group I introns, possessing the conserved motifs characteristic of this group. However, other insertions lack these motifs and form a distinct group that includes other fungal ribosomal introns. Alignments with almost 70 additional sequences from fungal nuclear SSU rDNA introns indicate that introns inserted at the same site along the rDNA gene are generally homologous, but they also suggest the possibility of some horizontal transfers. Two of the ericoid fungal introns showed strong homology with a conserved motif found in endonuclease genes from nuclear rDNA introns.

Amino Acid Sequence↗
PubMed2006

Petaloidy and petal identity MADS-box genes in the balsaminoid genera Impatiens and Marcgravia.

Impatiens and Marcgravia have striking morphological innovations associated with the flowers. One of the sepals in Impatiens is spurred and petaloid, while in Marcgravia the petals are fused into a cap and nectary cups are associated with the inflorescence. Balsaminaceae (Impatiens) and Marcgraviaceae have surprisingly been shown to be closely related, since both belong to the balsaminoid clade of Ericales (basal asterids). However, several thorough morphological studies thus far have not revealed shared derived characters (synapomorphies) that support a close relationship between these families. In the balsaminoid clade, transitions from entirely green flowers to flowers with heterotopic petaloid organs can be observed. The primary role of class B genes in core eudicots is to specify the identity of petal and stamen floral organs. E-class genes, of which SEP3 is a representative, have been identified as redundant mediators that confer transcriptional activation potential on protein complexes that specify organ identity. Given the conserved function of organ-identity MADS-box genes in model plants, but the rapid molecular evolution in angiosperms, it remains controversial whether these genes have been involved in shaping floral diversity. We have identified a SEP3-like gene and a total of five class B genes from Impatiens hawkeri and Marcgravia umbellata and report their quantitative expression in the floral organs. In Impatiens, two AP3/DEF-like genes were identified with strongly divergent C-terminal domains, one truncated and one unusually long. Both genes show a gradual decrease in expression towards the outer perianth organs, but no GLO-like gene expression is observed in the petaloid sepal. Remarkably, SEP3-like gene expression in the Impatiens perianth is absent from the green sepals but present in the petaloid sepal and in the petals. Dimeric protein interactions of the cloned Impatiens genes were studied in yeast and by using gel retardation. In Marcgravia, strong overlapping class B gene expression is limited to the stamens, but a SEP3-like gene is strongly expressed in the Marcgravia nectary, indicating that both Impatiens and Marcgravia show heterotopic expression of a SEP3-like gene. We discuss several candidate mechanisms for heterotopic petaloidy involving modified gene expression and protein interaction of SEP3-like and class B genes.

Amino Acid Sequence↗
PubMed1998

Herbal remedies in psychiatric practice.

Patients' use of alternative and complementary health services has created a need for physicians to become informed about the current literature regarding these treatments. Herbal remedies may be encountered in psychiatric practice when they are used to treat psychiatric symptoms; produce changes in mood, thinking, or behavior as a side effect; or interact with psychiatric medications. English-language articles and translated abstracts or articles (where available) found on MEDLINE and sources from the alternative/complementary health field were reviewed. Each herb was assessed for its safety, side effects, drug interactions, and efficacy in treating target symptoms or diagnoses. A synopsis of the information available for each herb is presented. In many cases the quantity and quality of data were insufficient to make definitive conclusions about efficacy or safety. However, there was good evidence for the efficacy of St John's wort for the treatment of depression and for ginkgo in the treatment of memory impairment caused by dementia. More research is required for most of the herbs reviewed, but the information published to date is still of clinical interest in diagnosing, counseling, and treating patients who may be taking botanical remedies.

Anti-Anxiety Agents↗
PubMed1999

Combining different phases in the development of medical treatments within a single trial.

In the development of medical treatments, identification of promising therapies and inference on selected treatments are usually performed in subsequent separate trials. An adaptive two-stage design is proposed for the situation of multiple treatments to be compared with a control, allowing integration of both steps within a single confirmatory trial controlling the multiple level alpha. After the interim analysis, the trial may be terminated early or is continued with a second stage, where the set of treatments may be reduced due to lack of efficacy or to safety problems. The procedure is highly flexible with respect to the distributional assumptions, stopping rules and selection criteria and allows a completely free recalculation of the sample size for the second stage. Simulations show that the method may be substantially more powerful than classical one-stage multiple treatment designs with the same total sample size. As in conventional strategies with a series of separate experiments, a reasonable selection strategy has to be applied in order to prevent proceeding with non-optimal treatments.

Clinical Trials as Topic↗
PubMed2000

Anticandidal activity of certain South Indian medicinal plants.

The anticandidal activity of 20 household South Indian medicinal plants and/or plant products was studied using 30 Candida albicans isolates obtained from vaginal candidiasis patients of Rajah Muthiah Medical College and Hospital and compared with the anticandidal activity of garlic. Water and ethanol extracts were prepared and their minimum inhibitory concentrations (MIC) and minimum fungicidal concentrations (MFC) were determined. Water extracts of three plants did not show any anticandidal activity, while Murrya koenigii did not exhibit any anticandidal activity in either extract. Other plants exhibited more activity in ethanol extracts showing that their active principle is more soluble in a non-polar solvent.

Allium↗
PubMed2007

Use of limestone karst forests by Bornean orangutans (Pongo pygmaeus morio) in the Sangkulirang peninsula, east Kalimantan, Indonesia.

The Indonesian province of East Kalimantan is home to some of the largest remaining contiguous tracts of lowland Dipterocarp forest on the island of Borneo. Nest surveys recently conducted in these forests indicated the presence of a substantial population of Eastern Bornean orangutans (Pongo pygmaeus morio) in the Berau and East Kutai regencies in the northern half of the province. The Sangkulirang Peninsula contains extensive limestone karst forests in close proximity to the lowland Dipterocarp forests inhabited by orangutans in these regencies. Orangutans have been sighted in these limestone karst forests, but the importance of this forest type for orangutans has been unclear. Therefore, we conducted 49 km of nest surveys in limestone karst forest to obtain the first quantitative estimates of orangutan densities in this habitat, and walked 28 km of surveys in nearby lowland Dipterocarp forests for comparison. We also gathered basic ecological data along our transects in an attempt to identify correlates of orangutan abundance across these habitat types. Undisturbed limestone karst forests showed the lowest orangutan densities (147 nests/km(2), 0.82 indiv/km(2)), disturbed limestone forests had intermediate densities (301 nests/km(2), 1.40 indiv/km(2)), and undisturbed lowland Dipterocarp forests contained the highest density (987 nests/km(2), 5.25 indiv/km(2)), significantly more than the undisturbed limestone karst forests. This difference was not correlated with variation in liana abundance, fig stem density, or stump density (an index of forest disturbance). Therefore, other factors, such as the relatively low tree species diversity of limestone karst forests, may explain why orangutans appear to avoid these areas. We conclude that limestone karst forests are of low relevance for safeguarding the future of orangutans in East Kalimantan.

Animals↗
PubMed2005

Behavioral response of the borer beetle Hoplocerambyx spinicornis to volatile compounds of the tree Shorea robusta.

Essential oils isolated from leaves (LO), bast (BO), heartwood (HO), and ethereal extract of resin (EER) of Shorea robusta were bioassayed with electroantennograph (EAG) and wind tunnel to study the behavioral response of male and female beetles, Hoplocerambyx spinicornis Newm., the most injurious heartwood borer of the tree. LO, BO, HO, and EER were shown to exhibit the electrophysiological activity in the female beetle, while LO and BO in the male beetle. In wind-tunnel studies, only BO elicited the attractant activity to both the sexes. A possible correlation of the constituents of the BO identified by GC/MS with the bioactivity is also presented.

Animals↗
PubMed2005

Two novel trimeric resveratrol derivatives from Cotylelobium lanceolatum.

Two new resveratrol (= 5-[(E)-2-(4-hydroxyphenyl)ethenyl]benzene-1,3-diol) trimers, cotylelophenols A (1) and B (2), were isolated from the stem of Cotylelobium lanceolatum (Dipterocarpaceae), together with ten known resveratrol oligomers (3-12). The structures of the isolates were established on the basis of spectroscopic analyses, including a detailed NMR spectroscopic investigation of 1 under different conditions. Compound 1 is the first resveratrol trimer with a rearranged 4-hydroxyphenyl group. Four possible biogenetic pathways towards resveratrol oligomers are proposed (Scheme).

Ericales↗
PubMed2005

New resveratrol tetramers from the stem bark of Upuna borneensis.

Five new resveratrol (=5-[(E)-2-(4-hydroxyphenyl)ethenyl]benzene-1,3-diol) tetramers, upunaphenols H-J (1-3) and trans-(4) and cis-upunaphenol K (5), were isolated from the stem of Upuna borneensis (Dipterocarpaceae). Their structures were elucidated on the basis of 1D- and 2D-NMR as well as FAB-MS data. Compounds 1-3 bear a rare biphenyl bond in their frameworks. Compounds 1 and 2 have an unprecedented nonacyclic fused ring system, and compounds 2 and 3 have symmetrical structures.

Ericales↗
PubMed1998

Antibacterial activity of Camellia sinensis extracts against dental caries.

Different bacteria were separated from saliva and teeth of cariogenic patients and identified by a variety of morphological and biochemical tests. Extracts of green tea strongly inhibited Escherichia coli, Streptococcus salivarius and Streptococcus mutans. The antibacterial effect of green and black tea extracts were compared with those of amoxicillin, cephradine and eugenol.

Adolescent↗