Diversity of antagonistic bacteria isolated from medicinal plant Peganum harmala L.

The antimicrobial activity of plant extract of Peganum harmala, a medicinal plant has been studied already. However, knowledge about bacterial diversity associated with different parts of host plant antagonistic to different human pathogenic bacteria is limited. In this study, bacteria were isolated from root, leaf and fruit of plant. Among 188 bacterial isolates isolated from different parts of the plant only 24 were found to be active against different pathogenic bacteria i.e. Escherichia coli, Methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecium, Enterococcus faecalis and Pseudomonas aeruginosa. These active bacterial isolates were identified on the basis of 16S rRNA gene analysis. Total population of bacteria isolated from plant was high in root, following leaf and fruit. Antagonistic bacteria were also more abundant in root as compared to leaf and fruit. Two isolates (EA5 and EA18) exhibited antagonistic activity against most of the targeted pathogenic bacteria mentioned above. Some isolates showed strong inhibition for one targeted pathogenic bacterium while weak or no inhibition for others. Most of the antagonistic isolates were active against MRSA, following E. faecium, P. aeruginosa, E. coli and E. faecalis. Taken together, our results show that medicinal plants are good source of antagonistic bacteria having inhibitory effect against clinical bacterial pathogens.     

Biogeography of bloom-forming microcystin producing and non-toxigenic populations of Dolichospermum lemmermannii (Cyanobacteria)

In the last decades, the cyanobacterium Dolichospermum lemmermannii showed an increasing spread to Southern Europe, raising serious concerns due to its ability to produce cyanotoxins. The widening of its geographic distribution and the observation of strains showing high optimum temperature underline its ecological heterogeneity, suggesting the existence of different ecotypes. To investigate its biogeography, new isolates from different European water bodies, together with strains maintained by the Norwegian Institute for Water Research Culture Collection of Algae, were genetically characterised for the 16S rRNA gene and compared with strains obtained from public repositories. Geographic distance highly influenced the differentiation of genotypes, further suggesting the concurrent role of geographic isolation, physical barriers and environmental factors in promoting the establishment of phylogenetic lineages adapted to specific habitats. Differences among populations were also examined by morphological analysis and evaluating the toxic potential of single strains, which revealed the exclusive ability of North European strains to produce microcystins, whereas the populations in Southern Europe tested negative for a wide range of cyanotoxins. The high dispersion ability and the existence of toxic genotypes indicate the possible spread of harmful blooms in other temperate regions.     

Latitudinal comparison of altitudinal changes in forest structure,leaf-type,and species richness in humid monsoon Asia

A new template for mountain vegetation zonation along latitudinal gradients is proposed for examining geographical pattern of various forest attributes in humid monsoon Asia. The contrasting temperature regime in tropical and temperate mountains, i.e., the former is a non-seasonal, temperature-sum controlled environment, and the latter is a seasonal, low temperature limiting environment, leads to different altitudinal patterns of tree height distribution and species richness. In the tropical mountains, both tree height and species richness decrease steeply, and the tree height often stepwise. The decline of tree height and species diversity in the temperate mountains is far less pronounced except near the forest limit. Both trends are explained by their temperature regime.     

The mitochondrial genome of Gatzara jezoensis (Neuroptera: Myrmeleontidae) and phylogenetic analysis of Neuroptera

Phylogenetic relationship within Neuroptera is controversial, particularly for the various hypotheses based on both morphological and molecular evidence. In the present study, we determined the complete mitochondrial genome (mitogenome) of Gatzara jezoensis, which is the second representative of the tribe Dendroleontini. The G. jezoensis mitogenome contained the conserved set of 37 mitochondrial genes and a putative control region, with a conserved gene arrangement which was similar to that of most sequenced neuropteran mitogenomes. All transfer RNAs exhibited the canonical cloverleaf secondary structure, except for trnS^(AGN). The control region contained two conserved elements (ploy-T stretch and ATGGTTCAAYAAAATAAYYCYCTC motif) and abundant microsatellite-like elements. The phylogenetic analysis of sequenced neuropteran mitogenomes using the concatenated protein-coding genes (PCGs) and ribosomal genes recovered the monophyly of Myrmeleontidae, which revealed this dataset could generate the more robust phylogeny of Neuroptera than that of 13 PCGs dataset.     

Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.     

De novo organogenesis and plant regeneration in <Emphasis Type="Italic">Pongamia pinnata</Emphasis>, oil producing tree legume

Role of Thidiazuron (TDZ) in inducing adventitious organogenesis in Pongamia was studied. TDZ at different concentrations (0, 0.45, 2.27, 4.54, 6.71, 9.08, 11.35, 13.12 and 22.71 μM) were used for induction of caulogenic bud formation in deembryonated cotyledon explants. Each cotyledon was cut into three segments and identified as proximal, middle and distal. Duration of TDZ exposure, influence of the segment and orientation of the explant were studied. TDZ at 11.35 μM concentration was optimum for the induction of shoots and rapid elongation. Shoots induced at higher concentration elongated after several passages in growth regulator free medium, thereby extending the period of differentiation. Exposure of the explant for 20 days yielded more number of buds than 10 days. Proximal segment of the cotyledon was more responsive. Contact of abaxial surface in the medium was more effective and generated more buds than the adaxial side. Buds differentiated and elongated on transfer to MS basal medium for 8–12 passages of 15 days each. Rooting and elongation of shoots was achieved in charcoal supplemented half-strength MS medium. Rooted plantlets survived on transfer to sand soil mixture. The plants were hardened and transferred to green house. This is the first report on in vitro regeneration of Pongamia pinnata via adventitious organogenesis using TDZ. This protocol may find application in studies in genetic transformation, isolation of somaclonal variants and in induction of mutants. It also provides a system to study the inhibitory role of TDZ on shoot differentiation.     

A cladistic and comparative analysis of kinematic components of the fast-start of fishes,with a note on body size constraints

The fast-start is an ecologically relevant behavior pattern in fishes. The present article analyses the distribution of five continuous kinematic traits (latency for response initiation, time to maximum angular velocity, time to maximum displacement velocity, maximum angular velocity, and maximum displacement velocity) in eight of the eleven species described in Eaton (66:65–81, 1977). Phylogenetic generalized least square estimation of ancestor states demonstrated evolutionary changes in maximum angular velocity and maximum displacement velocity, consistent with species differences in the same variables. These changes in maximum velocity are also correlated (phylogenetically independent contrasts) with the mean body sizes of all species, pointing to the possibility that body size was an evolutionary constraint on maximum velocities. The conservation of the other traits suggest that they are mainly constrained by neural control, and a trade-off between neural and body size-constraints is proposed ex hypothesi. An erratum to this article can be found at     

Curiously Modern DNA for a ``250 Million-Year-Old' Bacterium

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the ∼59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. Received: 12 April 2001 / Accepted: 9 June 2001     

Priors for the Bayesian star paradox

We show that the Bayesian star paradox, first proved mathematically by Steel and Matsen for a specific class of prior distributions, occurs in a wider context including less regular, possibly discontinuous, prior distributions.     

Statistical properties of the ordinary least-squares,generalized least-squares,and minimum-evolution methods of phylogenetic inference

Summary Statistical properties of the ordinary least-squares (OLS), generalized least-squares (GLS), and minimum-evolution (ME) methods of phylogenetic inference were studied by considering the case of four DNA sequences. Analytical study has shown that all three methods are statistically consistent in the sense that as the number of nucleotides examined (m) increases they tend to choose the true tree as long as the evolutionary distances used are unbiased. When evolutionary distances (d_ij's) are large and sequences under study are not very long, however, the OLS criterion is often biased and may choose an incorrect tree more often than expected under random choice. It is also shown that the variance-covariance matrix of d_ij's becomes singular as d_ij's approach zero and thus the GLS may not be applicable when d_ij's are small. The ME method suffers from neither of these problems, and the ME criterion is statistically unbiased. Computer simulation has shown that the ME method is more efficient in obtaining the true tree than the OLS and GLS methods and that the OLS is more efficient than the GLS when d_ij's are small, but otherwise the GLS is more efficient.Offprint requests to: M. Nei