Inter-clonal variation in phototactic behaviour and key life-history traits in a metapopulation of the cyclical parthenogen Daphnia ambigua: the effect of fish kairomones

We quantified genetic variation for ecological relevant traits in the presence and the absence of fish chemicals of eleven Daphnia ambigua clones that were isolated from six interconnected ponds that differed in water transparency. In a cohort life table experiment, we tested whether genetic variation for a set of key life history traits was present among these clones. In addition the phototactic behaviour of these clones cultured in the presence and the absence of fish kairomones was quantified using a biotest. We detected a significant effect of fish kairomones on the phototactic behaviour and a highly significant genetic variation among clones for this trait in D. ambigua clones isolated from ponds in De Maten. Differences in size at maturity among D. ambigua clones in De Maten were highly significant, whereas differences in spina length among D. ambigua clones in De Maten were not significant. The presence of fish chemicals did not affect the studied life-history traits. We observed a significant positive relationship between average phototactic behaviour for each population and size at maturity both in the presence as in the absence of fish kairomones. Most of the genetic differences could be attributed to a clone isolated from one clearwater pond that is not directly connected to the remainder of the pond complex.     

Structure and urovirulence characteristics of the fecal Escherichia coli population among healthy women

The fecal Escherichia coli population structure may influence the occurrence and etiology of extraintestinal infection, but is poorly understood. Accordingly, fecal E. coli from 39 healthy women (30 putative colonies per subject) were characterized for clonal identity, urinary tract infection-associated virulence traits, and phylogenetic background. The 120 unique E. coli clones (mean, three per sample) were distributed by phylogenetic group as follows: A (33%), D (31%), B1 (19%), and B2 (17%). However, 36% of women carried ≥1 clone from group B2, and 87% had clones from groups B2 and/or D. Of the B2 clones, 90% were from pauciclonal fecal samples (≤4 clones), compared with 47% and 52% of A and B1 clones (P = .001 and P = .007, respectively). Group B2 and D clones more often were dominant within the source sample than group A and B1 clones (60% vs. 41%: P = .05). Dominant clones exhibited higher virulence scores than non-dominant clones (mean 4.4 vs. 3.1: P = .015). In multilevel regression models, pauciclonal sample, B2, and clonal prevalence significantly predicted virulence score. In conclusion, within the intestinal E. coli population, virulence-associated traits, clonal prevalence, and low fecal clonal diversity are related. Virulence-associated traits of group B2/D E. coli may enhance fitness within the gut, thereby increasing strains’ likelihood of causing extraintestinal infection.     

Inheritance pattern of tetraploid Dioscorea alata and evidence of double reduction using microsatellite marker segregation analysis

Recent studies have shown that the basic chromosome number of the three major edible yams, Dioscorea alata, Dioscorea rotundata and Dioscorea trifida, is x?=?20, and that the clones with 2n?=?40 chromosomes are diploids. D. alata breeding programmes were limited to the production of diploid hybrids until 2006, when the tetraploids (2n?=?80) were found to be fertile and polyploid hybrids were produced by conventional hybridisation. However, the nature of the polyploidy (autotetraploidy or allotetraploidy) was not known in D. alata tetraploid clones. In the present study, the inheritance pattern of simple sequence repeat markers was determined in a tetraploid progeny using a Bayesian approach and by examining double reduction events. Results obtained confirm the autotetraploid nature of the 2n?=?80 clones of D. alata.     

Pyrethrin accumulation in elicited hairy root cultures of <Emphasis Type="Italic">Chrysanthemum cinerariaefolium</Emphasis>

The flowers of Pyrethrum (Chrysanthemum cinerariaefolium) are known to contain Pyrethrins that are naturally occurring potential insecticide. Hairy roots were induced from leaves of C. cinerariaefolium using Agrobacterium rhizogenes strain A4. The root clones were characterized in to four groups i.e. thick, unbranched (D2 and D5), thin, highly branched (D3), thick, branched (B2) and thick, highly branched (D1, D6). Six established hairy root clones showed the presence of pyrethrin and were selected for elicitation studies. Growth kinetics studies revealed highest growth index in hairy root clone D1 (592.0) followed by D6 and D3 on dry weight basis after 40 days of culture. The maximum pyrethrin content was found in the clone D3 (7.2 mg/g dw) which is comparable to the flowers obtained from the variety “Avadh”. Hairy root clone D2 (5.2 mg/g dw) and D6 (1.3 mg/g dw) contained pyrethrin but in less amount as compared to clone D3. The PCR analysis showed the presence of rol B and rol C genes in all the six hairy root clones while rol A was detected only in D2 clone. The methanolic extract of D3 clone showed antifungal activities against phytopathogenic fungal strains which were found maximum against Curvuleria andropogonis followed by Colletotrichum acutatum and Rhizoctonia solani. Hairy root clones D2, D3 and D6 were elicited with culture filtrate of endophytic fungus (Fusarium oxysporum) and bacteria (Bacillus subtilis). The culture filtrate (4.0?%v/v) of both the fungal and bacterial origin was found to be effective in enhancing the pyrethrin content in all the tested hairy root clones. Clone D3 showed maximum pyrethrin content on elicitation with F. oxysporum (9.7 mg/g dw) and B. subtilis (9.7 mg/g dw) culture filtrate, which is 32?% higher than the non elicited D3 hairy roots (7.2 mg/g dw). F. oxysporum also enhanced the hairy root growth resulting into the higher biomass yield of D3 (50?%) and D2 (76?%) in comparison to control non elicited hairy root clones of D3 and D2, respectively leading to higher pyrethrin yield.     

Pleistocene glaciations and polyphyletic origins of polyploidy in an arctic cladoceran

RFLP analysis of the ND4-ND5 genes of the mtDNA genome in Daphnia middendorffiana and three closely allied species was used to investigate its origin and age. Populations of D. middendorffiana from arctic Canada were found to possess three distinct mtDNA lineages, only one of which appears unique to this species. The other two mtDNA lineages are either closely allied or identical to haplotypes in D. pulicaria, suggesting that it is the maternal parent of many clones of D. middendorffiana. Within D. pulicaria, mtDNA lineages have largely disjunct distributions, suggesting that populations of this species persisted in three glacial refugia (arctic, western, eastern) during the Pleistocene. Hybridizations between these refugial stocks and other species such as D. melanica and D. pulex likely generated many of the polyploid lineages of D. middendorffiana following the Wisconsinan glaciation. The presence of one unique mtDNA lineage in D. middendorffiana suggests that at least some of its clones are more ancient, but further studies are needed to rule out the possibility of their recent derivation from an as yet undetected sexual species. As a general result, this study suggests that polyploid cladocerans are unlikely to predate the Pleistocene.     

Chronic responses of different clones of Daphnia longispina (field and ephippia) to different food levels

Resting eggs are a fundamental reproductive strategy among freshwater cladocerans. Under adverse environmental conditions, whole Daphnia populations can disappear from a lake and a new community will arise from ephippial eggs. Since these new populations are subjected to genetic variation, their responses to environmental stress or contaminants can be different from the “original” population. In the present study, life history responses (reproduction and growth) of Daphnia longispina to different food concentrations was studied. Two Daphnia populations were tested: (a) field clones and (b) ephippial clones. Food (Selenastrum capricornutum) concentration was the stressor tested (absence of food, and low to high food concentrations). The results showed that reproductive responses of D. longispina to the tested food concentrations varied among clones, independently from their origin.     

Theileria parva: cell culture analysis of clones of macroschizont-infected bovine lymphoblastoid cells

Three clones (H7, D7, and C5) were established from single cells of a bovine lymphoblastoid cell line (IR.TPM.1) infected with macroschizonts of the protozoan parasite Theileria parva. The cloning efficiency using feeder layers was 0.3–0.4. The mean parasite size (the number of parasite nuclei per cell) was different in each clone and was correlated to the growth rate. The fast growing clone, C5 (population doubling time 24 hr), contained smaller (mean parasite nuclear number, 12) parasites than a slow growing clone, D7 (population doubling time, 73 hr; mean number of parasite nuclei per cell, 35.3). The third clone, H7, had an intermediate growth rate (population doubling time, 49 hr) and parasite size (mean nuclei number, 18.1). There was variation in the incidence of microschizonts among the clones but microschizont-free clones were not isolated. When the clones were subjected to 4.3 × 10^?7M aminopterin, 20–25% of the cell population of clones H7 and C5 and the uncloned parent line lost their parasites in 4 days, while it took 7 days to reach a similar result (31% parasite-free cells) in clone D7. We were unable to isolate parasite-free clones from cells treated with aminopterin. Hydroxyurea (4 × 10^?4M) inhibited the growth of clone C5, but the macroschizonts continued to proliferate, and the incidence of cells with microschizonts increased. The size profile analysis showed that most of the aminopterin-treated cells were 9.0 μm, the hydroxyurea-treated cells 14.7 μm, and the untreated cells 10.8 μm in diameter.     

Variability in shoot cultures regenerated from hairy roots of Gentiana punctata

Differences among three clones of Gentiana punctata L. hairy root shoot regenerants were investigated in relation to their growth patterns, production of secondary metabolites and 2D protein profiles. Prominent differences in growth parameters were stable thus qualifying regenerant clones as true somaclones. Marked differences in protein spots were registered among the regenerant clones but not in comparison with the non-transformed control. Southern blot hybridization of regenerants showed the absence of rolA, B and C genes, initially present in the main hairy root lines. Orf13 and rolD were present and orf8 was missing in all three regenerant clones whereas orf3 was missing only in clone 2. Although lacking the three major rol genes, plants of regenerant clones retained characteristics of the hairy root phenotype.     

Phylogeography of ostreopsis along west Pacific coast, with special reference to a novel clade from Japan

Background

A dinoflagellate genus Ostreopsis is known as a potential producer of Palytoxin derivatives. Palytoxin is the most potent non-proteinaceous compound reported so far. There has been a growing number of reports on palytoxin-like poisonings in southern areas of Japan; however, the distribution of Ostreopsis has not been investigated so far. Morphological plasticity of Ostreopsis makes reliable microscopic identification difficult so the employment of molecular tools was desirable.

Methods/Principal Finding

In total 223 clones were examined from samples mainly collected from southern areas of Japan. The D8–D10 region of the nuclear large subunit rDNA (D8–D10) was selected as a genetic marker and phylogenetic analyses were conducted. Although most of the clones were unable to be identified, there potentially 8 putative species established during this study. Among them, Ostreopsis sp. 1–5 did not belong to any known clade, and each of them formed its own clade. The dominant species was Ostreopsis sp. 1, which accounted for more than half of the clones and which was highly toxic and only distributed along the Japanese coast. Comparisons between the D8–D10 and the Internal Transcribed Spacer (ITS) region of the nuclear rDNA, which has widely been used for phylogenetic/phylogeographic studies in Ostreopsis, revealed that the D8–D10 was less variable than the ITS, making consistent and reliable phylogenetic reconstruction possible.

Conclusions/Significance

This study unveiled a surprisingly diverse and widespread distribution of Japanese Ostreopsis. Further study will be required to better understand the phylogeography of the genus. Our results posed the urgent need for the development of the early detection/warning systems for Ostreopsis, particularly for the widely distributed and strongly toxic Ostreopsis sp. 1. The D8–D10 marker will be suitable for these purposes.     

Molecular organization of heterochromatin in malaria mosquitoes of the Anopheles maculipennis subgroup

Although heterochromatin makes up a significant portion of the malaria mosquito genome, its organization, function, and evolution are poorly understood. Sibling species of the Anopheles maculipennis subgroup, the European malaria mosquitoes, are characterized by striking differences in the morphology of pericentric heterochromatin; however, the molecular basis for the rapid evolutionary transformation of heterochromatin is not known. This study reports an initial survey of the molecular organization of the pericentric heterochromatin in nonmodel species from the A. maculipennis subgroup. Molecular identity and chromosomal localization were established for short DNA fragments obtained by microdissection from the pericentric diffuse β-heterochromatin of A. atroparvus. Among 102 sequenced clones of the Atr2R library, twenty had sequence similarity to transposable elements (TEs) from the Anopheles gambiae and Aedes aegypti genomes. At least six protein-coding single-copy genes from A. gambiae and four single-copy genes from Drosophila melanogaster were homologous to eight clones from the library. Most of these conserved genes were heterochromatic in A. gambiae but euchromatic in D. melanogaster. The remaining 74 clones were characterized as noncoding repetitive DNA. Comparative chromosome mapping of twelve clones in the sibling species A. atroparvus and A. messeae demonstrated that the noncoding repetitive sequences and the TEs have undergone independent chromosome-specific and species-specific gains and losses in the morphologically different pericentric heterochromatic regions, in accordance with the “library model.”     

UDP-GlcNAc:Glycoprotein N-acetylglucosamine-1-phosphotransferase mediates the initial step in the formation of the methylphosphomannosyl residues on the high mannose oligosaccharides of Dictyostelium discoideum glycoproteins

The Dictyostelium discoideum gene gpt1 encodes a protein XP_638036 with sequence similarity to the α/β subunits of mammalian UDP-GlcNAc:Glycoprotein N-acetylglucosamine-1-phosphotransferase. We now demonstrate that extracts of D. discoideum clones with mutations in this gene transfer GlcNAc-P from UDP-GlcNAc to mannose residues at less than 5% the wild type value. Further, the lysosomal hydrolases of these mutant clones fail to bind to a cation-independent mannose 6-phosphate receptor affinity column, indicating a lack of methylphosphomannosyl residues on the high mannose oligosaccharides of these proteins. We conclude that the gpt1 gene product catalyzes the initial step in the formation of methylphosphomannosyl residues on D. discoideum lysosomal hydrolases.     

Bacterial Diversity of Weathered Terrestrial Icelandic Volcanic Glasses

The diversity of microbial communities inhabiting two terrestrial volcanic glasses of contrasting mineralogy and age was characterised. Basaltic glass from a <0.8 Ma hyaloclastite deposit (Valafell) harboured a more diverse Bacteria community than the younger rhyolitic glass from ～150-300 AD (D?madalshraun lava flow). Actinobacteria dominated 16S rRNA gene clone libraries from both sites, however, Proteobacteria, Acidobacteria and Cyanobacteria were also numerically abundant in each. A significant proportion (15-34%) of the sequenced clones displayed <85% sequence similarities with current database sequences, thus suggesting the presence of novel microbial diversity in each volcanic glass. The majority of clone sequences shared the greatest similarity to uncultured organisms, mainly from soil environments, among these clones from Antarctic environments and Hawaiian and Andean volcanic deposits. Additionally, a large number of clones within the Cyanobacteria and Proteobacteria were more similar to sequences from other lithic environments, included among these Icelandic clones from crystalline basalt and rhyolite, however, no similarities to sequences reported from marine volcanic glasses were observed. PhyloChip analysis detected substantially greater numbers of phylotypes at both sites than the corresponding clone libraries, but nonetheless also identified the basaltic glass community as the richer, containing approximately 29% unique phylotypes compared to rhyolitic glass.     

Development of selection method for Glycyrrhiza uralensis superior clones with high-glycyrrhizic acid contents using DNA sequence polymorphisms in glycyrrhizic acid biosynthetic genes

Glycyrrhiza plants are important resources for sweeteners and medicines, because underground parts of them contain glycyrrhizic acid (GL), which has sweet taste and various pharmacological activities (ex. anti-inflammatory, antiallergy, antiviral activity, etc.). Although such importance of them, their supply still depends principally on the collection of wild plants. Therefore, it is an important issue to develop stable and efficient production system of Glycyrrhiza plants. To overcome this problem, we established the hydroponic cultivation system of Glycyrrhiza uralensis and selected superior G. uralensis clones with high-GL contents in the containment greenhouse. In this study, we aimed to develop a method of selecting these superior G. uralensis clones by DNA sequence polymorphisms in biosynthetic genes. Among the DNA sequences of GL biosynthetic key enzyme gene (CYP88D6), we found Glycyrrhiza species and clone-specific polymorphisms in intronic regions. By using these polymorphisms, discrimination among Glycyrrhiza species and G. uralensis clones became possible. Furthermore, the appearance frequency of superior clone-specific alleles in cloned CYP88D6 sequences was correlated with GL contents in crude drugs collected from the Japanese market. We also observed the tendency that G. uralensis seedlings having superior clone-specific alleles of CYP88D6 gene showed higher secondary metabolite productivity than those without the alleles. These results indicated that superior clone-specific alleles of CYP88D6 gene could be applied as DNA markers for selecting G. uralensis clones accumulating high secondary metabolites.     

Some somatic sequences are absent or exceedingly rare in Xenopus oocyte RNA

A variety of Xenopus laevis cDNA clones derived from somatic cell RNAs were hybridized to oocyte pA⁺ RNA separated on Northern gels. We were unable to detect oocyte pA⁺ sequences complementary to three undefined tadpole cDNA clones. With one of these clones, a complex pattern of bands appears during embryogenesis. With the other two clones, a single band appears. Two additional tadpole clones hybridize to both oocyte and tadpole RNA, but yield a more complex RNA pattern from embryos than from oocytes. One of these additional tadpole clones has complementarity to actin DNA, suggesting that the additional RNA band which appears during embryogenesis is α-actin mRNA (E. A. Sturgess, J. E. M. Ballantine, H. R. Woodland, P. R. Mohun, C. D. Lane, and G. J. Dimitriadis, 1980, J. Embryol. Exp. Morphol.58, 303–320). We have also failed to detect hybridization to oocyte pA⁺ RNA with one vitellogenin and three adult globin cDNA clones. Reconstruction experiments with purified globin mRNA from anemic adult blood cells set the lower level of sensitivity for globin mRNA at one part in 10⁶. The data suggest that some Xenopus mRNA sequences are absent or very rare in the oocyte pA⁺ RNA population.     

Widely differing degrees of sequence conservation of the two types of rDNA insertion within the melanogaster species sub-group of Drosophila

We have examined the distribution of sequences homologous to the type I and type II rDNA insertions of Drosophila melanogaster in its sibling species. Each of the six species we have examined has sequences homologous to the type I insertion, which have undergone extensive divergence by the criterion of their EcoRI, BstI and HindIII restriction patterns. We have isolated cosmid clones containing type I sequences from D. simulans and D. mauritiana, the two species most closely related to D. melanogaster. Southern hybridisation analysis of these clones indicates that, as in D. melanogaster, the type I sequences can exist independently of rDNA and can also dissociate to give sub-components homologous to the right hand segment of the D. melanogaster type I insertion. The type II sequences, on the other hand are present in five out of the six species, but their restriction endonuclease cleavage profile is highly conserved. The differences in the degree of conservation of the two types of insertion sequence are discussed.     

Seasonal dynamics of sestonic protease inhibition: impact on Daphnia populations

Daphnia populations often show rapid microevolutionary adaptation to environmental changes. Here, we investigated the possibility that microevolution of Daphnia populations could be driven by natural sestonic Protease Inhibition (PI). We hypothesized that PI changes seasonally, which might lead to concomitant changes in tolerance to PI in a co-occurring Daphnia magna population. In order to test this, seston from a eutrophic pond was sampled regularly over two successive years. Extracts of these freeze-dried samples were used to determine their Inhibitory Potential (IP) on D. magna gut proteases. In the summer seston the IP against chymotrypsins exceeded that of spring seston 200-fold. In order to test for possible impacts on the co-existing D. magna population, we isolated clones before (spring) and after (fall) the peak of the IP. Microsatellite analyses revealed that the two subpopulations were genetically distinct. Individual exposure of three clones from each population to varying concentrations of a cyanobacterium that contains chymotrypsin inhibitors revealed a decrease in population and somatic growth rate for each clone, but no seasonal effects on Daphnia’s tolerance. In order to include maternal effects, we conducted a multi-clonal competition experiment on various cyanobacterial concentrations. However, no evidence for seasonally increased tolerance of D. magna to dietary protease inhibitors could be found.     

Nitrite Reductase Genes (nirK and nirS) as Functional Markers To Investigate Diversity of Denitrifying Bacteria in Pacific Northwest Marine Sediment Communities

Genetic heterogeneity of denitrifying bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying nirK and nirS genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for denitrifying bacteria. nirS sequences could be amplified from samples of both sampling sites, whereas nirK sequences were detected only in samples from the Washington margin. To assess the underlying nir gene structure, PCR products of both genes were cloned and screened by restriction fragment length polymorphism (RFLP). Rarefraction analysis revealed a high level of diversity especially for nirS clones from Puget Sound and a slightly lower level of diversity for nirK and nirS clones from the Washington margin. One group dominated within nirK clones, but no dominance and only a few redundant clones were seen between sediment samples for nirS clones in both habitats. Hybridization and sequencing confirmed that all but one of the 228 putative nirS clones were nirS with levels of nucleotide identities as low as 45.3%. Phylogenetic analysis grouped nirS clones into three distinct subclusters within the nirS gene tree which corresponded to the two habitats from which they were obtained. These sequences had little relationship to any strain with known nirS sequences or to isolates (mostly close relatives of Pseudomonas stutzeri) from the Washington margin sediment samples. nirK clones were more closely related to each other than were the nirS clones, with 78.6% and higher nucleotide identities; clones showing only weak hybridization signals were not related to known nirK sequences. All nirK clones were also grouped into a distinct cluster which could not be placed with any strain with known nirK sequences. These findings show a very high diversity of nir sequences within small samples and that these novel nir clusters, some very divergent from known sequences, are not known in cultivated denitrifiers.     

Species and clone-dependent effects of tilapia fish (Cichlidae) on the morphology and life-history of temperate and tropical <Emphasis Type="Italic">Daphnia</Emphasis>

In aquatic systems, tilapia introductions may result in marked changes in the structure of prey communities. In this study, we experimentally examined the effects of tilapia-mediated water at the individual and population levels of prey by exposing three Daphnia species to predation cues. We hypothesized that tilapia-mediated water determines reduced age and size at primipara, greater and faster reproduction, enhanced intrinsic rates of population increase (r), and longer tail spines in Daphnia; but that the magnitude of these changes would be species and clone-dependent. When three tropical D. laevis and one temperate D. similis clones were exposed to predation cues, adaptive changes were observed in some of the aforementioned parameters for each clone. The three D. laevis clones exhibited changes in all life-history and morphological measures. Temperate Daphnia spinulata displayed no changes but decreased r values in the presence of predators. The observed changes in the species and clones tested here suggest that, overall, both temperate and tropical Daphnia can detect and adaptively react to the risk of tilapia predation. However, only a fraction of the possible defenses may be displayed by individual clones. In contrast, D. spinulata seems more vulnerable to tilapia predation, given its long body length and absence of adaptive changes. Our study indicates that Daphnia can respond to tilapia-mediated water, and that interspecific and clonal variation exists between temperate and tropical species.     

Differential In Vitro Kinetics of Drug Resistance Mutation Acquisition in HIV-1 RT of Subtypes B and C

Background

HIV-1 subtype B is the most prevalent in developed countries and, consequently, it has been extensively studied. On the other hand, subtype C is the most prevalent worldwide and therefore is a reasonable target for future studies. Here we evaluate the acquisition of resistance and the viability of HIV-1 subtype B and C RT clones from different isolates that were subjected to in vitro selection pressure with zidovudine (ZDV) and lamivudine (3TC).

Methods/Principal Findings

MT4 cells were infected with chimeric virus pseudotyped with RT from subtype B and C clones, which were previously subjected to serial passage with increasing concentrations of ZDV and 3TC. The samples collected after each passage were analyzed for the presence of resistance mutations and VL. No differences were found between subtypes B and C in viral load and resistance mutations when these viruses were selected with 3TC. However, the route of mutations and the time to rebound of subtype B and C virus were different when subjected to ZDV treatment. In order to confirm the role of the mutations detected, other clones were generated and subjected to in vitro selection. RT subtype B virus isolates tended to acquire different ZDV resistance mutations (Q151M and D67N or T215Y, D67D/N and F214L) compared to subtype C (D67N, K70R, T215I or T215F).

Conclusions/Significance

This study suggests that different subtypes have a tendency to react differently to antiretroviral drug selection in vitro. Consequently, the acquisition of resistance in patients undergoing antiretroviral therapy can be dependent on the subtypes composing the viral population.