External fertilisation and paternal care in the paedomorphic salamander Siren intermedia Barnes, 1826 (Urodela: Sirenidae)

Parental care is widespread in the animal kingdom and enhances offspring survival. Amphibians exhibit an extraordinary diversity of care strategies, including guarding, transport and even feeding of young. Among amphibians, females are usually the carers, but here we present a case of male parental care in the aquatic salamander Siren intermedia, accompanied by records of external fertilisation. Sirenids are a phylogenetically distinct group within basal salamanders, of which the precise systematic position has long been debated. Our observations of external fertilisation and paternal care of S. intermedia lead us to conclude that apparently both internal fertilisation and maternal care evolved after the split between the more basal groups (Cryptobranchoidea and Sirenoidea) and all other salamanders (suborder Salamandroidea).     

Repeated Exposure to Lutzomyia intermedia Sand Fly Saliva Induces Local Expression of Interferon-Inducible Genes Both at the Site of Injection in Mice and in Human Blood

During a blood meal, Lutzomyia intermedia sand flies transmit Leishmania braziliensis, a parasite causing tegumentary leishmaniasis. In experimental leishmaniasis, pre-exposure to saliva of most blood-feeding sand flies results in parasite establishment in absence of any skin damages in mice challenged with dermotropic Leishmania species together with saliva. In contrast, pre-immunization with Lu. intermedia salivary gland sonicate (SGS) results in enhanced skin inflammatory exacerbation upon co-inoculation of Lu. intermedia SGS and L. braziliensis. These data highlight potential unique features of both L. braziliensis and Lu. intermedia. In this study, we investigated the genes modulated by Lu. intermedia SGS immunization to understand their potential impact on the subsequent cutaneous immune response following inoculation of both SGS and L. braziliensis. The cellular recruitment and global gene expression profile was analyzed in mice repeatedly inoculated or not with Lu. intermedia. Microarray gene analysis revealed the upregulation of a distinct set of IFN-inducible genes, an immune signature not seen to the same extent in control animals. Of note this INF-inducible gene set was not induced in SGS pre-immunized mice subsequently co-inoculated with SGS and L. braziliensis. These data suggest the parasite prevented the upregulation of this Lu. intermedia saliva-related immune signature. The presence of these IFN-inducible genes was further analyzed in peripheral blood mononuclear cells (PBMCs) sampled from uninfected human individuals living in a L. braziliensis-endemic region of Brazil thus regularly exposed to Lu. intermedia bites. PBMCs were cultured in presence or absence of Lu. intermedia SGS. Using qRT-PCR we established that the IFN-inducible genes induced in the skin of SGS pre-immunized mice, were also upregulated by SGS in PBMCs from human individuals regularly exposed to Lu. intermedia bites, but not in PBMCs of control subjects. These data demonstrate that repeated exposure to Lu. intermedia SGS induces the expression of potentially host-protective IFN-inducible genes.     

The identification of genes specific to Prevotella intermedia and Prevotella nigrescens using genomic subtractive hybridization

Prevotella intermedia and Prevotella nigrescens, which are often isolated from periodontal sites, were once considered two different genotypes of P. intermedia. Although the genomic sequence of P. intermedia was determined recently, little is known about the genetic differences between P. intermedia and P. nigrescens. The subtractive hybridization technique is a powerful method for generating a set of DNA fragments differing between two closely related bacterial strains or species. We used subtractive hybridization to identify the DNA regions specific to P. intermedia ATCC 25611 and P. nigrescens ATCC 25261. Using this method, four P. intermedia ATCC 25611-specific and three P. nigrescens ATCC 25261-specific regions were determined. From the species-specific regions, insertion sequence (IS) elements were isolated for P. intermedia. IS elements play an important role in the pathogenicity of bacteria. For the P. intermedia-specific regions, the genes adenine-specific DNA-methyltransferase and 8-amino-7-oxononanoate synthase were isolated. The P. nigrescens-specific region contained a Flavobacterium psychrophilum SprA homologue, a cell-surface protein involved in gliding motility, Prevotella melaninogenica ATCC 25845 glutathione peroxide, and Porphyromonas gingivalis ATCC 33277 leucyl-tRNA synthetase. The results demonstrate that the subtractive hybridization technique was useful for distinguishing between the two closely related species. Furthermore, this technique will contribute to our understanding of the virulence of these species.     

Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation

Background

Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. It is of clinical significance to identify the main drive of its various adaptation and pathogenicity. In order to explore the intra-species genetic differences among strains of Prevotella intermedia of different niches, we isolated a strain Prevotella intermedia ZT from the infected root canal of a Chinese patient with periapical periodontitis and gained a draft genome sequence. We annotated the genome and compared it with the genomes of other taxa in the genus Prevotella.

Results

The raw data set, consisting of approximately 65X-coverage reads, was trimmed and assembled into contigs from which 2165 ORFs were predicted. The comparison of the Prevotella intermedia ZT genome sequence with the published genome sequence of Prevotella intermedia 17 and Prevotella intermedia ATCC25611 revealed that ~14% of the genes were strain-specific. The Preveotella intermedia strains share a set of conserved genes contributing to its adaptation and pathogenic and possess strain-specific genes especially those involved in adhesion and secreting bacteriocin. The Prevotella intermedia ZT shares similar gene content with other taxa of genus Prevotella. The genomes of the genus Prevotella is highly dynamic with relative conserved parts: on average, about half of the genes in one Prevotella genome were not included in another genome of the different Prevotella species. The degree of conservation varied with different pathways: the ability of amino acid biosynthesis varied greatly with species but the pathway of cell wall components biosynthesis were nearly constant. Phylogenetic tree shows that the taxa from different niches are scarcely distributed among clades.

Conclusions

Prevotella intermedia ZT belongs to a genus marked with highly dynamic genomes. The specific genes of Prevotella intermedia indicate that adhesion, competing with surrounding microbes and horizontal gene transfer are the main drive of the evolution of Prevotella intermedia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1272-3) contains supplementary material, which is available to authorized users.     

Introgressive hybridization between Plantago major L. taxa

Occurrence and direction of introgressive hybridization between Plantago major taxa were tested. Plantago major plants were collected from 10 Egyptian locations. Four populations of two European taxa were used for comparison. These are ecologically and geographically separated and were identified as the subspecies Plantago major ssp. major and Plantago major ssp. intermedia. In the Egyptian populations, most individuals fall within the variation range of P. major ssp. intermedia. Only one population, from Burg El-Arab, morphologically resembled clearly P. major ssp. major and showed some ISSR fragments that characterize pure populations of this taxon. All individuals of population 2 (Alexandria) and some individuals of populations 1, 3, 5, 6 and 10 (Alexandria, Aswan) morphologically corresponded to P. major ssp. intermedia. All individuals collected from Egypt had ISSR fragments characterizing both pure P. major ssp. major and pure P. major ssp. intermedia. Most of these individuals had a higher percentage of intermedia-type fragments than major-type fragments, suggesting that P. major ssp. intermedia in Egypt shows some introgression towards P. major ssp. major. The pure populations were distinct from each other, while the Egyptian populations were intermediate according to principal coordinate analysis (PCoA) of ISSR data. In the populations collected from Egypt, major and intermedia cannot be seen as separate species. The study suggests that the dominant taxa introgressed to the minority population(s). Taxon frequency may be a key component in determining the direction of introgression.     

Development of Prevotella intermedia-specific PCR primers based on the nucleotide sequences of a DNA probe Pig27

The aim of this study was to develop Prevotella intermedia-specific PCR primers based on the P. intermedia-specific DNA probe. The P. intermedia-specific DNA probe was screened by inverted dot blot hybridization and confirmed by Southern blot hybridization. The nucleotide sequences of the species-specific DNA probes were determined using a chain termination method. Southern blot analysis showed that the DNA probe, Pig27, detected only the genomic DNA of P. intermedia strains. PCR showed that the PCR primers, Pin-F1/Pin-R1, had species-specificity for P. intermedia. The detection limits of the PCR primer sets were 0.4 pg of the purified genomic DNA of P. intermedia ATCC 49046. These results suggest that the PCR primers, Pin-F1/Pin-R1, could be useful in the detection of P. intermedia as well as in the development of a PCR kit in epidemiological studies related to periodontal diseases.     

Editor's choice: The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale,intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat

Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria.     

Pronounced differences in genetic structure despite overall ecological similarity for two Ambystoma salamanders in the same landscape

Studies linking genetic structure in amphibian species with ecological characteristics have focused on large differences in dispersal capabilities. Here, we test whether two species with similar dispersal potential but subtle differences in other ecological characteristics also exhibit strong differences in genetic structure in the same landscape. We examined eight microsatellites in marbled salamanders (Ambystoma opacum) from 29 seasonal ponds and spotted salamanders (Ambystoma maculatum) from 19 seasonal ponds in a single geographic region in west-central Massachusetts. Despite overall similarity in ecological characteristics of spotted and marbled salamanders, we observed clear differences in the genetic structure of these two species. For marbled salamanders, we observed strong overall genetic differentiation (F _ST = 0.091, F′ _ST = 0.375), three population-level clusters of populations (K = 3), a strong pattern of isolation by distance (r = 0.58), and marked variation in family-level structure (from 1 to 23 full-sibling families per site). For spotted salamanders, overall genetic differentiation was weaker (F _ST = 0.025, F′ _ST = 0.102), there was no evidence of population-level clustering (K = 1), the pattern of isolation by distance (r = 0.17) was much weaker compared to marbled salamanders, and there was less variation in family-level structure (from 10 to 36 full-sibling families per site). We suspect that a combination of breeding site fidelity, effective population size, and generation interval is responsible for these marked differences. Our results suggest that marbled salamanders, compared to spotted salamanders, are more sensitive to fragmentation from various land-use activities and would be less likely to recolonize extirpated sites on an ecologically and conservation-relevant time frame.     

Astacin-like metalloproteases are a gene family of toxins present in the venom of different species of the brown spider (genus Loxosceles)

Brown spiders have a worldwide distribution, and their venom has a complex composition containing many different molecules. Herein, we report the existence of a family of astacin-like metalloprotease toxins in Loxosceles intermedia venom, as well as in the venom of different species of Loxosceles. Using a cDNA library from the L. intermedia venom gland, we cloned two novel cDNAs encoding astacin-like metalloprotease toxins, LALP2 and LALP3. Using an anti-serum against the previously described astacin-like toxin in L. intermedia venom (LALP1), we detected the presence of immunologically-related toxins in the venoms of L. intermedia, Loxosceles laeta, and Loxosceles gaucho. Zymographic experiments showed gelatinolytic activity of crude venoms of L. intermedia, L. laeta, and L. gaucho (which could be inhibited by the divalent metal chelator 1,10-phenanthroline) at electrophoretic mobilities identical to those reported for immunological cross-reactivity. Moreover, mRNAs extracted from L. laeta and L. gaucho venom glands were screened for astacin-like metalloproteases, and cDNAs obtained using LALP1-specific primers were sequenced, and their deduced amino acid sequences confirmed they were members of the astacin family with the family signatures (HEXXHXXGXXHE and MXY), LALP4 and LALP5, respectively. Sequence comparison of deduced amino acid sequences revealed that LALP2, LALP3, LALP4, and LALP5 are related to the astacin family. This study identified the existence of gene family of astacin-like toxins in the venoms of brown spiders and raises the possibility that these molecules are involved in the deleterious effects triggered by the venom.     

A Comparison of Techniques used to Distinguish Strains of Prevotella intermedia from Prevotella nigrescens

This study compared the potential of three techniques to differentiate between the speciesPrevotella intermedia (ATCC 25611) and Prevotella nigrescens (ATCC 33563, ATCC 25261) including recent clinical isolates identified only as P. intermedia using Rapid ID 32A. The techniques used were: RAPD-PCR (random amplification of polymorphic DNA by polymerase chain reaction) using the arbitrary primer L10, partial 16S rRNA gene sequencing using general bacterial primers TPU1 and RTU3, and PCR with species specific oligonucleotide primers designed to regions of the 16S rDNA chosen by analysis of the full sequences as available in the EMBL database. Cluster analysis of binary matrix data from RAPD-PCR fingerprints confirmed that P. intermedia and P. nigrescens are genetically distinct and although there is intraspecies heterogeneity, clinical isolates can be identified as P. intermedia or P. nigrescens by this method. Partial 16S rRNA sequencing and species specific PCR are easily accessible with molecular information readily available. Specific PCR requires time-consuming optimisation but may be the technique of choice for clinical samples. It is concluded that all techniques are appropriate but that no one technique would be best for all applications.     

Polyamines in turions and young plants of hydrocharis morsus-ranae and utricularia intermedia

Spermidine is the most abundant polyamine in dormant turions of Hydrocharis morsus-ranae and Utricularia intermedia, and it is also the dominant polyamine in sprouts of U. intermedia. The putrescine level is high in young leaves of H. morsus-ranae. Cadaverine and homospermidine occur respectively in vernalized turions of H. morsus-ranae and of U. intermedia.     

The taxonomic status of Western Pacific mysid species of Neomysis awatschensis (Brandt, 1851) group

The discussion of the taxonomic status of West Pacific mysid species Neomysis awatschensis (Brandt, 1851), N. intermedia (Czerniavsky, 1882) and N. nigra Nakazawa, 1910 has continued over the last century. Examination of a large taxonomic collection of the Zoological Institute of the Russian Academy of Sciences, including syntypes of N. awatschensis and N. intermedia, revealed that N. intermedia is a junior synonym of N. awatschensis and N. nigra is a valid species, not a synonym of N. awatschensis. N. nigra was first recorded in Russian waters in the Possyet Bay (Sea of Japan).     

Compared chemical properties of dermonecrotic and lethal toxins from spiders of the genusLoxosceles (Araneae)

Loxosceles spider venom usually causes a typical dermonecrotic lesion in bitten patients, but it may also cause systemic effects that may be lethal. Gel filtration on Sephadex G-100 ofLoxosceles gaucho, L. laeta, orL. intermedia spider venoms resulted in three fractions (A, containing higher molecular mass components, B containing intermediate molecular mass components, and C with lower molecular mass components). The dermonecrotic and lethal activities were detected exclusively in fraction A of all three species. Analysis by SDS-PAGE showed that the major protein contained in fraction A has molecular weight approximately 35 kDa inL. gaucho andL. intermedia, but 32 kDa inL. laeta venom. These toxins were isolated from venoms ofL. gaucho, L. laeta, andL. intermedia by SDS-PAGE followed by blotting to PVDF membrane and sequencing. A database search showed a high level of identity between each toxin and a fragment of theL. reclusa (North American spider) toxin. A multiple sequence alignment of theLoxosceles toxins showed many common identical residues in their N-terminal sequences. Identities ranged from 50.0% (L. gaucho andL. reclusa) to 61.1% (L. intermedia andL. reclusa). The purified toxins were also submitted to capillary electrophoresis peptide mapping afterin situ partial hydrolysis of the blotted samples. The results obtained suggest thatL. intermedia protein is more similar toL. laeta toxin thanL. gaucho toxin and revealed a smaller homology betweenL. intermedia andL gaucho. Altogether these findings suggest that the toxins responsible for most important activities of venoms ofLoxosceles species have a molecular mass of 32–35 kDa and are probably homologous proteins.     

Orientation of field populations ofBrachymeria intermedia [Hym.: Chalcididae], to host and host-habitat cues

Brachymeria intermedia (Nees), a pupal parasitoid of the gypsy moth, was caught in the field using plexiglas traps coated with Tangletrap (2). Significantly greater numbers of females were collected in traps baited with gypsy moth pupae than in traps with male or femaleB. intermedia or traps painted yellow.B. intermedia collected in traps during the first 3 weeks of native gypsy moth pupation were primarily female. A preponderance of males were caught during the fourth week. The hyperparasite,Brachymeria compsilurae (Cwfd) was also trapped in small numbers. Gypsy moth pupae were hung in interior and exterior areas of woodland sites. A greater number ofB. intermedia emerged from pupae in woodland edge sites than from pupae in interior woodland sites.     

Intraspecies Variability Affects Heterotypic Biofilms of Porphyromonas gingivalis and Prevotella intermedia: Evidences of Strain-Dependence Biofilm Modulation by Physical Contact and by Released Soluble Factors

It is well known that strain and virulence diversity exist within the population structure of Porphyromonas gingivalis. In the present study we investigate intra- and inter-species variability in biofilm formation of Porphyromonas gingivalis and partners Prevotella intermedia and Prevotella nigrescens. All strains tested showed similar hydrophobicity, except for P. gingivalis W83 which has roughly half of the hydrophobicity of P. gingivalis ATCC33277. An intraspecies variability in coaggregation of P. gingivalis with P. intermedia was also found. The association P. gingivalis W83/P. intermedia 17 produced the thickest biofilm and strain 17 was prevalent. In a two-compartment system P. gingivalis W83 stimulates an increase in biomass of strain 17 and the latter did not stimulate the growth of P. gingivalis W83. In addition, P. gingivalis W83 also stimulates the growth of P. intermedia ATCC25611 although strain W83 was prevalent in the association with P. intermedia ATCC25611. P. gingivalis ATCC33277 was prevalent in both associations with P. intermedia and both strains of P. intermedia stimulate the growth of P. gingivalis ATCC33277. FISH images also showed variability in biofilm structure. Thus, the outcome of the association P. gingivalis/P. intermedia seems to be strain-dependent, and both soluble factors and physical contact are relevant. The association P. gingivalis-P. nigrescens ATCC33563 produced larger biomass than each monotypic biofilm, and P. gingivalis was favored in consortia, while no differences were found in the two-compartment system. Therefore, in consortia P. gingivalis-P. nigrescens physical contact seems to favor P. gingivalis growth. The intraspecies variability found in our study suggests strain-dependence in ability of microorganisms to recognize molecules in other bacteria which may further elucidate the dysbiosis event during periodontitis development giving additional explanation for periodontal bacteria, such as P. gingivalis and P. intermedia, among others, to persist and establish chronic infections in the host.     

Reconstruction of chromosome rearrangements between the two most ancestral duckweed species <Emphasis Type="Italic">Spirodela polyrhiza</Emphasis> and <Emphasis Type="Italic">S. intermedia</Emphasis>

The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.     

Immunity to Lutzomyia intermedia Saliva Modulates the Inflammatory Environment Induced by Leishmania braziliensis

Background

During blood feeding, sand flies inject Leishmania parasites in the presence of saliva. The types and functions of cells present at the first host-parasite contact are critical to the outcome on infection and sand fly saliva has been shown to play an important role in this setting. Herein, we investigated the in vivo chemotactic effects of Lutzomyia intermedia saliva, the vector of Leishmania braziliensis, combined or not with the parasite.

Methods and Findings

We tested the initial response induced by Lutzomyia intermedia salivary gland sonicate (SGS) in BALB/c mice employing the air pouch model of inflammation. L. intermedia SGS induced a rapid influx of macrophages and neutrophils. In mice that were pre-sensitized with L. intermedia saliva, injection of SGS was associated with increased neutrophil recruitment and a significant up-regulation of CXCL1, CCL2, CCL4 and TNF-α expression. Surprisingly, in mice that were pre-exposed to SGS, a combination of SGS and L. braziliensis induced a significant migration of neutrophils and an important modulation in cytokine and chemokine expression as shown by decreased CXCL10 expression and increased IL-10 expression.

Conclusion

These results confirm that sand fly saliva modulates the initial host response. More importantly, pre-exposure to L. intermedia saliva significantly modifies the host''s response to L. braziliensis, in terms of cellular recruitment and expression of cytokines and chemokines. This particular immune modulation may, in turn, favor parasite multiplication.     

Coniogramme intermedia Hieron. (Hemionitidaceae Pichi Sermolli) in the northern Sikhote-Alin

The distributional pattern of Coniogramme intermedia within the Russian Far East has been characterized. The characteristics of location, species diversity and structure of plant groupings in the inhabited places are given. Some measures are proposed to preserve endangered communities of coniferous and broad-leaved forests with the participation of Coniogramme intermedia.