Rare and fleeting: an example of interspecific recombination in animal mitochondrial DNA

Recombination is thought to occur only rarely in animal mitochondrial DNA (mtDNA). However, detection of mtDNA recombination requires that cells become heteroplasmic through mutation, intramolecular recombination or 'leakage' of paternal mtDNA. Interspecific hybridization increases the probability of detecting mtDNA recombinants due to higher levels of sequence divergence and potentially higher levels of paternal leakage. During a study of historical variation in Atlantic salmon (Salmo salar) mtDNA, an individual with a recombinant haplotype containing sequence from both Atlantic salmon and brown trout (Salmo trutta) was detected. The individual was not an F1 hybrid but it did have an unusual nuclear genotype which suggested that it was a later-generation backcross. No other similar recombinant haplotype was found from the same population or three neighbouring Atlantic salmon populations in 717 individuals collected during 1948-2002. Interspecific recombination may increase mtDNA variability within species and can have implications for phylogenetic studies.     

The glypican 3-hosted murine mir717 gene: sequence conservation, seed region polymorphisms and putative targets

Mir717 (mmu-mir-717) was first reported in mouse and resides in the intron 3 of glypican 3 (Gpc3) gene. Our present study revealed that this microRNA (miRNA) gene is conserved among 26 mammalian species and harbors polymorphic sites within the mature seed region in mice. Our finding represents a rare four layer genomic overlap consisting of growth associated quantitative trait locus (QTL), body mass associated Gpc3 gene, highly conserved miRNA gene and mature miRNA seed single nucleotide polymorphism (SNP) identified in the lean mouse strain 129/Sv. Additionally, genes potentially targeted by Mir717 include 91 genes associated with obesity and related phenotypes in mammals. Our analysis provides a basis for further experiments to causally connect the identified SNP and Mir717 gene itself to obesity regulation. Furthermore, our bioinformatics analysis now enables functional annotation of Mir717 orthologs in other species, thus determining the effect of its target genes on fat-related traits.     

Discovery of larval Gnathostoma nipponicum in frogs and snakes from Jeju-do (Province), Republic of Korea

A survey was performed to find out the intermediate hosts of Gnathostoma nipponicum in Jeju-do (Province), the Republic of Korea. In August 2009 and 2010, a total of 82 tadpoles, 23 black-spotted pond frogs (Rana nigromaculata), 7 tiger keelback snakes (Rhabdophis tigrinus tigrinus), 6 red-tongue viper snakes (Agkistrodon ussuriensis), and 2 cat snakes (Elaphe dione) were collected in Jeju-do and examined by the pepsin-HCl digestion method. Total 5 gnathostome larvae were detected in 3 (50%) of 6 A. ussuriensis, 70 larvae in 3 of 7 (42.9%) R. tigrinus tigrinus, and 2 larvae in 2 of 82 (8.7%) frogs. No gnathostome larvae were detected in tadpoles and cat snakes. The larvae detected were a single species, and 2.17 × 0.22 mm in average size. They had characteristic head bulbs, muscular esophagus, and 4 cervical sacs. Three rows of hooklets were arranged in the head bulbs, and the number of hooklets in each row was 29, 33, and 36 posteriorly. All these characters were consistent with the advanced third-stage larvae of G. nipponicum. It has been first confirmed in Jeju-do that R. nigromaculata, A. ussuriensis, and R. tigrinus tigrinus play a role for intermediate and/or paratenic hosts for G. nipponicum.     

Alien invasions in aquatic ecosystems: Toward an understanding of brook trout invasions and potential impacts on inland cutthroat trout in western North America

Experience from case studies of biologicalinvasions in aquatic ecosystems has motivated aset of proposed empirical rules forunderstanding patterns of invasion and impactson native species. Further evidence is neededto better understand these patterns, andperhaps contribute to a useful predictivetheory of invasions. We reviewed the case ofbrook trout (Salvelinus fontinalis)invasions in the western United States andtheir impacts on native cutthroat trout (Oncorhynchus clarki). Unlike many biologicalinvasions, a considerable body of empiricalresearch on brook trout and cutthroat trout isavailable. We reviewed life histories of eachspecies, brook trout invasions, their impactson cutthroat trout, and patterns and causes ofsegregation between brook trout and cutthroattrout. We considered four stages of theinvasion process: transport, establishment,spread, and impacts to native species. Most ofthe research we found focused on impacts. Interspecific interactions, especiallycompetition, were commonly investigated andcited as impacts of brook trout. In many casesit is not clear if brook trout invasions have ameasurable impact. Studies of speciesdistributions in the field and a variety ofexperiments suggest invasion success of brooktrout is associated with environmental factors,including temperature, landscape structure,habitat size, stream flow, and humaninfluences. Research on earlier stages ofbrook trout invasions (transport,establishment, and spread) is relativelylimited, but has provided promising insights. Management alternatives for controllingbrook trout invasions are limited, and actions tocontrol brook trout focus on direct removal,which is variably successful and can haveadverse effects on native species. Themanagement applicability of research has beenconfounded by the complexity of the problem andby a focus on understanding processes atsmaller scales, but not on predicting patternsat larger scales. In the short-term, animproved predictive understanding of brooktrout invasions could prove to be most useful,even if processes are incompletely understood. A stronger connection between research andmanagement is needed to identify more effectivealternatives for controlling brook troutinvasions and for identifying managementpriorities.     

Relevance of genetics for conservation policies: the case of Minorcan cork oaks

Background and Aims

Marginal populations of widely distributed species can be of high conservation interest when they hold a significant or unique portion of the genetic diversity of the species. However, such genetic information is frequently lacking. Here the relevance of genetic surveys to develop efficient conservation strategies for such populations is illustrated using cork oak (Quercus suber) from Minorca (Balearic Islands, Spain) as a case study. Cork oak is highly endangered on the island, where no more than 67 individuals live in small, isolated stands in siliceous sites. As a consequence, it was recently granted protected status.

Methods

Two Bayesian clustering approaches were used to analyse the genetic structure of the Minorcan population, on the basis of nuclear microsatellite data. The different groups within the island were also compared with additional island and continental populations surrounding Minorca.

Key Results

Very high genetic diversity was found, with values comparable with those observed in continental parts of the species'' range. Furthermore, the Minorcan oak stands were highly differentiated from one another and were genetically related to different continental populations of France and Spain.

Conclusions

The high levels of genetic diversity and inter-stands differentiation make Minorcan cork oak eligible for specific conservation efforts. The relationship of Minorcan stands to different continental populations in France and Spain probably reflects multiple colonization events. However, discrepancy between chloroplast DNA- and nuclear DNA-based groups does not support a simple scenario of recent introduction. Gene exchanges between neighbouring cork oak stands and with holm oak have created specific and exceptional genetic combinations. They also constitute a wide range of potential genetic resources for research on adaptation to new environmental conditions. Conservation guidelines that take into account these findings are provided.     

Biochemical and structural insights into intramembrane metalloprotease mechanisms

Intramembrane metalloproteases are nearly ubiquitous in living organisms and they function in diverse processes ranging from cholesterol homeostasis and the unfolded protein response in humans to sporulation, stress responses, and virulence of bacteria. Understanding how these enzymes function in membranes is a challenge of fundamental interest with potential applications if modulators can be devised. Progress is described toward a mechanistic understanding, based primarily on molecular genetic and biochemical studies of human S2P and bacterial SpoIVFB and RseP, and on the structure of the membrane domain of an archaeal enzyme. Conserved features of the enzymes appear to include transmembrane helices and loops around the active site zinc ion, which may be near the membrane surface. Extramembrane domains such as PDZ (PSD-95, DLG, ZO-1) or CBS (cystathionine-β-synthase) domains govern substrate access to the active site, but several different mechanisms of access and cleavage site selection can be envisioned, which might differ depending on the substrate and the enzyme. More work is needed to distinguish between these mechanisms, both for enzymes that have been relatively well-studied, and for enzymes lacking PDZ and CBS domains, which have not been studied. This article is part of a Special Issue entitled: Intramembrane Proteases.     

Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

Background

Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).

Results

Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.

Conclusion

The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.     

Late Quaternary vegetation, biodiversity and fire dynamics on the southern Brazilian highland and their implication for conservation and management of modern Araucaria forest and grassland ecosystems

Palaeoecological background information is needed for management and conservation of the highly diverse mosaic of Araucaria forest and Campos (grassland) in southern Brazil. Questions on the origin of Araucaria forest and grasslands; its development, dynamic and stability; its response to environmental change such as climate; and the role of human impact are essential. Further questions on its natural stage of vegetation or its alteration by pre- and post-Columbian anthropogenic activity are also important. To answer these questions, palaeoecological and palaeoenvironmental data based on pollen, charcoal and multivariate data analysis of radiocarbon dated sedimentary archives from southern Brazil are used to provide an insight into past vegetation changes, which allows us to improve our understanding of the modern vegetation and to develop conservation and management strategies for the strongly affected ecosystems in southern Brazil.     

Virtual screening and in vitro assay of potential drug like inhibitors from spices against Glutathione-S-Transferase of Meloidogyne incognita

Glutathione S-transferases (GSTs) enzymes are critical antioxidant and detoxification system responsible for long-term existence of nematodes in host species. Hence, 16 phytochemicals predicted and reported to have potential nematicidal activity have been docked to GST enzyme of Meloidogyne incognita to assess their binding affinity and inhibitory activity. In vitro effects of these phytochemicals from in silico results have been done for validation of docking studies and efficacy in GST inhibition of following compounds such as alpha- pinene, alpha- terpineol, beta- caryophyllene, capsaicin, cinnamic acid, citronellol, curcumin, eugenol, geraniol, isoeugenol, linalool, myristicin, neral, NVA (N-vanillylnonanamide), piperine, vanillin have been revealed. Nematode inhibition in vitro bioassay for selected compounds could conclude that maximum mortality was observed with highest concentrations of beta- caryophyllene (78%) followed by eugenol (61.6%), cinnamic acid (55%) and N-vanillylnonanamide (49%). These findings thus suggest that the above phytochemicals could be potentially developed as nematicidal molecules against M. incognita infections.     

Phylogeography of the endangered rosewood Dalbergia nigra (Fabaceae): insights into the evolutionary history and conservation of the Brazilian Atlantic Forest

The Brazilian rosewood (Dalbergia nigra) is an endangered tree endemic to the central Brazilian Atlantic Forest, one of the world''s most threatened biomes. The population diversity, phylogeographic structure and demographic history of this species were investigated using the variation in the chloroplast DNA (cpDNA) sequences of 185 individuals from 19 populations along the geographical range of the species. Fifteen haplotypes were detected in the analysis of 1297 bp from two non-coding sequences, trnV-trnM and trnL. We identified a strong genetic structure (F_ST=0.62, P<0.0001), with a latitudinal separation into three phylogeographic groups. The two northernmost groups showed evidence of having maintained historically larger populations than the southernmost group. Estimates of divergence times between these groups pointed to vicariance events in the Middle Pleistocene (ca. 350 000–780 000 years ago). The recurrence of past climatic changes in the central part of the Atlantic forest, with cycles of forest expansion and contraction, may have led to repeated vicariance events, resulting in the genetic differentiation of these groups. Based on comparisons among the populations of large reserves and small, disturbed fragments of the same phylogeographic group, we also found evidence of recent anthropogenic effects on genetic diversity. The results were also analysed with the aim of contributing to the conservation of D. nigra. We suggest that the three phylogeographic groups could be considered as three distinct management units. Based on the genetic diversity and uniqueness of the populations, we also indicate priority areas for conservation.     

Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats

Background

Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens.

Results

Following in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes.

Conclusions

Overall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1498-0) contains supplementary material, which is available to authorized users.     

Suppression of NS3 and MP is important for the stable inheritance of RNAi-mediated rice stripe virus (RSV) resistance obtained by targeting the fully complementary RSV-CP gene

Rice stripe virus (RSV) is a viral disease that seriously impacts rice production in East Asia, most notably in Korea, China, and Japan. Highly RSV-resistant transgenic japonica rice plants were generated using a dsRNAi construct designed to silence the entire sequence region of the RSV-CP gene. Transgenic rice plants were inoculated with a population of viruliferous insects, small brown planthoppers (SBPH), and their resistance was evaluated using ELISA and an infection rate assay. A correlation between the expression of the RSV-CP homologous small RNAs and the RSV resistance of the transgenic rice lines was discovered. These plants were also analyzed by comparing the expression pattern of invading viral genes, small RNA production and the stable transmission of the RSV resistance trait to the T3 generation. Furthermore, the agronomic trait was stably transmitted to the T4 generation of transgenic plants.     

Marcescent corollas as functional structures: effects on the fecundity of two insect-pollinated plants

Background and aims

Persistence of withered corollas after anthesis (‘corolla marcescence’) is widespread in angiosperms, yet its functional significance does not seem to have been explored for any species. This note reports the results of experiments assessing the fecundity effects of marcescent corollas in two southern Spanish insect-pollinated plants, Lavandula latifolia (Lamiaceae) and Viola cazorlensis (Violaceae).

Methods

The effect of marcescent corollas on seed production was evaluated experimentally on wild-growing plants. Newly open flowers were randomly assigned to either control or treatment groups in experimental plants. After anthesis, withered corollas of treatment flowers were removed and those in control flowers were left in place. Fruits produced by treatment and control flowers were collected shortly before dehiscence and the number of seeds counted.

Key Results

In V. cazorlensis, removal of withered corollas had no effect on percentage of fruit set, but mean seeds per fruit increased from 9·5 to 11·4. In L. latifolia, corolla removal had no effect on the number of seeds per fruit, but reduced the proportion of flowers ripening fruit from 60 % to 40 %. The detrimental effect of corolla removal on L. latifolia fecundity resulted from the drastic increase in fruit infestation by seed-predatory cecidomyiid larvae, which occurred in 4 % and 34 % of control and treatment fruits, respectively.

Conclusions

Because of their potential effects on plant fecundity, marcescent corollas should not be dismissed a priori as biologically irrelevant leftovers from past floral functions. The simplicity of the experimental layout required to test for short-term fecundity effects of corolla marcescence should help to achieve a better understanding of the ecological and evolutionary correlates of this widespread but poorly understood trait.     

A pharmacological investigation of Hippophae salicifolia (HS) and Hippophae rhamnoides turkestanica (HRT) against multiple stress (C-H-R): an experimental study using rat model

Hippophae salicifolia (HS) and Hippophae rhamnoides turkestanica (HRT) are abundantly found species of Hippophae in Himalayan region of India. As these plants thrive under extreme climatic conditions, it is suspected that these plants must have a unique adaptogenic property against high-altitude stress. To keeping these views in our mind, the present study was planned to evaluate the mechanism of action of aqueous extract of HS and aqueous extract of HRT against multiple stress [cold-hypoxia-restraint (C-H-R)] for their adaptogenic activity. The present study reported the adaptogenic activity of HS in facilitating tolerance to multiple stress, CHR in rats. Pre-treatment with aqueous extract of HS significantly attenuated reactive oxygen species (ROS) production, protein oxidation, and lipid peroxidation and also showed role in maintaining antioxidant status as similar to control rats. Since protein oxidation was decreased by pre-treatment of HS, protein homeostasis was also sustained by regulation of heat shock proteins (HSP70 and HSP60). Interestingly, heme oxygenase-1 (HO-1), Vascular Endothelial Growth Factor (VEGF), and nitric oxide (NO) level was also increased in HS pre-treated rats depicted its adaptogenic activity against multiple stress, CHR. Conclusively, aqueous extract of HS could use an adaptogen for high altitude-associated multiple stress (CHR).     

Identification and classification of detoxification enzymes from Culex quinquefasciatus (Diptera: Culicidae)

Molecular characterization of the insecticide resistance has become a hot research topic ever since the first disease transmitting arthropod (Anopheles gambiae) genome sequence has unveiled in 2002. A recent publication of the Culex quinquefasciatus genome sequence has opened up new opportunities for molecular and comparative genomic analysis of multiple mosquito genomes to characterize the insecticide resistance. Here, we utilized a whole genome sequence of Cx. quinquefasciatus to identify putatively active members of the detoxification supergene families, namely cytochrome P450s (P450s), glutathione-S-transferases (GSTs), and choline/carboxylesterases (CCEs). The Culex genome analysis revealed 166 P450s, 40 GSTs, and 62 CCEs. Further, the comparative genomic analysis shows that these numbers are considerably higher than the other dipteran mosquitoes. These observed speciesspecific expansions of the detoxification super gene family members endorse the popular understanding of the involvement of these gene families in protecting the organism against multitudinous classes of toxic substances during its complex (aquatic and terrestrial) life cycle. Thus, the generated data set may provide an initial point to start with to characterize the insecticide resistance at a molecular level which could then lead the development of an easy to use molecular marker to monitor the incipient insecticide resistance in field environs.     

Arsenate reduction: thiol cascade chemistry with convergent evolution

The frequent abundance of arsenic in the environment has guided the evolution of enzymes for the reduction of arsenate. The arsenate reductases (ArsC) from different sources have unrelated sequences and structural folds, and can be divided into different classes on the basis of their structures, reduction mechanisms and the locations of catalytic cysteine residues. The thioredoxin-coupled arsenate reductase class is represented by Staphylococcus aureus pI258 ArsC and Bacillus subtilis ArsC. The ArsC from Escherichia coli plasmid R773 and the eukaryotic ACR2p reductase from Saccharomyces cerevisiae represent two distinct glutaredoxin-linked ArsC classes. All are small cytoplasmic redox enzymes that reduce arsenate to arsenite by the sequential involvement of three different thiolate nucleophiles that function as a redox cascade. In contrast, the ArrAB complex is a bacterial heterodimeric periplasmic or a surface-anchored arsenate reductase that functions as a terminal electron acceptor and transfers electrons from the membrane respiratory chain to arsenate. Finally, the less well documented arsenate reductase activity of the monomeric arsenic(III) methylase, which is an S-adenosylmethionine (AdoMet)-dependent methyltransferase. After each oxidative methylation cycle and before the next methylation step, As(V) is reduced to As(III). Methylation by this enzyme is also considered an arsenic-resistance mechanism for bacteria, fungi and mammals.     

Sugar hydrazone-metal complexes: transition- and non-transition metal complexes of monosaccharide S-alkylhydrazonecarbodithioates and dehydro-L-ascorbic acid bis(S-alkylhydrazonecarbodithioates)

Copper(II), nickel(II) and palladium(II) complexes with aldehydo-D-arabinose-, L-arabinose-, D-galactose-, D-glucose- and D-mannose- S-methyl- and S-benzylhydrazonecarbodithioates were synthesized and characterized by elemental analyses, infrared and UV-Vis. In these complexes the aldehydo sugar hydrazone acts as a mononegative NS bidentate ligand. The reaction of Cu(II) chloride, however, proceeded with reduction, and copper(I) complexes were isolated. The hydrazone molecule in these Cu(I) complexes acts as neutral NS bidentate ligand. Dehydro-L-ascorbic acid bis(S-methylhydrazinecarbodithioate) and bis(hydrazinecarbothioamide), as well as their corresponding Cu(II), Ni(II), zinc(II) and Pd(II) complexes were prepared and characterized. Electrospray (ES) and field desorption (FD) mass spectra suggest that the Cu(II), Ni(II), and Pd(II) complexes are monomeric (square planar), whereas the Zn(II) are dimeric and pentacoordinate.     

Population Dynamics of Plant Nematodes in Cultivated Soil: Effect of Summer Cover Crops in Newly Cleared Land

Five nematode species were studied for ability to develop on seven summer cover crops in rotation with tomato transplants grown every third year. Increase of Tylenchorhynchus claytoni, Trichodorus christiei, Pratylenchus brachyurus, Helicotylenchus dihystera, and Xiphinema americanum in newly cleared soil varied with different cover crops. No substantial nematode population increases occurred until the third summer of crop growth. All species except X. americanum and H. dihystera developed best on sudangrass and millet. Crotalaria caused substantial increase of H. dihystera and P. brachyurus but suppressed the other species. Marigold suppressed all species except X. americanum which increased substantially on marigold during the 5th year. Cotton favored rapid increase of T. christiei, and moderate increases of all species except T. claytoni which was suppressed. Beggarweed favored moderate increases of T. christiei and H. dihystera but suppressed the other species. Hairy indigo favored rapid increase of H. dihystera, moderate increases of T. christiei and X. americanum, and suppressed the other species. Number of marketable transplants was reduced after 2 years of sudangrass and cotton; these crops favored increases of T. christiei and T. claytoni. The better cover crops prevented increases of most plant parasitic nematodes in land cropped to tomato, a suitable host.