Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks

Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range protein-protein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.     

Diversity of Halimeda (Bryopsidales,Chlorophyta) in New Caledonia: a Combined Morphological and Molecular Study

Halimeda is a genus of calcified and segmented green macroalgae in the order Bryopsidales. In New Caledonia, the genus is abundant and represents an important part of the reef flora. Previous studies recorded 19 species that were identified using morphological criteria. The aim of this work was to reassess the diversity of the genus in New Caledonia using morpho‐anatomical examinations and molecular analyses of the plastid tufA and rbcL genes. Our results suggest the occurrence of 22 species. Three of these are reported for the first time from New Caledonia: Halimeda kanaloana, H. xishaensis, and an entity resembling H. stuposa. DNA analyses revealed that the species H. fragilis exhibits cryptic or pseudocryptic diversity in New Caledonia. We also show less conclusive evidence for cryptic species within H. taenicola     

Impacts and management of unowned and owned cats at a seabird colony on Reunion Island (Western Indian Ocean)

Biological Invasions - Cats (Felis catus) introduced on islands have strong impacts on biodiversity, and the main conservation actions to protect native fauna is cat eradication or control (i.e.,...     

Effects of crayfish on leaf litter breakdown and shredder prey: are native and introduced species functionally redundant?

Recent increases in biological invasions frequency may have important consequences on native communities. However, functional redundancy between invasive and native species could reduce non-native species effects on native ecosystems. Despite this, even small differences in functional traits between these species may still have unpredictable effects on colonized ecosystems. Invasive crayfish, as ecosystem engineers, potentially have wide and complex effects on recipient ecosystems, even when replacing a native counterpart. We used laboratory microcosms to test whether native (Astacus astacus) and invasive crayfish species (Orconectes limosus, Pacifastacus leniusculus and Procambarus clarkii) are actually functionally redundant in their effects on prey/shredder density and leaf litter breakdown. Results show that crayfish strongly influenced macroinvertebrate numbers and leaf litter breakdown and indicate that differences in direct (prey and leaf litter consumption) and indirect (prey habitat use and leaf litter breakdown) effects between crayfish species do exist. While the replacement of A. astacus by O. limosus may have induced only minor changes in freshwater ecosystems, invasions by the larger and more aggressive P. clarkii and P. leniusculus will likely have strong effects on invaded ecosystem. Overall, there seems to be no functional redundancy between these four species and outcomes of crayfish invasion will likely be species specific.     

Antitumor activity and distribution of pyrroloiminoquinones in the sponge genus Zyzzya

A detailed analysis of four different collections of the sponge genus Zyzzya yielded nine pyrroloiminoquinones of the makaluvamine, batzelline, and isobatzelline/damirone classes. Dereplication analyses of additional Zyzzya extracts did not disclose more potent or additional new compounds. Comparative testing of these compounds in the National Cancer Institute's 60 cell line human tumor screen revealed varying levels of potency and differential cytotoxicity, apparently related to the unsaturation levels in and substitution patterns on the core ring system. Further studies on the topoisomerase II-mediated DNA cleavage were conducted. Reductive activation of the pyrroloiminoquinones led to DNA damage in vitro, which correlated with half wave potentials and reversibility parameters. DNA damage could be abrogated by ascorbate. Fluorescence displacement was used to measure intercalation with DNA; intercalation efficiency did not correlate with DNA-damaging proficiency. Makaluvamine H (5) emerged as the most potent and differential of our isolates, roughly comparable to makaluvamines C (in vitro) and I (in vivo). 3,7-Dimethyl guanine was isolated from one of the Zyzzya collections and from the sponge Latrunculia purpurea.     

Ethyl acetate extract and its major constituent, isorhamnetin 3-O-rutinoside, from Nitraria retusa leaves, promote apoptosis of human myelogenous erythroleukaemia cells

Objective: Fractionation of ethyl acetate extract (EA) obtained from Nitraria retusa leaves was assessed using different methods of chromatography, and isorhamnetin3‐O‐rutinoside (I3‐O‐R) was isolated from this extract. Its structure was determined using data obtained from ¹H and ¹³C NMR spectra, as well as by various correlation experiments (COSY, HMQC and HMBC). Both EA extract and I3‐O‐R were investigated for their ability to induce apoptosis in human chronic myelogenous erythroleukaemia cells (K562). Materials and methods: Apoptosis of cells from the K562 line was detected by DNA fragmentation, PARP cleavage and by evaluating activities of caspases 3 and 8. Results: Apoptosis, revealed by DNA fragmentation and PARP cleavage, was observed after 48‐h incubation of these human myelogenous erythroleukaemia cells (K562), with the tested products. Likewise, caspase 3 and caspase 8 activities were induced in the presence of the EA extract and I3‐O‐R after 48 h of incubation. Conclusion: Our results strongly suggest the involvement of the extrinsic pathway of apoptosis in cells treated by both the original EA extract and its major component, I3‐O‐R.     

The More We Search,the More We Find: Discovery of a New Lineage and a New Species Complex in the Genus Asparagopsis

In the past few decades, in the marine realm in particular, the use of molecular tools has led to the discovery of hidden taxonomic diversity, revealing complexes of sister species. A good example is the red algal genus Asparagopsis. The two species (A. armata and A. taxiformis) recognized in this genus have been introduced in many places around the world. Within the nominal species A. taxiformis, previous molecular analyses have uncovered several lineages, suggesting the existence of sister species or subspecies. Although the genus has been well studied in some regions (e.g., the Mediterranean Sea and Hawaii), it remains poorly investigated in others (e.g., South Pacific). Our study mainly focused on these latter areas to clarify lineages and better determine lineage status (i.e., native vs. introduced). A total of 188 specimens were collected from 61 sites, 58 of which had never been sampled before. We sequenced the DNA from samples for three markers and obtained 112 sequences for the chloroplastic RuBisCo spacer, 118 sequences for the nuclear LSU rRNA gene, and 174 for the mitochondrial spacer cox2-3. Phylogenetic analyses using all three markers suggested the existence of two cryptic sister species with the discovery of a new clade within A. armata. This clade was found only in Western Australia, Tasmania and New Zealand, and is thus restricted to a subregional biogeographic unit. We also discovered a new, fifth lineage for A. taxiformis restricted to the South Pacific and Western Australia. Except for this newly described lineage, all other lineages showed a global distribution influenced by introduction events. These results illustrate the difficulty in accurately defining cosmopolitan species. Our findings also highlight the need for targeted (i.e., in poorly studied areas) and geographically extensive sampling efforts when studying taxa that have been introduced globally and that are likely to hide species complexes.     

Relationship correlation of antioxidant and antiproliferative capacity of Cyperus rotundus products towards K562 erythroleukemia cells

A Total Oligomers Flavonoids (TOFs) and ethyl acetate extracts of Cyperus rotundus were analyzed, in vitro, for their antioxidant activity using several biochemical assays: the xanthine (X)/xanthine oxidase (XO), the lipid peroxidation induced by H₂O₂ in K562 human chronic myelogenous leukemia cells and the DNA damage in pKS plasmid DNA assay induced by H₂O₂/UV-photolysis and for their apoptotic effect. TOF and ethyl acetate extracts were found to be efficient in inhibiting xanthine oxidase with IC₅₀ values of 240 and 185 μg/ml and superoxide anion with IC₅₀ values of 150 and 215 μg/ml, respectively. Also, all the extracts tested were effective in reducing the production of thiobarbituric acid reactive substances (TBARS) and were able to protect against H₂O₂/UV-photolysis induced DNA damage. The highest activity, measured as equivalents of MDA concentration, was observed in the ethyl acetate extract (MDA = 2.04 nM). In addition, the data suggest that only TOF enriched extract exerts growth inhibition on K562 cells through apoptosis induction. Therefore, these extracts were subjected to further separation by chromatographic methods. Thus, three major compounds (catechin, afzelechin and galloyl quinic acid) were isolated from the TOF enriched extract and five major compounds (luteolin, ferulic acid, quercetin, 3-hydroxy, 4-methoxy-benzoic acid and 6,7-dimethoxycoumarin) from ethyl acetate extract. Their structures were determined by spectroscopic data analysis and comparison with the literature. In addition, we evaluate the biological activities of the catechin, ferulic acid and luteolin. This investigation has revealed that the luteolin was the most active in reducing the production of TBARS (MDA = 1.5 nM), inhibiting significantly the proliferation of K562 cells (IC₅₀ = 25 μg/ml) and protecting against H₂O₂/UV-photolysis induced DNA damage. In conclusion, the study reveals that the ability of C. rotundus to inhibit the enzyme xanthine oxidase (XO), the lipid peroxidation and to exert apoptotic effect, may explain possible mechanisms by which C. rotundus exhibits its health benefits.