Phylogeny of <Emphasis Type="Italic">Banana Streak Virus</Emphasis> Reveals Recent and Repetitive Endogenization in the Genome of Its Banana Host (<Emphasis Type="Italic">Musa</Emphasis> sp.)

Banana streak virus (BSV) is a plant dsDNA pararetrovirus (family Caulimoviridae, genus badnavirus). Although integration is not an essential step in the BSV replication cycle, the nuclear genome of banana (Musa sp.) contains BSV endogenous pararetrovirus sequences (BSV EPRVs). Some BSV EPRVs are infectious by reconstituting a functional viral genome. Recent studies revealed a large molecular diversity of episomal BSV viruses (i.e., nonintegrated) while others focused on BSV EPRV sequences only. In this study, the evolutionary history of badnavirus integration in banana was inferred from phylogenetic relationships between BSV and BSV EPRVs. The relative evolution rates and selective pressures (d_N/d_S ratio) were also compared between endogenous and episomal viral sequences. At least 27 recent independent integration events occurred after the divergence of three banana species, indicating that viral integration is a recent and frequent phenomenon. Relaxation of selective pressure on badnaviral sequences that experienced neutral evolution after integration in the plant genome was recorded. Additionally, a significant decrease (35%) in the EPRV evolution rate was observed compared to BSV, reflecting the difference in the evolution rate between episomal dsDNA viruses and plant genome. The comparison of our results with the evolution rate of the Musa genome and other reverse-transcribing viruses suggests that EPRVs play an active role in episomal BSV diversity and evolution.     

Response of a complex foraging phenotype to artificial selection on its component traits

In nature, where predators must often track dynamic and dispersed prey populations, predator consumption rate, conversion efficiency, dispersal, and prey finding are likely to be important links between foraging and predator–prey population dynamics. Small differences in predator foraging caused by variation in any of the abovementioned traits might lead to significant differences in predator success as well as population dynamics. We used artificial selection to create lines of the predatory mite, Phytoseiulus persimilis in order to determine the potential for or constraints on the evolution of predator foraging behaviors. All four foraging traits demonstrated considerable phenotypic variation. They also exhibited significant realized heritabilities after artificial selection, except that prey finding did not respond to downward selection. Lines that responded to selection did so rapidly, and high-consumption, high-conversion efficiency, and high- and low-dispersal were stable for at least four generations after artificial selection was relaxed. There were some indirect responses to selection among the foraging traits. For example, there was positive correlation between consumption and dispersal. However, none of the correlated responses were of the magnitude of the direct responses we measured on the same trait. We also observed some correlations between foraging traits and life-history traits such as low-consumption and development time (negative), high-consumption and fecundity (positive), and high-conversion efficiency and fecundity (positive), but these were more likely to represent non-genetic constraints. Intrinsic rates of increase in low-consumption and low-conversion efficiency lines were lower than in their respective high lines and the unselected control, whereas rates of increase in dispersal and olfactory response lines did not differ from the unselected control. Thus, traits that make up foraging share partially overlapping genetic architectures with highly heritable phenotypic components, suggesting that each foraging trait will be able to respond rapidly to changes in the density and distribution of resources.     

Peroxynitrite activates NF-E2-related factor 2/antioxidant response element through the pathway of phosphatidylinositol 3-kinase: the role of nitric oxide synthase in rat glutathione S-transferase A2 induction.

The protective adaptive response to electrophiles and reactive oxygen species is mediated by the induction of phase II detoxifying genes through antioxidant response elements (AREs). Our previous study showed that sulfur amino acid deprivation (SAAD) produces peroxides and induces rat glutathione S-transferase A2 (rGSTA2) through NF-E2-related factor 2 (Nrf2)/ARE activation via the pathway of phosphatidylinositol 3-kinase (PI3-kinase). The current study was designed to investigate the role of peroxynitrite in Nrf2/ARE activation and rGSTA2 induction. L-Arginine deficiency or N(G)-nitro-L-arginine methyl ester (L-NAME) reduced peroxide production induced by SAAD in H4IIE cells. Northern and Western blot analyses revealed that the levels of rGSTA2 mRNA and protein were significantly increased 24h after incubation of the cells in SAAD medium, which was inhibited by L-arginine deficiency or L-NAME. Subcellular fractionation and gel shift analyses revealed that SAAD increased the level of nuclear Nrf2 and activated ARE, which were also blocked by L-arginine deficiency or L-NAME. Whereas the exogenous NO donor S-nitroso-N-acetyl-penicillamine (SNAP) alone failed to significantly induce rGSTA2, SNAP enhanced SAAD-inducible rGSTA2 expression, verifying the notion that peroxynitrite derived from NO contributes to rGSTA2 induction. 3-Morpholinosydnonimine (SIN-1), which decomposes and yields peroxynitrite, increased the rGSTA2 mRNA and protein levels in a dose-dependent manner. SIN-1 increased the level of nuclear Nrf2 and activated Nrf2/ARE, which was supershifted by anti-Nrf2 and anti-Maf antibodies. SIN-1 increased the activity of PI3-kinase, as monitored by phosphorylation of Akt. SIN-1-inducible rGSTA2 expression was inhibited by PI3-kinase inhibitors. These results provide evidence that peroxynitrite plays an essential role in nuclear translocation of Nrf2 and ARE activation through the pathway of PI3-kinase and that nitric oxide synthase is involved in the induction of rGSTA2.     

Human-mediated processes affecting distribution and genetic structure of Squalidus multimaculatus,a freshwater cyprinid with small spatial range

Endemic species typically have a narrow niche breadth, and are likely more vulnerable to extinction than more widespread taxa. Squalidus multimaculatus is a small cyprinid endemic to the Korean Peninsula, and its reported geographical range was restricted to several small rivers located along the southeast coast. Several populations of S. multimaculatus have supposedly been subject to a variety of recent anthropogenic actions. Here, we analyzed the pattern of genetic diversity within and among populations of S. multimaculatus using nine microsatellite loci to quantify the relative contributions of human-mediated processes to the contemporary distribution and genetic structure. Overall, low levels of genetic diversity were exhibited in the populations of S. multimaculatus. Genetic differentiations among populations were not completely represented by their geographical proximity, likely resulting from the low intrapopulation genetic variability and anthropogenic transplants. The most conspicuous outcome of the anthropogenic activities was the introgression of alleles from a closely related species, S. gracilis majimae. Our study showed that anthropogenic transplanting, even with only a small number of individuals, can challenge our conservation goal to maintain the species integrity that has long been shaped in evolutionary processes.     

Connecting fruit production to seedling establishment in two co-occurring <Emphasis Type="Italic">Miconia</Emphasis> species: consequences of seed dispersal by birds in upper Amazonia

This study investigated links between seed production by two species of Miconia (Melastomataceae), whose seeds are dispersed by birds, and later stages of recruitment in lowland forests of eastern Ecuador. Seed dispersal and survival in later stages are crucial for understanding and predicting patterns of plant population dynamics as well as for understanding patterns of diversity in tropical forests. A major goal was to determine if the spatial template of seed deposition established by birds predicted probability of recruitment. We used observational and experimental approaches to compare patterns of recruitment in Miconia fosteri and M. serrulata. We calculated probabilities of transition between successive stages of recruitment for each species in three habitats. The number of plants with fruit, number of fruits removed, and, to a lesser extent, patterns of seed deposition varied between species and among habitats, whereas seed survival, germination, and establishment showed little variation among habitats. The location of seed deposition directly influenced the cumulative probabilities of survival. Among-habitat differences in the probabilities of recruitment set by seed deposition were not modified by later stages, although probability of recruitment was 2.5 times higher for M. serrulata than for M. fosteri after 1 year. The more critical stages for recruitment were seed removal and deposition. Our results from multiple life-cycle stages suggest that habitat associations among plants that reach reproductive maturity become established at early life stages and were mostly a consequence of seed dispersal by birds. These results differ from those obtained in temperate zones and suggest fundamental differences in the importance of recruitment processes. Dispersers, such as manakins, play significant roles in recruitment and population dynamics of M. fosteri, M. serrulata and numerous other understory plants of Neotropical forests. Their role in plant recruitment could be much greater than previously considered in megadiverse tropical forests. Thus, loss of dispersers could have long-term and far-reaching implications for maintenance of diversity.     

A novel bifunctional endo-/exo-type cellulase from an anaerobic ruminal bacterium

An anaerobic microorganism termed AN-C16-KBRB was isolated from the bovine rumen and demonstrated cellulolytic activity on a NB agar plate containing azo-carboxymethyl cellulose. The 16S rRNA gene of the strain was 98% similar to that of Clostridiaceae bacterium SK082 (AB298754) as the highest homology. A novel celEdx16 gene encoding a bifunctional endo-/exocellulase (CelEdx16) was cloned by the shotgun method from AN-C16-KBRB, and the enzyme was characterized. The celEdx16 gene had an open reading frame of 1,104-base pairs, which encoded 367 amino acids to yield a protein of molecular mass 40.4 kDa. The amino acid sequence was 53% identical to that of an endoglucanase from Clostridium thermocellum. CelEdx16 was overexpressed in Escherichia coli and purified using Ni-NTA affinity chromatography. The specific endocellulase and exocellulase activities of CelEdx16 were 15.9 and 3.6 × 10⁻² U mg⁻¹, respectively. The Michaelis–Menten constant (K _m values) and the maximal reaction velocities (V _max values) of CelEdx16 were 47.1 μM and 9.6 × 10⁻³ μmole min⁻¹ when endocellulase activity was measured and 106.3 μM and 2.1 × 10⁻⁵ μmole min⁻¹ when exocellulase activity was assessed. CelEdx16 was optimally active at pH 5.0 and 40°C.     

Plant cover estimation based on the beta distribution in grassland vegetation

Cover is the most frequently used measure of abundance in vegetation surveys of grasslands, and various qualitative and semi-quantitative methods have been developed for visual estimation of this metric. Field survey is usually made with a point-grid plate. The frequency distributions of cover derived from point-grid counts follow a beta distribution. Combining point-grid counts from a field survey and the beta distribution for a statistical analysis, we developed an effort-saving cover-measurement method. Cover is measured with a transparent plastic plate on which, for example, 10 × 10 = 100 points are arranged in a lattice with 1-cm grid spacing (thus, one point count represents 1 cm² of cover). N quadrats are set out at randomly dispersed sites in a grassland, and, in each, the plastic plate is used for making counts. The number of grid points located above a given species is counted in every quadrat until the number of counted points reaches a given value c, which is determined in advance. If the number of counted points reaches c in a quadrat, the count is stopped and the quadrat is classified in the category “>c”. In quadrats where c is not attained, full point counts above the species bodies are made. Let g be the number of observed quadrats whose cover is ≤c. Using these g cover measurements and the number of quadrats (N − g) with cover >c, we can quantitatively estimate cover for each species and the spatial pattern index value based on the maximum likelihood method. In trial counts using this method, the time savings varied between 5% and 41%, depending on the shape of the cover frequency distribution. The mean cover value estimates agreed well with conventional measures without a stopping point (i.e., based on full counts of all points in each quadrat).     

Toxicity of unsaturated fatty acids to the biohydrogenating ruminal bacterium, <Emphasis Type="Italic">Butyrivibrio fibrisolvens</Emphasis>

Background  

Health-promoting polyunsaturated fatty acids (PUFA) are abundant in forages grazed by ruminants and in vegetable and fish oils used as dietary supplements, but only a small proportion of PUFA finds its way into meat and milk, because of biohydrogenation in the rumen. Butyrivibrio fibrisolvens plays a major role in this activity. The aim of this study was to investigate the mechanisms by which PUFA affect the growth of B. fibrisolvens, how PUFA are metabolized and the metabolic response to growth in the presence of PUFA.     

Comparative Genomics Identifies Candidate Genes for Infectious Salmon Anemia (ISA) Resistance in Atlantic Salmon (<Emphasis Type=Italic>Salmo salar</Emphasis>)

Infectious salmon anemia (ISA) has been described as the hoof and mouth disease of salmon farming. ISA is caused by a lethal and highly communicable virus, which can have a major impact on salmon aquaculture, as demonstrated by an outbreak in Chile in 2007. A quantitative trait locus (QTL) for ISA resistance has been mapped to three microsatellite markers on linkage group (LG) 8 (Chr 15) on the Atlantic salmon genetic map. We identified bacterial artificial chromosome (BAC) clones and three fingerprint contigs from the Atlantic salmon physical map that contains these markers. We made use of the extensive BAC end sequence database to extend these contigs by chromosome walking and identified additional two markers in this region. The BAC end sequences were used to search for conserved synteny between this segment of LG8 and the fish genomes that have been sequenced. An examination of the genes in the syntenic segments of the tetraodon and medaka genomes identified candidates for association with ISA resistance in Atlantic salmon based on differential expression profiles from ISA challenges or on the putative biological functions of the proteins they encode. One gene in particular, HIV-EP2/MBP-2, caught our attention as it may influence the expression of several genes that have been implicated in the response to infection by infectious salmon anemia virus (ISAV). Therefore, we suggest that HIV-EP2/MBP-2 is a very strong candidate for the gene associated with the ISAV resistance QTL in Atlantic salmon and is worthy of further study.