Phylogeny and genetic diversity of palolo worms (Palola, Eunicidae) from the tropical North Pacific and the Caribbean

Palolo worms (Palola, Eunicidae) are best known for their annual mass spawnings, or "risings," in the South Pacific. Palola currently contains 14 morphologically similar species, mostly from shallow tropical waters. In this study, 60 specimens of Palola from nine locations in the tropical North Pacific and the Caribbean were sequenced for the two mitochondrial markers cytochrome c oxidase subunit I and 16S ribosomal RNA to infer phylogenetic relationships, genetic diversity, and phylogeography within the taxon. Phylogenetic analysis was performed using Bayesian statistics and parsimony. Vouchers of the same specimens were examined morphologically. Two major clades (A and B) can be distinguished within the monophyletic Palola. A number of individuals in clade B bear rows of ventral eyespots in the posterior body region, typical for swarming P. viridis and probably a synapomorphy for clade B. No morphological synapomorphy was found for clade A. Haplotypes from divergent clades often co-occur in the same location. Some haplotypes are geographically widespread, in one case covering the entire east-west expansion of the tropical Pacific. These results imply that despite the apparent absence of teleplanic larvae in eunicid polychaetes, long-distance dispersal is possible in at least some lineages of Palola. With the first taste of palolo I understood the Samoans' love for it. Certainly it suggested a salty caviar, but with something added, a strong, rich whiff of the mystery and fecundity of the ocean depths. -R. Steinberg. Pacific and Southeast Asian cooking. Time-Life Books, New York, 1970.     

The influence of 5% and 10% dietary apple pectin on parameters of fermentation in faeces and caecal digesta of weaning pigs

In order to determine the effect of pectin on fermentation parameters in the faeces and caecal digesta of weaned pigs 18 castrated male crossbred pigs with an average body weight of 8 kg were fitted with T-cannulas at the caecum. The animals were randomly distributed into three groups and fed with diets supplemented with 0, 5 and 10% pectin. Faeces were collected over a period of 3 days. Thereafter the diets were withdrawn for 24 h followed by ad libitum feeding to enhance the feed intake. Caecal chyme was collected 0, 8 and 24 h postprandial. In the faeces the addition of 5% pectin to the diet lowered the content of dry matter and lactic acid. The pH and the digestibility of pectins, the concentration of total SCFA, acetate, propionate, butyrate, bicarbonate and chloride increased. Dietary pectin of 10% increased the content of total SCFA and acetate further. When the diets were withdrawn and fed ad libitum 24 h later, a decline of the pH and an increased concentration of lactate in the caecal chyme could be observed in all groups up to 8 h after feeding. With an interval of 8 to 24 h after feeding, a further decline in pH and a rise of lactate only occurred when the diet was not supplemented with pectin. It was concluded that pectin might be beneficial for the development of fermentative processes in the large intestine.     

Expression of the Cameleon calcium biosensor in fungi reveals distinct Ca2+ signatures associated with polarized growth,development, and pathogenesis

Calcium is a universal messenger that translates diverse environmental stimuli and developmental cues into specific cellular and developmental responses. While individual fungal species have evolved complex and often unique biochemical and structural mechanisms to exploit specific ecological niches and to adjust growth and development in response to external stimuli, one universal feature to all is that Ca²⁺-mediated signaling is involved. The lack of a robust method for imaging spatial and temporal dynamics of subcellular Ca²⁺ (i.e., “Ca²⁺ signature”), readily available in the plant and animal systems, has severely limited studies on how this signaling pathway controls fungal growth, development, and pathogenesis. Here, we report the first successful expression of a FRET (Förster Resonance Energy Transfer)-based Ca²⁺ biosensor in fungi. Time-lapse imaging of Magnaporthe oryzae, Fusarium oxysporum, and Fusarium graminearum expressing this sensor showed that instead of a continuous gradient, the cytoplasmic Ca²⁺ ([Ca²⁺]_c) change occurred in a pulsatile manner with no discernable gradient between pulses, and each species exhibited a distinct Ca²⁺ signature. Furthermore, occurrence of pulsatile Ca²⁺ signatures was age and development dependent, and major [Ca²⁺]_c transients were observed during hyphal branching, septum formation, differentiation into specialized plant infection structures, cell–cell contact and in planta growth. In combination with the sequenced genomes and ease of targeted gene manipulation of these and many other fungal species, the data, materials and methods developed here will help understand the mechanism underpinning Ca²⁺-mediated control of cellular and developmental changes, its role in polarized growth forms and the evolution of Ca²⁺ signaling across eukaryotic kingdoms.     

An alternate sucrose binding mode in the E203Q Arabidopsis invertase mutant: an X-ray crystallography and docking study

In the present study, we report on the X-ray crystallographic structure of a GH32 invertase mutant, (i.e., the Arabidopsis thaliana cell-wall invertase 1-E203Q, AtcwINV1-mutant) in complex with sucrose. This structure was solved to reveal the features of sugar binding in the catalytic pocket. However, as demonstrated by the X-ray structure the sugar binding and the catalytic pocket arrangement is significantly altered as compared with what was expected based on previous X-ray structures on GH-J clan enzymes. We performed a series of docking and molecular dynamics simulations on various derivatives of AtcwINV1 to reveal the reasons behind this modified sugar binding. Our results demonstrate that the E203Q mutation introduced into the catalytic pocket triggers conformational changes that alter the wild type substrate binding. In addition, this study also reveals the putative productive sucrose binding modus in the wild type enzyme.     

P2-P1' macrocyclization of P2 phenylglycine based HCV NS3 protease inhibitors using ring-closing metathesis

Macrocyclization is a commonly used strategy to preorganize HCV NS3 protease inhibitors in their bioactive conformation. Moreover, macrocyclization generally leads to greater stability and improved pharmacokinetic properties. In HCV NS3 protease inhibitors, it has been shown to be beneficial to include a vinylated phenylglycine in the P2 position in combination with alkenylic P1' substituents. A series of 14-, 15- and 16-membered macrocyclic HCV NS3 protease inhibitors with the linker connecting the P2 phenylglycine and the alkenylic P1' were synthesized by ring-closing metathesis, using both microwave and conventional heating. Besides formation of the expected macrocycles in cis and trans configuration as major products, both ring-contracted and double-bond migrated isomers were obtained, in particular during formation of the smaller rings (14- and 15-membered rings). All inhibitors had K(i)-values in the nanomolar range, but only one inhibitor type was improved by rigidification. The loss in inhibitory effect can be attributed to a disruption of the beneficial π-π interaction between the P2 fragment and H57, which proved to be especially deleterious for the d-phenylglycine epimers.     

DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters

The spatial and temporal organization of DNA replication was investigated in living cells with a green fluorescent protein fusion to the DNA polymerase clamp PCNA. In situ extractions and photobleaching experiments revealed that PCNA, unlike RPA34, shows little if any turnover at replication sites, suggesting that it remains associated with the replication machinery through multiple rounds of Okazaki fragment synthesis. Photobleaching analyses further showed that the transition from earlier to later replicons occurs by disassembly into a nucleoplasmic pool of rapidly diffusing subcomponents and reassembly at newly activated sites. The fact that these replication sites were de novo assembled in close proximity to earlier ones suggests that activation of neighboring origins may occur by a domino effect possibly involving local changes in chromatin structure and accessibility.