Biogeography of sponge chemical ecology: comparisons of tropical and temperate defenses

Examples from both marine and terrestrial systems have supported the hypothesis that predation is higher in tropical than in temperate habitats and that, as a consequence, tropical species have evolved more effective defenses to deter predators. Although this hypothesis was first proposed for marine sponges over 25 years ago, our study provides the first experimental test of latitudinal differences in the effectiveness of sponge chemical defenses. We collected 20 common sponge species belonging to 14 genera from tropical Guam and temperate Northeast Spanish coasts (Indo-Pacific and Mediterranean biogeographic areas) and conducted field-based feeding experiments with large and small fish predators in both geographic areas. We use the term global deterrence to describe the deterrent activity of a sponge extract against all of the predators used in our experiments and to test the hypothesis that sponges from Guam are chemically better defended than their Mediterranean counterparts. Sympatric and allopatric deterrence refer to the average deterrent activity of a sponge against sympatric or allopatric predators. All of the sponges investigated in this study showed deterrent properties against some predators. However, 35% of the sponge species were deterrent in at least one but not in all the experiments, supporting the idea that predators can respond to chemical defenses in a species-specific manner. Tropical and temperate sponges have comparable global, sympatric, and allopatric deterrence, suggesting not only that chemical defenses from tropical and temperate sponges are equally strong but also that they are equally effective against sympatric and allopatric predators. Rather than supporting geographic trends in the production of chemical defenses, our data suggest a recurrent selection for chemical defenses in sponges as a general life-history strategy.     

Structural characterisation of a perdeuteriomethylated exopolysaccharide by NMR spectroscopy: characterisation of the novel exopolysaccharide produced by Lactobacillus delbrueckii subsp. bulgaricus EU23

The exopolysaccharide (EPS) from Lactobacillus delbrueckii subsp. bulgaricus EU23 was perdeuteriomethylated and the perdeuteriomethylated EPS (pdm-EPS) purified by elution from a C(18) Sep-Pak cartridge. Both 1D and 2D NMR spectra were recorded for the pdm-EPS and these were interpreted to provide assignments for the individual 1H and 13C resonances of the sugar residues of the repeating unit. Using a combination of the results from monomer analysis and linkage analysis of the native EPS and the ROESY and HMBC NMR spectra of the pdm-EPS the following structure has been determined for the repeating unit:A process for characterising polysaccharides having low solubility in aqueous solution is reported.     

Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18

We present the 4.8-Mb complete genome sequence of Salmonella enterica serovar Typhi strain Ty2, a human-specific pathogen causing typhoid fever. A comparison with the genome sequence of recently isolated S. enterica serovar Typhi strain CT18 showed that 29 of the 4,646 predicted genes in Ty2 are unique to this strain, while 84 genes are unique to CT18. Both genomes contain more than 200 pseudogenes; 9 of these genes in CT18 are intact in Ty2, while 11 intact CT18 genes are pseudogenes in Ty2. A half-genome interreplichore inversion in Ty2 relative to CT18 was confirmed. The two strains exhibit differences in prophages, insertion sequences, and island structures. While CT18 carries two plasmids, one conferring multiple drug resistance, Ty2 has no plasmids and is sensitive to antibiotics.     

The position of arginine 124 controls the rate of iron release from the N-lobe of human serum transferrin. A structural study

Human serum transferrin (hTF) is a bilobal iron-binding and transport protein that carries iron in the blood stream for delivery to cells by a pH-dependent mechanism. Two iron atoms are held tightly in two deep clefts by coordination to four amino acid residues in each cleft (two tyrosines, a histidine, and an aspartic acid) and two oxygen atoms from the "synergistic" carbonate anion. Other residues in the binding pocket, not directly coordinated to iron, also play critical roles in iron uptake and release through hydrogen bonding to the liganding residues. The original crystal structures of the iron-loaded N-lobe of hTF (pH 5.75 and 6.2) revealed that the synergistic carbonate is stabilized by interaction with Arg-124 and that both the arginine and the carbonate adopt two conformations (MacGillivray, R. T. A., Moore, S. A., Chen, J., Anderson, B. F., Baker, H., Luo, Y. G., Bewley, M., Smith, C. A., Murphy, M. E., Wang, Y., Mason, A. B., Woodworth, R. C., Brayer, G. D., and Baker, E. N. (1998) Biochemistry 37, 7919-7928). In the present study, we show that the two conformations are also found for a structure at pH 7.7, indicating that this finding was not strictly a function of pH. We also provide structures for two single point mutants (Y45E and L66W) designed to force Arg-124 to adopt each of the previously observed conformations. The structures of each mutant show that this goal was accomplished, and functional studies confirm the hypothesis that access to the synergistic anion dictates the rate of iron release. These studies highlight the importance of the arginine/carbonate movement in the mechanism of iron release in the N-lobe of hTF. Access to the carbonate via a water channel allows entry of protons and anions, enabling the attack on the iron.     

Increased yield of total RNA from fine-needle aspirates for use in expression microarray analysis

Fine-needle aspirate samples hold the potential for gaining valuable insight into the molecular details and prognostic indicators for certain types of cancer in a limited volume of relatively pure tumor cells. Although limited, such clinical samples can be used with high efficiency when analyzed in conjunction with gene-dense expression microarrays. For this reason, it is essential to retrieve as much high-quality genetic material as possible from each fine-needle aspirate sample. We have conducted a study to improve the efficiency of extracting high quality total RNA to use in microarray analysis from single ex vivo fine-needle aspirate samples of 11 breast cancers added to RNAlater RNA Stabilization Reagent immediately upon collection. Approximately half the total RNA from fine-needle aspirate samples of breast cancers was isolated from the supernatant, and that RNA had similar quality and gene expression profile to the RNA that was isolated from the corresponding cell pellet. We recommend that the supernatant not be discarded when extracting RNA from fine-needle aspirate samples stored in RNAlater.     

Trawling damage to Northeast Atlantic ancient coral reefs

This contribution documents widespread trawling damage to cold-water coral reefs at 840-1300 m depth along the West Ireland continental shelf break and at 200 m off West Norway. These reefs are spectacular but poorly known. By-catches from commercial trawls for deep-water fish off West Ireland included large pieces (up to 1 m(2)) of coral that had been broken from reefs and a diverse array of coral-associated benthos. Five azooxanthellate scleractinarian corals were identified in these by-catches, viz. Desmophyllum cristagalli, Enallopsammia rostrata, Lophelia pertusa, Madrepora oculata and Solenosmilia variabilis. Dating of carbonate skeletons using (14)C accelerator mass spectrometry showed that the trawled coral matrix was at least 4550 years old. Surveys by remotely operated vehicles in Norway showed extensive fishing damage to L. pertusa reefs. The urgent need for deep-water coral conservation measures is discussed in a Northeast Atlantic context.     

Treating mites in a bat colony: a case study

Since many bats used in research are wild-caught, dealing with mite infestation can present a unique challenge to the animal care staff. The authors tested the efficacy of fipronil spray for eliminating mites from a bat colony.     

Vaccination with a Melan-A peptide selects an oligoclonal T cell population with increased functional avidity and tumor reactivity

Both the underlying molecular mechanisms and the kinetics of TCR repertoire selection following vaccination against tumor Ags in humans have remained largely unexplored. To gain insight into these questions, we performed a functional and structural longitudinal analysis of the TCR of circulating CD8(+) T cells specific for the HLA-A2-restricted immunodominant epitope from the melanocyte differentiation Ag Melan-A in a melanoma patient who developed a vigorous and sustained Ag-specific T cell response following vaccination with the corresponding synthetic peptide. We observed an increase in functional avidity of Ag recognition and in tumor reactivity in the postimmune Melan-A-specific populations as compared with the preimmune blood sample. Improved Ag recognition correlated with an increase in the t(1/2) of peptide/MHC interaction with the TCR as assessed by kinetic analysis of A2/Melan-A peptide multimer staining decay. Ex vivo analysis of the clonal composition of Melan-A-specific CD8(+) T cells at different time points during vaccination revealed that the response was the result of asynchronous expansion of several distinct T cell clones. Some of these T cell clones were also identified at a metastatic tumor site. Collectively, these data show that tumor peptide-driven immune stimulation leads to the selection of high-avidity T cell clones of increased tumor reactivity that independently evolve within oligoclonal populations.