Genetic diversity despite population collapse in a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata)

Sawfish (family Pristidae) are among the most critically endangered marine fish in the world, yet very little is known about how genetic bottlenecks, genetic drift, and inbreeding depression may be affecting these elasmobranchs. In the US Atlantic, the smalltooth sawfish (Pristis pectinata) has declined to 1-5% of its abundance in the 1900s, and its core distribution has contracted to southwest Florida. We used 8 polymorphic microsatellite markers to show that this remnant population still exhibits high genetic diversity in terms of average allelic richness (18.23), average alleles per locus (18.75, standard deviation [SD] 6.6) and observed heterozygosity (0.43-0.98). Inbreeding is rare (mean individual internal relatedness = -0.02, SD 0.14; F(IS) = -0.011, 95% confidence interval [CI] = -0.039 to 0.011), even though the estimated effective population size (N(e)) is modest (250-350, 95% CI = 142-955). Simulations suggest that the remnant smalltooth sawfish population will probably retain >90% of its current genetic diversity over the next century even at the lower estimate of N(e). There is no evidence of a genetic bottleneck accompanying last century's demographic bottleneck, and we discuss hypotheses that could explain this. We also discuss features of elasmobranch life history and population biology that could make them less vulnerable than other large marine vertebrates to genetic change associated with reduced population size.     

Duplication dup(1)(q41q44) defined by fluorescence in situ hybridization: delineation of the 'trisomy 1q42-->qter syndrome'

We report on a novel case of pure partial tandem duplication 1q42q43 confirmed by fluorescence in situ hybridization (FISH). We compare the manifestations of our patient with similar cases previously reported. We conclude that the most common clinical manifestations of trisomy 1q42qter are prenatal and postnatal growth retardation, relative macrocephaly, triangular face, prominent forehead, broad nasal bridge, abnormal philtrum, micro/retrognathia, cardiac defects and mental retardation. We would like to emphasize the importance of the FISH technique in the identification of the duplicated segment.     

Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor

Combined quantum mechanical/molecular mechanical (QM/MM) simulations are carried out to analyze factors that dictate the proton transfer in carbonic anhydrase II (CAII), an enzyme that has been used as a prototypical example of long-range proton transfers in biomolecules. In contrast to the long-held conjecture in the experimental literature, the computed potentials of mean force (PMF) suggest that the proton transfer in CAII is not very sensitive to the orientation of the acceptor group (His 64) and, therefore, the number of water molecules that bridge the donor (zinc-water) and acceptor groups. Perturbative analysis indicates that a series of polar and charged residues close to the transfer pathways make the dominant contribution to the barrier and exothermicity of the proton transfer reaction, thus supporting the proposal from previous studies of Warshel and co-workers using a somewhat simpler QM/MM model that electrostatic interactions play a major role in the proton transfer in CAII. The PMF results are in striking contrast to previous analysis using the same QM/MM method but an ensemble of minimum energy path (MEP) calculations, which found a steep dependence of the barrier height on the number of bridging water molecules. Analysis of the configurations sampled in the PMF and MEP simulations suggests that this difference arises because the PMF simulations sample a largely stepwise mechanism while the local MEP calculations artificially favored concerted transfers due to the specific protocol used to generate the initial configurations. Therefore, this study presents a compelling argument for carrying out proper conformational sampling in the study of long-range proton transfers. Finally, we illustrate that Phi analysis, which has been widely used in protein folding studies, can potentially generate new mechanistic information for long-range proton transfers regarding the sequence of events. The results of the perturbation analysis and the Phi analysis provide opportunities for experimentally testing the mechanistic proposals from this study and our recent work in which a stepwise "proton hole" transfer pathway has been proposed.     

A streamlined, bi-organelle, multiplex PCR approach to species identification: Application to global conservation and trade monitoring of the great white shark, Carcharodon carcharias

The great white shark, Carcharodoncarcharias, is the most widely protectedelasmobranch in the world, and is classified asVulnerable by the IUCN and listed on AppendixIII of CITES. Monitoring of trade in whiteshark products and enforcement of harvest andtrade prohibitions is problematic, however, inlarge part due to difficulties in identifyingmarketed shark parts (e.g., dried fins, meatand processed carcasses) to species level. Toaddress these conservation and managementproblems, we have developed a rapid, moleculardiagnostic assay based on species-specific PCRprimer design for accurate identification ofwhite shark body parts, including dried fins. The assay is novel in several respects: Itemploys a multiplex PCR assay utilizing bothnuclear (ribosomal internal transcribed spacer2) and mitochondrial (cytochrome b) locisimultaneously to achieve a highly robustmeasure of diagnostic accuracy; it is verysensitive, detecting the presence of whiteshark DNA in a mixture of genomic DNAs from upto ten different commercially fished sharkspecies pooled together in a single PCR tube;and it successfully identifies white shark DNAfrom globally distributed animals. Inaddition to its utility for white shark trademonitoring and conservation applications, thishighly streamlined, bi-organelle, multiplex PCRassay may prove useful as a general model forthe design of genetic assays aimed at detectingbody parts from other protected and threatenedspecies.     

Nodal and BMP expression during the transition to pentamery in the sea urchin <Emphasis Type="Italic">Heliocidaris erythrogramma</Emphasis>: insights into patterning the enigmatic echinoderm body plan

Background

The molecular mechanisms underlying the development of the unusual echinoderm pentameral body plan and their likeness to mechanisms underlying the development of the bilateral plans of other deuterostomes are of interest in tracing body plan evolution. In this first study of the spatial expression of genes associated with Nodal and BMP2/4 signalling during the transition to pentamery in sea urchins, we investigate Heliocidaris erythrogramma, a species that provides access to the developing adult rudiment within days of fertilization.

Results

BMP2/4, and the putative downstream genes, Six1/2, Eya, Tbx2/3 and Msx were expressed in the earliest morphological manifestation of pentamery during development, the five hydrocoele lobes. The formation of the vestibular ectoderm, the specialized region overlying the left coelom that forms adult ectoderm, involved the expression of putative Nodal target genes Chordin, Gsc and BMP2/4 and putative BMP2/4 target genes Dlx, Msx and Tbx. The expression of Nodal, Lefty and Pitx2 in the right ectoderm, and Pitx2 in the right coelom, was as previously observed in other sea urchins.

Conclusion

That genes associated with Nodal and BMP2/4 signalling are expressed in the hydrocoele lobes, indicates that they have a role in the developmental transition to pentamery, contributing to our understanding of how the most unusual body plan in the Bilateria may have evolved. We suggest that the Nodal and BMP2/4 signalling cascades might have been duplicated or split during the evolution to pentamery.

     

Effects <Emphasis Type="Italic">per se</Emphasis> of Organic Solvents in the Cerebral Acetylcholinesterase of Rats

Acetylcholinesterase (AChE) was studied in different rat brain regions (cerebellum, hypothalamus, striatum, hippocampus and cortex) in the presence of different organic solvents normally used in the in vitro assay. The organic solvents used were acetone (C₃H₆O), acetonitrile (C₂H₃N), ethyl alcohol (C₂H₆O), isopropyl alcohol (C₃H₈O), methyl alcohol (CH₄O), tert-butyl alcohol (C₄H₁₀O) and dimethyl sulfoxide (DMSO, C₂H₆OS) ranging from 0.6 to 10%. Ethyl and methyl alcohol presented no effect on AChE activity at any of the concentrations and brain structures tested. In the hippocampus, isopropyl alcohol did not demonstrate a significant inhibitory effect, even at high concentrations. Tert-butyl alcohol presented an interesting result, increased AChE activity (P < .05) in the hypothalamus (1.8%), cortex (1.8 and 2.5) and striatum (1.2, 1.8 and 2.5%) and decreased activity at a concentration of 10% in the cortex (P < .05) and striatum (P < .01). Acetone and acetonitrile presented similar results, both significantly inhibiting AChE in all structures (5%, P < .05 and 10%, P < .01). DMSO exhibited a highly inhibitory effect at practically all concentrations tested (P < .01). In conclusion, for testing new compounds on AChE activity in vitro, methyl and ethyl alcohol may be the best organic solvent choice.     

Nervous and muscle system development in <Emphasis Type="Italic">Phascolion strombus</Emphasis> (Sipuncula)

Recent interpretations of developmental gene expression patterns propose that the last common metazoan ancestor was segmented, although most animal phyla show no obvious signs of segmentation. Developmental studies of non-model system trochozoan taxa may shed light on this hypothesis by assessing possible cryptic segmentation patterns. In this paper, we present the first immunocytochemical data on the ontogeny of the nervous system and the musculature in the sipunculan Phascolion strombus. Myogenesis of the first anlagen of the body wall ring muscles occurs synchronously and not subsequently from anterior to posterior as in segmented spiralian taxa (i.e. annelids). The number of ring muscles remains constant during the initial stages of body axis elongation. In the anterior-posteriorly elongated larva, newly formed ring muscles originate along the entire body axis between existing myocytes, indicating that repeated muscle bands do not form from a posterior growth zone. During neurogenesis, the Phascolion larva expresses a non-metameric, paired, ventral nerve cord that fuses in the mid-body region in the late-stage elongated larva. Contrary to other trochozoans, Phascolion lacks any larval serotonergic structures. However, two to three FMRFamide-positive cells are found in the apical organ. In addition, late larvae show commissure-like neurones interconnecting the two ventral nerve cords, while early juveniles exhibit a third, medially placed FMRFamidergic ventral nerve. Although we did not find any indications for cryptic segmentation, certain neuro-developmental traits in Phascolion resemble the conditions found in polychaetes (including echiurans) and myzostomids and support a close relationship of Sipuncula and Annelida.