Eating catch of the day: the diet of porbeagle shark Lamna nasus (Bonnaterre 1788) based on stomach content analysis,and the interaction with trawl fisheries in the south-western Atlantic (52° S–56° S)

This work examined the diet of the porbeagle shark Lamna nasus in the south-west Atlantic Ocean (SWAO, Argentina, 52° S–56° S) by analysing the stomach content information obtained by scientific observers who sampled specimens captured as by-catch on-board commercial fishing vessels from 2010 to 2020. A total of 148 fishing sites were analysed, in which the estimated catch was composed mainly of hoki Macruronus magellanicus (56.00%) and southern blue whiting Micromesistius australis (33.13%). From 413 porbeagle sharks sampled (292 females and 121 males) ranging from 71 to 241 cm total length (L_T) (mean: 179.76 ± 26.74 cm), 310 (75.06%) contained food in the stomachs. The forage fish were mainly hoki M. magellanicus (23.53%) and southern blue whiting M. australis (19.05%), followed by the Patagonian sprat Sprattus fuegensis (4.48%) and nototheniids (1.4%). Cephalopods and crustaceans accounted for 10% of the diet. The estimated trophic level was 4.35. Generalized linear models revealed that the consumption of hoki M. magellanicus and southern blue whiting M. australis increased with the L_T of the porbeagle shark. Moreover, smaller porbeagle sharks preyed upon both small and large teleost fish, whereas larger porbeagle sharks predated exclusively upon large fish. The diet of porbeagle shark involved interactions with fisheries as it fed upon the fish species that constituted the main catch in the analysed fishing sites, as well as the main catches of the austral trawl fisheries. The ecological role of porbeagle shark observed in the SWAO exposed implications for fisheries management from a multispecies perspective.     

Sea urchin Hox genes: insights into the ancestral Hox cluster

We describe the Hox cluster in the radially symmetric sea urchin and compare our findings to what is known from clusters in bilaterally symmetric animals. Several Hox genes from the direct-developing sea urchin Heliocidaris erythrogramma are described. CHEF gel analysis shows that the Hox genes are clustered on a < or = 300 kilobase (kb) fragment of DNA, and only a single cluster is present, as in lower chordates and other nonvertebrate metazoans. Phylogenetic analyses of sea urchin, amphioxus, Drosophila, and selected vertebrate Hox genes confirm that the H. erythrogramma genes, and others previously cloned from other sea urchins, belong to anterior, central, and posterior groups. Despite their radial body plan and lack of cephalization, echinoderms retain at least one of the anterior group Hox genes, an orthologue of Hox3. The structure of the echinoderm Hox cluster suggests that the ancestral deuterostome had a Hox cluster more similar to the current chordate cluster than was expected Sea urchins have at least three Abd-B type genes, suggesting that Abd-B expansion began before the radiation of deuterostomes.      

Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.     

Male-biased sexual size dimorphism in sharks: the narrowmouth catshark Schroederichthys bivius as case study

Hydrobiologia - In shark populations, variation in sexual size dimorphism (SSD) appears to be related with the reproductive mode. Here, we aimed to investigate the reproductive biology of the...     

An optimized microarray platform for assaying genomic variation in <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> field populations

We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.     

Fucosylated protein of retinal cone photoreceptor outer segments: morphological and biochemical analyses

Cone outer segments (OS) of the goldfish retina are diffusely labeled after intravitreal injection of [(3)H]fucose while rod OS remain unlabeled. By electron microscopic radioautography, the OS of red- and blue-sensitive cones are heavily labeled while green- sensitive cone OS are lightly labeled. The time-course and pattern of OS labeling in all cone types from 30 min to 24 h resemble that of incorporation of other sugars into rhodopsin in rod OS. The nature of the cone OS-specific fucosylated component(s) was examined using biochemical techniques. Cone OS were prelabeled by intravitreal injection of [(3)H]fucose 24 h before sacrifice. Photoreceptor OS were isolated using a discontinuous sucrose density gradient and it was verified by electron microscopic radioautography that the only source of radioactivity in the preparations was cone OS. The different cone types could be recognized by the heaviness of labeling, characteristic membrane spacing, and 'staining' of green cone OS in vitro with horseradish peroxidase. After acid hydrolysis of prelabeled photoreceptor membranes, 90 percent of the counts were in the neutral sugar fraction which was analyzed by thin-layer chromatography. Approximately 70 percent of the radioactivity co-chromatographed with authentic fucose. SDS-PAGE/fluorography of prelabeled photoreceptor membranes revealed a single radioactive component that was lightly stained with coomassie blue and showed an apparent molecular weight of 33,000. This cone-derived band was separated from unlabeled rod opsin which was well stained and showed an apparent mol wt of 38,000. Isoelectric focusing under denaturing conditions produced two major and one minor band of radioactivity with isoelectric points of 8.2, 8.6, and 8.8 respectively. No radioactivity was found in association with a stained band corresponding in isoelectric point to that of bovine opsin (pl, 6.2). The fucosylated component was readily digested by pronase, indicating its protein nature. Washing of the isolated OS with isotonic and hypotonic buffers failed to extract major amounts of the radioactivity, suggesting that the fucosylated component is an integral membrane protein. The presence of a fucosylated protein thus represents a major difference between cone and rod OS in the goldfish and has enabled us to identify cone OS in preparations of isolated photoreceptor membranes and to demonstrate the separation of a cone-derived glycoprotein from rod opsin.