Close relatives in population samples: Evaluation of the consequences for genetic stock identification

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.     

An insight into the reproductive biology of the bearded goby Sufflogobius bibarbatus

Preliminary results obtained from histological analyses of the male reproductive organs, supplemented with field and behavioural data, indicate that Sufflogobius bibarbatus, a small, slow growing gobiid exhibiting low fecundity, which plays an important role in the food web off Namibia, where large areas of the shelf are hypoxic, spawns demersally. Large males defend benthic nests, possibly at the edge of the hypoxic shelf. Male reproductive strategy appears to be flexible, and tentative evidence to suggest that polygyny and sneaking may also occur is presented.     

Echinocephalus caniculus n. sp. (Nematoda: Gnathostomatidae Railliet, 1895) from the lesser spotted dogfish Scyliorhinus canicula (L.) (Elasmobranchii: Scyliorhinidae Gill, 1862) off Tunisia,with a key to species of the genus Echinocephalus

Systematic Parasitology - Echinocephalus caniculus n. sp. (Nematoda, Gnathostomatidae Railliet, 1895) was isolated from the spiral valve of the lesser spotted dogfish Scyliorhinus canicula (L.)...     

Two new species of Echinobothrium van Beneden, 1849 (Cestoda: Diphyllidea) from the Persian Gulf

Two new species of diphyllidean cestodes are described from the Persian Gulf, Echinobothrium persiense n. sp. from Rhinobatos punctifer Compagno & Randall and Echinobothrium hormozganiense n. sp. from Mustelus mosis Hemprich & Ehrenberg. E. persiense is the first record of a species of Echinobothrium van Beneden, 1849 from R. punctifer and these two new species increase the number of diphyllideans known from the Persian Gulf from one to three. The number of apical hooks of E. persiense (hook formula: {5-6 6/5 5-6}) is distinct from all other species in the genus except for E. affine Diesing, 1863, E. harfordi McVicar, 1976, E. bonasum Williams & Campbell, 1980, E. fautleyae Tyler & Caira, 1999, E. syrtense (Neifar, Tyler & Euzet, 2001) Tyler, 2006 (emend), E. chisholmae Jones & Beveridge, 2001, E. tetabuanense Ivanov & Caira, 2012, E. sematanense Ivanov & Caira, 2012 and E. weipaense Ivanov & Caira, 2012. Echinobothrium persiense can be distinguished from all other species of the genus with 11 apical hooks by a combination of the following features: armed cephalic peduncle, testes arranged in a single column, lateral hooklets arranged in two groups, U-shaped ovary, cephalic peduncle length (124-181 μm), genital pore and cirrus-sac position, and by having 10-14 spines per row on the cephalic peduncle. Echinobothrium hormozganiense has a hook formula of {12-15 16/15 12-15} and is similar to E. musteli Pintner, 1889, E. notoguidoi Ivanov, 1997 and E. diamanti Ivanov & Lipshitz, 2006 by possessing additional spines between the rostellum and the bothria. It differs from E. musteli by having an H-shaped ovary and lateral hooklets arranged in two lateral groups, and the number of spines per row on the cephalic peduncle (18-21) readily differentiates it from E. notoguidoi (24-26) and E. diamanti (95-118). With these two new species, Echinobothrium van Beneden, 1849 now includes 45 valid species.     

Species of Colletotrichum on Agavaceae

Species of Colletotrichum cause diseases on a wide range of hosts, frequently infecting plants in the Agavaceae (monocotyledons: Liliales). Three species of Colletotrichum restricted to the Agavaceae were detected through morphological studies of specimens and molecular sequence analyses of the LSU of the nu-rDNA and the ITS region of the nu-rDNA from cultures. Colletotrichum agaves on Agave is fully described and illustrated. Colletotrichum dracaenophilum is described as a new species for isolates having long conidia and occurring on Dracaena sanderiana from China. Colletotrichum phormii and Glomerella phormii are determined to be the correct scientific names for the asexual and sexual states, respectively, of a species commonly referred to as C. rhodocyclum and G. phacidiomorpha occurring mainly on Phormium. In addition, C. gloeosporioides and C. boninense were isolated from plants in the Agavaceae. All species of Colletotrichum described on Agavaceae were evaluated based on type specimens. A key to the five species of Colletotrichum on Agavaceae is included. This paper includes one new species, Colletotrichum dracaenophilum, and three new combinations, Colletotrichum phormii, Glomerella phormii, and Phaeosphaeriopsis phacidiomorpha.     

Mass and Information Feedbacks through Receptor Endocytosis Govern Insulin Signaling as Revealed Using a Parameter-free Modeling Framework

Insulin and other hormones control target cells through a network of signal-mediating molecules. Such networks are extremely complex due to multiple feedback loops in combination with redundancy, shared signal mediators, and cross-talk between signal pathways. We present a novel framework that integrates experimental work and mathematical modeling to quantitatively characterize the role and relation between co-existing submechanisms in complex signaling networks. The approach is independent of knowing or uniquely estimating model parameters because it only relies on (i) rejections and (ii) core predictions (uniquely identified properties in unidentifiable models). The power of our approach is demonstrated through numerous iterations between experiments, model-based data analyses, and theoretical predictions to characterize the relative role of co-existing feedbacks governing insulin signaling. We examined phosphorylation of the insulin receptor and insulin receptor substrate-1 and endocytosis of the receptor in response to various different experimental perturbations in primary human adipocytes. The analysis revealed that receptor endocytosis is necessary for two identified feedback mechanisms involving mass and information transfer, respectively. Experimental findings indicate that interfering with the feedback may substantially increase overall signaling strength, suggesting novel therapeutic targets for insulin resistance and type 2 diabetes. Because the central observations are present in other signaling networks, our results may indicate a general mechanism in hormonal control.     

Structure-function engineering of interferon-beta-1b for improving stability, solubility, potency, immunogenicity, and pharmacokinetic properties by site-selective mono-PEGylation

Recombinant interferon-beta-1b (IFN-beta-1b) is used clinically in the treatment of multiple sclerosis. In common with many biological ligands, IFN-beta-1b exhibits a relatively short serum half-life, and bioavailability may be further diminished by neutralizing antibodies. While PEGylation is an approach commonly employed to increase the blood residency time of protein therapeutics, there is a further requisite for molecular engineering approaches to also address the stability, solubility, aggregation, immunogenicity and in vivo exposure of therapeutic proteins. We investigated these five parameters of recombinant human IFN-beta-1b in over 20 site-selective mono-PEGylated or multi-PEGylated IFN-beta-1b bioconjugates. Primary amines were modified by single or multiple attachments of poly(ethylene glycol), either site-specifically at the N-terminus, or randomly on the 11 lysines. In two alternate approaches, site-directed mutagenesis was independently employed in the construction of designed IFN-beta-1b variants containing either a single free cysteine or lysine for site-specific PEGylation. Optimization of conjugate preparation with 12 kDa, 20 kDa, 30 kDa, and 40 kDa amine-selective PEG polymers was achieved, and a comparison of the structural and functional properties of the IFN-beta-1b proteins and their PEGylated counterparts was conducted. Peptide mapping and MALDI-TOF mass spectrometric analysis confirmed the attachment sites of the PEG polymer. Independent biochemical and bioactivity analyses, including antiviral and antiproliferation bioassays, circular dichroism, capillary electrophoresis, flow cytometric profiling, reversed phase and size exclusion HPLC, and immunoassays demonstrated that the functional activities of the designed IFN-beta-1b conjugates were maintained, while the formation of soluble or insoluble aggregates of IFN-beta-1b was ameliorated. Immunogenicity and pharmacokinetic studies of selected PEGylated IFN-beta-1b compounds in mice and rats demonstrated both diminished IgG responses, and over 100-fold expanded AUC exposure relative to the unmodified protein. The results demonstrate the capacity of this macromolecular engineering strategy to address both pharmacological and formulation challenges for a highly hydrophobic, aggregation-prone protein. The properties of a lead mono-PEGylated candidate, 40 kDa PEG2-IFN-beta-1b, were further investigated in formulation optimization and biological studies.