Generalization of learned predator recognition: an experimental test and framework for future studies

While some prey species possess an innate recognition of their predators, others require learning to recognize their predators. The specific characteristics of the predators that prey learn and whether prey can generalize this learning to similar predatory threats have been virtually ignored. Here, we investigated whether fathead minnows that learned to chemically recognize a specific predator species as a threat has the ability to generalize their recognition to closely related predators. We found that minnows trained to recognize the odour of a lake trout as a threat (the reference predator) generalized their responses to brook trout (same genus as lake trout) and rainbow trout (same family), but did not generalize to a distantly related predatory pike or non-predatory suckers. We also found that the intensity of antipredator responses to the other species was correlated with the phylogenetic distance to the reference predator; minnows responded with a higher intensity response to brook trout than rainbow trout. This is the first study showing that prey have the ability to exhibit generalization of predator odour recognition. We discuss these results and provide a theoretical framework for future studies of generalization of predator recognition.     

A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores

The internal phylogeny of the arachnid order Opiliones is investigated by including molecular data from five molecular markers for ca. 140 species totalling 43 families of Opiliones. The phylogenetic analyses consisted of a direct optimization (DO) approach using POY v. 4 and sophisticated tree search algorithms as well as a static alignment analysed under maximum likelihood. The four Opiliones suborders were well‐supported clades, but subordinal relationships did not receive support in the DO analysis, with the exception of the monophyly of Palpatores (=Eupnoi + Dyspnoi). Maximum‐likelihood analysis strongly supported the traditional relationship of Phalangida and Palpatores: (Cyphophthalmi ((Eupnoi + Dyspnoi) Laniatores)). Relationships within each suborder are well resolved and largely congruent between direct optimization and maximum‐likelihood approaches. Age estimates for the main Opiliones lineages suggest a Carboniferous diversification of Cyphophthalmi, while its sister group, Phalangida, diversified in the Early Devonian. Diversification of all suborders predates the Triassic, and most major lineages predate the Cretaceous. The following taxonomic changes are proposed. Dyspnoi: Hesperonemastoma is transferred to Sabaconidae. Insidiatores: Sclerobunidae stat. nov. is erected as a family for Zuma acuta. © The Willi Hennig Society 2009.     

Effect of chitosan type on protein and water recovery efficiency from surimi wash water treated with chitosan-alginate complexes

Previous research has shown that soluble protein recovery by chitosan (Chi) complexes with polyanions such as alginate (Alg) is more effective than using chitosan alone. In this study, Chi-Alg complexes were used to recover soluble proteins from surimi wash water (SWW) slightly acidified to pH 6. Six Chi samples differing in molecular weight (MW) and degree of deacetylation (DD) were used at 20, 40 and 100mg/L SWW Chi-Alg complexes prepared with a Chi:Alg mixing ratio previously optimized (MR=0.2). FTIR analysis of the solids recovered revealed the three characteristic amide bands observed in the same region for untreated SWW confirming protein adsorption by Chi-Alg. The superior effectiveness of Chi complexes was confirmed but differences among chitosan types could not be correlated to MW and DD. Experimental Chi samples with 94%, 93%, 75% and 93% DD and 22, 47, 225 and 3404 x 10(3)Da, respectively, showed 73-76% protein adsorption while a commercial chitosan sample with 84% DD and 3832 x 10(3)Da had 74-83% protein adsorption. An experimental chitosan, SY-1000 with 94% DD and 1.5 x 10(6)Da, showed the highest protein adsorption (79-86%) and turbidity reduction (85-92%) when used at 20mg/L SWW.     

A clone-free,single molecule map of the domestic cow (Bos taurus) genome

Background

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.

Results

The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).

Conclusion

Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI’s current designation of UMD3.1 sequence assembly as the “reference assembly” and the Btau4.6 as the “alternate assembly.” The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1823-7) contains supplementary material, which is available to authorized users.     

Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data

Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5 kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most‐parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species‐rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non‐monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter‐sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total‐evidence tree unambiguously optimizes trunk segmentation: a 23‐segmented trunk has a single origin in the blind clade. © The Willi Hennig Society 2011.     

2‐(Undecyloxy)‐ethanol is a major component of the male‐produced aggregation pheromone of Monochamus sutor

The small white‐marmorated longicorn beetle, Monochamus sutor (L.) (Coleoptera: Cerambycidae), is widely distributed throughout Europe and Asia. It is a potential vector of the pine wood nematode, Bursaphelenchus xylophilus (Steiner et Buhrer) Nickle, the causal agent of the devastating pine wilt disease. Volatiles were collected from both male and female beetles after maturation feeding. In analyses of these collections using gas chromatography (GC) coupled to mass spectrometry, a single male‐specific compound was detected and identified as 2‐(undecyloxy)‐ethanol. In analyses by GC coupled to electroantennography the only consistent responses from both female and male antennae were to this compound. Trapping tests were carried out in Spain, Sweden, and China. 2‐(Undecyloxy)‐ethanol was attractive to both male and female M. sutor beetles. A blend of the bark beetle pheromones ipsenol, ipsdienol, and 2‐methyl‐3‐buten‐2‐ol was also attractive to both sexes in Spain and Sweden, and further increased the attractiveness of the 2‐(undecyloxy)‐ethanol. The host plant volatiles α‐pinene, 3‐carene, and ethanol were weakly attractive, if at all, in all three countries and did not significantly increase the attractiveness of the blend of 2‐(undecyloxy)‐ethanol and bark beetle pheromones. 2‐(Undecyloxy)‐ethanol is thus proposed to be the major, if not only, component of the male‐produced aggregation pheromone of M. sutor, and its role is discussed. This compound has been reported as a pheromone of several other Monochamus species and is another example of the parsimony that seems to exist among the pheromones of many of the Cerambycidae. Traps baited with 2‐(undecyloxy)‐ethanol and bark beetle pheromones should be useful for monitoring and control of pine wilt disease, should M. sutor be proven to be a vector of the nematode.     

Tetrahydrohyperforin Inhibits the Proteolytic Processing of Amyloid Precursor Protein and Enhances Its Degradation by Atg5-Dependent Autophagy

Alzheimer''s disease (AD) is a neurodegenerative disorder characterized by the accumulation of amyloid-β (Aβ) peptide. We have previously shown that the compound tetrahydrohyperforin (IDN5706) prevents accumulation of Aβ species in an in vivo model of AD, however the mechanism that explains this reduction is not well understood. We show herein that IDN5706 decreases the levels of ER degradation enhancer, mannosidase alpha-like 1 (EDEM1), a key chaperone related to endoplasmic-reticulum-associated degradation (ERAD). Moreover, we observed that low levels of EDEM1 correlated with a strong activation of autophagy, suggesting a crosstalk between these two pathways. We observed that IDN5706 perturbs the glycosylation and proteolytic processing of the amyloid precursor protein (APP), resulting in the accumulation of immature APP (iAPP) in the endoplasmic reticulum. To investigate the contribution of autophagy, we tested the effect of IDN5706 in Atg5-depleted cells. We found that depletion of Atg5 enhanced the accumulation of iAPP in response to IDN5706 by slowing down its degradation. Our findings reveal that IDN5706 promotes degradation of iAPP via the activation of Atg5-dependent autophagy, shedding light on the mechanism that may contribute to the reduction of Aβ production in vivo.