Insights into the ecological performance of agroecosystems with ECOPATH II

The article provides insights on agroecosystem modeling and analysis with ECOPATH II.

Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

New insights into the diets of harbor seals (Phoca vitulina) in the Salish Sea revealed by analysis of fatty acid signatures

Harbor seals (Phoca fvitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available informationon harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

James's rule and causes and consequences of a latitudinal cline in the demography of John's Snapper (Lutjanus johnii) in coastal waters of Australia

Demographic parameters were derived from sectioned otoliths of John’s Snapper (Lutjanus johnii) from 4 regions across 9° of latitude and 23° of longitude in northern Australia. Latitudinal variation in size and growth rates of this species greatly exceeded longitudinal variation. Populations of John’s Snapper farthest from the equator had the largest body sizes, in line with James’s rule, and the fastest growth rates, contrary to the temperature-size rule for ectotherms. A maximum age of 28.6 years, nearly 3 times previous estimates, was recorded and the largest individual was 990 mm in fork length. Females grew to a larger mean asymptotic fork length (L∞) than did males, a finding consistent with functional gonochorism. Otolith weight at age and gonad weight at length followed the same latitudinal trends seen in length at age. Length at maturity was ~72–87% of L∞ and varied by ~23% across the full latitudinal gradient, but age at first maturity was consistently in the range of 6–10 years, indicating that basic growth trajectories were similar across vastly different environments. We discuss both the need for complementary reproductive data in age-based studies and the insights gained from experiments where the concept of oxygen- and capacity-limited thermal tolerance is applied to explain the mechanistic causes of James’s rule in tropical fish species.

Chromosome painting in the long-tailed field mouse provides insights into the ancestral murid karyotype

We report on the hybridization of mouse chromosomal paints to Apodemus sylvaticus, the long-tailed field mouse. The mouse paints detected 38 conserved segments in the Apodemus karyotype. Together with the species reported here there are now six species of rodents mapped with Mus musculus painting probes. A parsimony analysis indicated that the syntenies of nine M. musculus chromosomes were most likely already formed in the muroid ancestor: 3, 4, 7, 9, 14, 18, 19, X and Y. The widespread occurrence of syntenic segment associations of mouse chromosomes 1/17, 2/13, 7/19, 10/17, 11/16, 12/17 and 13/15 suggests that these associations were ancestral syntenies for muroid rodents. The muroid ancestral karyotype probably had a diploid number of about 2n = 54. It would be desirable to have a richer phylogenetic array of species before any final conclusions are drawn about the Muridae ancestral karyotype. The ancestral karyotype presented here should be considered as a working hypothesis. Copyright (C) 2004 S. Karger AG, Basel.

New Insights into the Evolution of Intronic Sequences of the beta-fibrinogen Gene and Their Application in Reconstructing Mustelid Phylogeny

Mustelidae is the largest and most diverse family in the order Carnivora. The phylogenetic relationships among the subfamilies have especially long been a focus of study. Herein we are among the first to employ two new introns (4 and 7) of the nuclear P-f

New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction

The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyr

Characterization of TRPC2, an Essential Genetic Component of VNS Chemoreception, Provides Insights into the Evolution of Pheromonal Olfaction in Secondary-Adapted Marine Mammals

Pheromones are chemical cues released and sensed by individuals of the same species, which are of major importance in regulating reproductive and social behaviors of mammals. Generally, they are detected by the vomeronasal system (VNS). Here, we first investigated and compared an essential genetic component of vomeronasal chemoreception, that is, TRPC2 gene, of four marine mammals varying the degree of aquatic specialization and related terrestrial species in order to provide insights into the evolution of pheromonal olfaction in the mammalian transition from land to water. Our results based on sequence characterizations and evolutionary analyses, for the first time, show the evidence for the ancestral impairment of vomeronasal pheromone signal transduction pathway in fully aquatic cetaceans, supporting a reduced or absent dependence on olfaction as a result of the complete adaptation to the marine habitat, whereas the amphibious California sea lion was found to have a putatively functional TRPC2 gene, which is still under strong selective pressures, reflecting the reliance of terrestrial environment on chemical recognition among the semiadapted marine mammals. Interestingly, our study found that, unlike that of the California sea lion, TRPC2 genes of the harbor seal and the river otter, both of which are also semiaquatic, are pseudogenes. Our data suggest that other unknown selective pressures or sensory modalities might have promoted the independent absence of a functional VNS in these two species. In this respect, the evolution of pheromonal olfaction in marine mammals appears to be more complex and confusing than has been previously thought. Our study makes a useful contribution to the current understanding of the evolution of pheromone perception of mammals in response to selective pressures from an aquatic environment.

Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited: New Insights from Ten Additional Colobines

Pancreatic RNase genes implicated in the adaptation of the colobine monkeys to leaf eating have long intrigued evolutionary biologists since the identification of a duplicated RNASE1 gene with enhanced digestive efficiencies in Pygathrix nemaeus. The recent emergence of two contrasting hypotheses, that is, independent duplication and one-duplication event hypotheses, make it into focus again. Current understanding of Colobine RNASE1 gene evolution of colobine monkeys largely depends on the analyses of few colobine species. The present study with more intensive taxonomic and character sampling not only provides a clearer picture of Colobine RNASE1 gene evolution but also allows to have a more thorough understanding about the molecular basis underlying the adaptation of Colobinae to the unique leaf-feeding lifestyle. The present broader and detailed phylogenetic analyses yielded two important findings: 1) All trees based on the analyses of coding, noncoding, and both regions provided consistent evidence, indicating RNASE1 duplication occurred after Asian and African colobines speciation, that is, independent duplication hypothesis; 2) No obvious evidence of gene conversion in RNASE1 gene was found, favoring independent evolution of Colobine RNASE1 gene duplicates. The conclusion drawn from previous studies that gene conversion has played a significant role in the evolution of Colobine RNASE1 was not supported. Our selective constraint analyses also provided interesting insights, with significant evidence of positive selection detected on ancestor lineages leading to duplicated gene copies. The identification of a handful of new adaptive sites and amino acid changes that have not been characterized previously also provide a necessary foundation for further experimental investigations of RNASE1 functional evolution in Colobinae.