Isolation and characteristics of a yeast from preserved fish hydrolysate notably resistant to propionic acid

A fermentative film-forming yeast, designated PR1, notably resistant to propionic acid, was isolated from hydrolysed fish gurry that had been initially adjusted to a pH of 3.5 with phosphoric acid and preserved with 0.2% propionic acid. Growth on a variety of culture media yielded only budding cells. Bipolar budding with multiple buds at each pole was commonly encountered. Neither ascospores nor pseudomycelium were produced. Colonies on orange serum agar were 3–5 mm in diameter whereas, on tryptic soy agar containing 0.5% glucose, giant colonies were formed that filled most of the area of the plates within 48 h. Off-odours were not produced nor were disaccharides utilized. The isolate exhibited poor growth in 0.4% propionic acid at pH 4.0 and was completely inhibited by 0.5% propionic acid.     

Multiple forms of glucose–adenosine triphosphate phosphotransferase in rat mammary gland

Measurements have been made of the total hexokinase activity and of the relative amounts of types I and II hexokinase in rat mammary gland and at different stages of the lactation cycle. The total hexokinase activity increased during lactation, that of type II increasing to a greater extent than that of type I; the type II/type I activity ratio rose from a pregnancy value of about 1 to a mid-lactation value of 3, returning to 1 on involution. The changes in type II hexokinase activity during the lactation cycle parallel the changes in the insulin sensitivity of mammary-gland tissue. A study of the effect of alloxan-diabetes on mammary-gland hexokinase during the mid-lactation period revealed that, although the total glucose-phosphorylating capacity of the mammary gland was almost unchanged, the relative contributions of type I and type II hexokinases altered, decreasing the type II/type I activity ratio to about 1.     

Oral vaccination with salmonella simultaneously expressing Yersinia pestis F1 and V antigens protects against bubonic and pneumonic plague

The gut provides a large area for immunization enabling the development of mucosal and systemic Ab responses. To test whether the protective Ags to Yersinia pestis can be orally delivered, the Y. pestis caf1 operon, encoding the F1-Ag and virulence Ag (V-Ag) were cloned into attenuated Salmonella vaccine vectors. F1-Ag expression was controlled under a promoter from the caf1 operon; two different promoters (P), PtetA in pV3, PphoP in pV4, as well as a chimera of the two in pV55 were tested. F1-Ag was amply expressed; the chimera in the pV55 showed the best V-Ag expression. Oral immunization with Salmonella-F1 elicited elevated secretory (S)-IgA and serum IgG titers, and Salmonella-V-Ag(pV55) elicited much greater S-IgA and serum IgG Ab titers than Salmonella-V-Ag(pV3) or Salmonella-V-Ag(pV4). Hence, a new Salmonella vaccine, Salmonella-(F1+V)Ags, made with a single plasmid containing the caf1 operon and the chimeric promoter for V-Ag allowed the simultaneous expression of F1 capsule and V-Ag. Salmonella-(F1+V)Ags elicited elevated Ab titers similar to their monotypic derivatives. For bubonic plague, mice dosed with Salmonella-(F1+V)Ags and Salmonella-F1-Ag showed similar efficacy (>83% survival) against approximately 1000 LD(50) Y. pestis. For pneumonic plague, immunized mice required immunity to both F1- and V-Ags because the mice vaccinated with Salmonella-(F1+V)Ags protected against 100 LD(50) Y. pestis. These results show that a single Salmonella vaccine can deliver both F1- and V-Ags to effect both systemic and mucosal immune protection against Y. pestis.     

Modelling the probability distribution of the number of DNA double-strand breaks due to sporadic alkylation of nucleotide bases

Metabolites and certain chemical agents (for example methyl methanesulfonate) can induce nucleotide bases on chromosomal strands to become alkylated. These alkylated sites have the potential to become single-strand chromosomal breaks, a form of DNA damage, if they are exposed to a sufficient temperature in vitro. It has been proposed that a single-strand break (SSB) sufficiently close to another SSB on the opposite chromosomal strand will form a double-strand break (DSB). DNA repair mechanisms are less able to repair DSBs compared to SSBs. Because of the complex three-dimensional structure of DNA, some chromosomal regions are more susceptible to alkylation than others. A question of interest is therefore whether these alkylated bases are randomly distributed or tend to be clustered. Pulsed-field gel electrophoresis allows the number of DNA fragments (and hence the number of DSBs) to be observed directly. The randomness of alkylation events can therefore be tested using the standard statistical hypothesis-testing framework. Under the null hypothesis, that the SSBs are randomly distributed on each of the strands, we can calculate the probability of observing a number of DSBs at least as large as that observed and hence the associated p-value. Previously, the probability distribution of the number of DSBs has been determined by Monte Carlo simulations; when considering the whole genome this can be very time consuming. In this paper, we theoretically derive an approximation to the distribution enabling appropriate probabilities to be calculated quickly. Based on previous findings we assume that the number of breaks on each strand is small compared to the number of nucleotide bases. We show that our method can give the correct probability distribution when alkylation events are relatively rare, discuss how rare these events have to be and suggest potential extensions to the model when a greater proportion of bases are alkylated.     

Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context

Hybridization can profoundly affect the genomic composition and phenotypes of closely related species, and provides an opportunity to identify mechanisms that maintain reproductive isolation between species. Recent evidence suggests that hybridization outcomes within a species pair can vary across locations. However, we still do not know how variable outcomes of hybridization are across geographic replicates, and what mechanisms drive that variation. In this study, we described hybridization outcomes across 27 locations in the North Fork Shoshone River basin (Wyoming, USA) where native Yellowstone cutthroat trout and introduced rainbow trout co‐occur. We used genomic data and hierarchical Bayesian models to precisely identify ancestry of hybrid individuals. Hybridization outcomes varied across locations. In some locations, only rainbow trout and advanced backcrossed hybrids towards rainbow trout were present, while trout in other locations had a broader range of ancestry, including both parental species and first‐generation hybrids. Later‐generation intermediate hybrids were rare relative to backcrossed hybrids and rainbow trout individuals. Using an individual‐based simulation, we found that outcomes of hybridization in the North Fork Shoshone River basin deviate substantially from what we would expect under null expectations of random mating and no selection against hybrids. Since this deviation implies that some mechanisms of reproductive isolation function to maintain parental taxa and a diversity of hybrid types, we then modelled hybridization outcomes as a function of environmental variables and stocking history that are likely to affect prezygotic barriers to hybridization. Variables associated with history of fish stocking were the strongest predictors of hybridization outcomes, followed by environmental variables that might affect overlap in spawning time and location.     

Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium

Type 2 diabetes (T2D) is a common, polygenic chronic disease with high heritability. The purpose of this whole-genome association study was to discover novel T2D-associated genes. We genotyped 500 familial cases and 497 controls with >300,000 HapMap-derived tagging single-nucleotide-polymorphism (SNP) markers. When a stringent statistical correction for multiple testing was used, the only significant SNP was at TCF7L2, which has already been discovered and confirmed as a T2D-susceptibility gene. For a replication study, we selected 10 SNPs in six chromosomal regions with the strongest association (singly or as part of a haplotype) for retesting in an independent case-control set including 2,573 T2D cases and 2,776 controls. The most significant replicated result was found at the AHI1-LOC441171 gene region.     

Hitchhiking the high seas: Global genomics of rafting crabs

Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next‐generation sequencing of genomewide restriction‐site‐associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species‐level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low—likely three closely related species—with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F_ST = 0.08–0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic‐level resolution for estimating contemporary population structure in organisms with large, highly connected populations.