Construction of Saccharomyces cerevisiae strains that accumulate relatively low concentrations of trehalose, and their application in testing the contribution of the disaccharide to stress tolerance

Genetically related diploid strains of Saccharomyces cerevisiae that accumulate varied amounts of trehalose during starvation for nitrogen have been constructed. Strains that produced greater than 5% trehalose (dry cell weight) were more tolerant of thermal, or freeze-thaw stresses than strains that produced less than 4% trehalose. Thus trehalose appears to play a role in stress tolerance of yeast. The significance of these results is that, for the first time, a series of related, unmutated strains have been used to test the effect of trehalose on thermotolerance. Previous studies employed either heat shock treatment, or mutated strains to provide trehalose variations, and as such the contribution of the disaccharide to stress tolerance could not necessarily be separated from other factors such as heat shock proteins.     

Genetic differentiation of populations of the copepod sea louse Lepeophtheirus salmonis (Krøyer) ectoparasitic on wild and farmed salmonids around the coasts of Scotland: Evidence from RAPD markers

Sea trout are the sea-going migratory form of the freshwater brown trout (Salmo trutta L.) and since 1989 there have been marked declines in their stocks on the west coasts both of Scotland and Ireland. Various factors have been attributed as possible causal agents in these stock declines, including fresh water acidification, overfishing, climatic fluctuations, habitat degradation and sea lice parasitic burdens. The putative impact of infestations of sea trout by the ectoparasitic copepod sea louse, Lepeophtheirus salmonis (Krøyer), has featured prominently in the controversy, especially with regard to the role of inshore commercial salmon farms as a possible source of infestation of wild salmonids by sea lice. This study focused on the population genetics of L. salmonis around the coasts of Scotland: We sampled fish from wild and cultured stocks and included salmon (Salmo salar L.), rainbow trout (Oncorhynchus mykiss Walbaum) and sea trout as host species. Analyses of allozyme variation of sea lice were confined to data for two polymorphic loci (Fum, Got-2) and conformed to our initial expectation — that the inclusion of a planktonic larval phase in the life cycle of the copepod, in addition to the high mobility of the host fish, would enhance gene flow and preclude genetic differentiation of L. salmonis populations as a result of random drift alone. DNA polymorphism was quantified by means of PCR and RAPD analysis. Six primers were screened for 16 samples (from wild and farmed salmon, wild sea trout and farmed rainbow trout) — including the east, north and west coasts of Scotland — and the data analyzed by AMOVA (Analysis of Molecular Variance). In contrast to the allozyme results, the RAPD analysis showed striking patterns of genetic differentiation around the coasts of Scotland. The overall pattern was one of genetic homogeneity of L. salmonis populations sampled from wild salmon and sea trout. All of the L. salmonis samples taken from farmed salmon and rainbow trout did, however, show highly significant levels of genetic differentiation, both between wild and farmed salmonids and among the various farms themselves. Evidence of high levels of small-scale spatial or temporal heterogeneity of RAPD marker band frequencies was shown for the one farm from which repeat samples (July and November, 1995) were analysed. Samples of sea lice taken from west coast wild sea trout subjected to RAPD analysis also revealed the occurrence of putative “farm markers” in some individual parasites, indicating that they had possibly originated from salmon farms.     

A cell‐based model system links chromothripsis with hyperploidy

A remarkable observation emerging from recent cancer genome analyses is the identification of chromothripsis as a one‐off genomic catastrophe, resulting in massive somatic DNA structural rearrangements (SRs). Largely due to lack of suitable model systems, the mechanistic basis of chromothripsis has remained elusive. We developed an integrative method termed “complex alterations after selection and transformation (CAST),” enabling efficient in vitro generation of complex DNA rearrangements including chromothripsis, using cell perturbations coupled with a strong selection barrier followed by massively parallel sequencing. We employed this methodology to characterize catastrophic SR formation processes, their temporal sequence, and their impact on gene expression and cell division. Our in vitro system uncovered a propensity of chromothripsis to occur in cells with damaged telomeres, and in particular in hyperploid cells. Analysis of primary medulloblastoma cancer genomes verified the link between hyperploidy and chromothripsis in vivo. CAST provides the foundation for mechanistic dissection of complex DNA rearrangement processes.     

Infestations of wild adult Atlantic salmon (Salmo salar L.) by the ectoparasitic copepod sea louse Lepeophtheirus salmonis Krøyer: prevalence,intensity and the spatial distribution of males and [2pt] females on the host fish

The copepod Lepeophtheirus salmonis Krøyer is a specific ectoparasite of North Atlantic and Pacific salmonids in their marine phases. We compared infestations of L. salmonis on wild Atlantic salmon (Salmo salarL.) captured in estuarine (Firth of Tay, east Scotland; 1995, 1996) and marine coastal waters (Strathy Point, north Scotland; 1998, 1999). Host fish from the Tay were caught by sweep netting, whilst those from Strathy Point were trapped in anchored bagnets. Fish capture method and exposure of the parasites to brackish conditions may both have detrimental effects on the retention of L. salmonis by the host, and hence possibly lead to their being under-estimated on returning adult fish. At Strathy Point, we recorded (i) an infestation prevalence of 100%, (ii) mean log abundances of pre-adult + adult L. salmonis at 19 (1998) and 24 (1999) per fish, (iii) 85/93% of all L. salmonis as being adults and (iv) overall 68/69% females. Fish caught in the upper Firth of Tay showed significantly lower prevalences, intensities and abundances of L. salmonis and probably had lost part or all of their lice burdens prior to capture, whereas those sampled from Strathy Point were apparently minimally affected by capture method or brackish water influences. The loss of parasites for the Tay fish was not markedly biased to males or females, or to pre-adult versus adult developmental stages. There were significantly greater abundances of L. salmonis on two sea-winter fish (30 lice per fish) than on one sea-winter fish (17 lice per fish) sampled at Strathy Point in 1998. There are several possible explanations for such age-related patterns of abundance, but the indications are that (i) initial infestation of smolts occurs in coastal waters, (ii) infestation of hosts in the open ocean is a persistent event, and (iii) oceanic reinfestation outweighs mortality losses of L. salmonis. This parasite typically occupies rather few zones on the host fish covering only a small percentage of the total available body surface area. Female predominance appears to be characteristic of L. salmonisinfestations of wild Atlantic salmon; this is in marked contrast to reports of extreme male dominance on farmed stocks. Adult females predominated on the epidermis adjacent to, and posterior of, the insertion of the anal fin and along the posterior dorsal midline between the dorsal and caudal fins. Males predominated on the sides of the head and along the dorsal midline between the head and the dorsal fin. Mate guarding/precopulatory pairs are formed between pre-adult II females and adult males. The significant correlation between the distribution of pre-adult females and adult males may be indicative of pre-adult females actively seeking out adult males, but more likely is due to the (large) adult females competitively ousting all smaller life stages (female and male) from those preferred zones. Given the relatively low fecundity of adult females, and observations of 100% prevalence of L. salmonis, the infective planktonic copepodid stage evidently is extremely efficient at locating and establishing upon its host fish in the pelagic environment.     

Clinical associations of serum interleukin-17 in systemic lupus erythematosus

Introduction

Serum interleukin (IL)-17 concentrations have been reported to be increased in systemic lupus erythematosus (SLE), but associations with clinical characteristics are not well understood. We characterized clinical associations of serum IL-17 in SLE.

Methods

We quantified IL-17 in serum samples from 98 SLE patients studied cross-sectionally, and in 246 samples from 75 of these patients followed longitudinally over two years. Disease activity was recorded using the SLE Disease Activity Index (SLEDAI)-2k. Serum IL-6, migration inhibitory factor (MIF), and B cell activating factor of the tumour necrosis factor family (BAFF) were also measured in these samples.

Results

Serum IL-17 levels were significantly higher in SLE patients compared to healthy donors (P <0.0001). No correlation was observed between serum IL-17 and SLEDAI-2k, at baseline or during longitudinal follow-up. However, we observed that SLEDAI-2k was positively correlated with IL-17/IL-6 ratio. Serum IL-17 was significantly increased in SLE patients with central nervous system (CNS) disease (P = 0.0298). A strong correlation was observed between serum IL-17 and IL-6 (r = 0.62, P <0.0001), and this relationship was observed regardless of disease activity and persisted when integrating cytokine levels over the period observed (r = 0.66, P <0.0001). A strong correlation of serum IL-17 was also observed with serum BAFF (r = 0.64, P <0.0001), and MIF (r = 0.36, P = 0.0016).

Conclusions

Serum IL-17 concentration correlates poorly with SLE disease activity but is significantly elevated in patients with CNS disease. IL-17/IL-6 ratio may be more useful than IL-17 or IL-6 alone to characterize Th17-driven disease, such as SLE. The association of other cytokines with serum IL-17 suggests that IL-17 may drive activation of diverse immune pathways in SLE.     

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

The emergence of high-throughput, next-generation sequencing technologies has dramatically altered the way we assess genomes in population genetics and in cancer genomics. Currently, there are four commonly used whole-genome sequencing platforms on the market: Illumina’s HiSeq2000, Life Technologies’ SOLiD 4 and its completely redesigned 5500xl SOLiD, and Complete Genomics’ technology. A number of earlier studies have compared a subset of those sequencing platforms or compared those platforms with Sanger sequencing, which is prohibitively expensive for whole genome studies. Here we present a detailed comparison of the performance of all currently available whole genome sequencing platforms, especially regarding their ability to call SNVs and to evenly cover the genome and specific genomic regions. Unlike earlier studies, we base our comparison on four different samples, allowing us to assess the between-sample variation of the platforms. We find a pronounced GC bias in GC-rich regions for Life Technologies’ platforms, with Complete Genomics performing best here, while we see the least bias in GC-poor regions for HiSeq2000 and 5500xl. HiSeq2000 gives the most uniform coverage and displays the least sample-to-sample variation. In contrast, Complete Genomics exhibits by far the smallest fraction of bases not covered, while the SOLiD platforms reveal remarkable shortcomings, especially in covering CpG islands. When comparing the performance of the four platforms for calling SNPs, HiSeq2000 and Complete Genomics achieve the highest sensitivity, while the SOLiD platforms show the lowest false positive rate. Finally, we find that integrating sequencing data from different platforms offers the potential to combine the strengths of different technologies. In summary, our results detail the strengths and weaknesses of all four whole-genome sequencing platforms. It indicates application areas that call for a specific sequencing platform and disallow other platforms. This helps to identify the proper sequencing platform for whole genome studies with different application scopes.     

Competition in the presence of a virus in an aquatic system: an SIS model in the chemostat

Recent research indicates that viruses are much more prevalent in aquatic environments than previously imagined. We derive a model of competition between two populations of bacteria for a single limiting nutrient in a chemostat where a virus is present. It is assumed that the virus can only infect one of the populations, the population that would be a more efficient consumer of the resource in a virus free environment, in order to determine whether introduction of a virus can result in coexistence of the competing populations. We also analyze the subsystem that results when the resistant competitor is absent. The model takes the form of an SIS epidemic model. Criteria for the global stability of the disease free and endemic steady states are obtained for both the subsystem as well as for the full competition model. However, for certain parameter ranges, bi-stability, and/or multiple periodic orbits is possible and both disease induced oscillations and competition induced oscillations are possible. It is proved that persistence of the vulnerable and resistant populations can occur, but only when the disease is endemic in the population. It is also shown that it is possible to have multiple attracting endemic steady states, oscillatory behavior involving Hopf, saddle-node, and homoclinic bifurcations, and a hysteresis effect. An explicit expression for the basic reproduction number for the epidemic is given in terms of biologically meaningful parameters. Mathematical tools that are used include Lyapunov functions, persistence theory, and bifurcation analysis.     

A laboratory investigation of the filtration and ingestion rates of the tilapia,Oreochromis niloticus,feeding on two species of blue-green algae

Synopsis Quantitative aspects of the filter-feeding of the tilapia,Oreochromis niloticus, on two species of the blue-green algae —Anabaena cylindrica andMicrocystis aeruginosa — were investigated in the laboratory. The ingestion rate of 85 mm SLO. niloticus was best fitted using a linear regression over the range of biovolume concentrations studied (3 × 10⁶ – 3 × 10⁸ m³ ml^–1). The ingestion rate of 40 mm SL fish gave a curvilinear relationship and was best fitted using a logarithmic regression. For each size class of fish, ingestion rates were higher when fed the largerAnabaena thanMicrocystis. The results of ingestion and filtration rates are comparable to work on other aquatic suspension feeders and tend to substantiate a universality in the fundamental regulatory mechanism of filter feeding.     

Nexilin,a Cardiomyopathy-Associated F-Actin Binding Protein,Binds and Regulates IRS1 Signaling in Skeletal Muscle Cells

Insulin stimulates glucose uptake through a highly organized and complex process that involves movement of the glucose transporter 4 (GLUT4) from intracellular storage sites to the plasma membrane. Previous studies in L6 skeletal muscle cells have shown that insulin-induced activation and assembly of insulin receptor substrate 1 (IRS1) and p85α the regulatory subunit of the Type 1A phosphatidylinositol-3-kinase (PI3K), within remodeled actin-rich membrane structures is critical for downstream signalling mediating the translocation of GLUT4. The mechanism for localization within actin cytoskeletal scaffolds is not known, as direct interaction of IRS1 or p85α with F-actin has not been demonstrated. Here we show that nexilin, a F-actin binding protein implicated in the pathogenesis of familial dilated cardiomyopathies, preferentially binds to IRS1 over IRS2 to influence glucose transport in skeletal muscle cells. Nexilin stably associates with IRS1 under basal conditions in L6 myotubes and this complex is disassembled by insulin. Exposure of L6 myotubes to Latrunculin B disrupts the spatial patterning of nexilin and its transient association with IRS1. Functional silencing of nexilin has no effect on insulin-stimulated IRS1 tyrosine phosphorylation, however it enhances recruitment of p85α to IRS1 resulting in increased PI-3, 4, 5-P₃ formation, coincident with enhanced AKT activation and glucose uptake. By contrast, overexpression of nexilin inhibits transmission of IRS1 signals to AKT. Based on these findings we propose that nexilin may tether IRS1 to actin-rich structures under basal conditions, confining IRS1 signaling to specific subcellular locations in the cell. Insulin-elicited release of this constraint may enhance the efficiency of IRS1/PI3K interaction and PI-3, 4, 5-P₃ production at localized sites. Moreover, the selective binding of nexilin to IRS1 and not IRS2 may contribute to the differential specificity of IRS isoforms in the modulation of GLUT4 trafficking in skeletal muscle cells.