Selection for resistance to a fungal pathogen in Drosophila melanogaster

An artificial selection experiment designed to explore the evolution of resistance to a fungal pathogen, Beauveria bassiana, in Drosophila melanogaster is reported here. The experiment was designed to test whether there is sufficient additive genetic variation in this trait for increased resistance to evolve, and, if so, whether there are correlated responses that might represent a cost to defence. After 15 generations of selection, flies from selected lines did not have higher overall fitness after infection compared with control lines. The response to selection for resistance against this pathogen is thus much weaker than against other species, in particular, parasitoids. There was, however, evidence for increased late-life fecundity in selected lines, which may indicate evolved tolerance of fungal infection. This increase was accompanied by reduced early-life fitness, which may reflect the well-known trade-off between early and late reproduction. In the absence of fungal infection, selected flies had lower fitness than control flies, and the possibility that this is also a trade-off with increased tolerance is explored.     

EFFECTS OF PARTHENOGENESIS AND GEOGRAPHIC ISOLATION ON FEMALE SEXUAL TRAITS IN A PARASITOID WASP

Population divergence in sexual traits is affected by different selection pressures, depending on the mode of reproduction. In allopatric sexual populations, aspects of sexual behavior may diverge due to sexual selection. In parthenogenetic populations, loss‐of‐function mutations in genes involved in sexual functionality may be selectively neutral or favored by selection. We assess to what extent these processes have contributed to divergence in female sexual traits in the parasitoid wasp Leptopilina clavipes in which some populations are infected with parthenogenesis‐inducing Wolbachia bacteria. We find evidence consistent with both hypotheses. Both arrhenotokous males and males derived from thelytokous strains preferred to court females from their own population. This suggests that these populations had already evolved population‐specific mating preferences when the latter became parthenogenetic. Thelytokous females did not store sperm efficiently and fertilized very few of their eggs. The nonfertility of thelytokous females was due to mutations in the wasp genome, which must be an effect of mutation accumulation under thelytoky. Divergence in female sexual traits of these two allopatric populations has thus been molded by different forces: independent male/female coevolution while both populations were still sexual, followed by female‐only evolution after one population switched to parthenogenesis.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Mechanisms of monoclonal antibody-mediated protection against virulent Semliki Forest virus.

Both neutralizing and nonneutralizing immunoglobulin G2a monoclonal antibodies (MAs) directed against the E2 glycoprotein of Semliki Forest virus (SFV) protected mice prophylactically and therapeutically against virulent SFV infection. The neutralizing MAs, however, conferred protection to mice at lower doses than did nonneutralizing MAs. The antibody-dependent, complement-mediated cytolysis of SFV-infected L cells was effectuated by both kinds of antibodies, but again neutralizing MAs were more effective. Removal of the Fc part of the neutralizing MA UM 5.1 by pepsin digestion resulted in a 100-fold reduction of the neutralization titer (10(4) versus 10(6)) and a complete loss of its capacity to mediate antibody-dependent, complement-mediated cytolysis. Passive protection of infected mice occurred only after administration of relatively high doses of F(ab')2 of MA UM 5.1 (30.0 micrograms versus 0.1 microgram). F(ab')2 fragments prepared from the nonneutralizing MA UM 4.2 had lost their protective capacity completely. Surprisingly, the nonneutralizing MA UM 4.2 retarded virus growth in mouse fibroblasts (L cells), although inhibition was at much higher doses than with the neutralizing MA UM 5.1. Furthermore, both MAs promoted the uptake of virulent SFV in the Fc receptor-bearing WEHI-3 cells. The results suggest that nonneutralizing MAs protect mice not only by antibody-dependent, complement-mediated cytolysis but also by growth inhibition and enhanced uptake of SFV in the nonpermissive macrophages of BALB/c mice. This hypothesis is supported by the absence of viremia in recipients of nonneutralizing MA UM 4.2 at 24 h after infection.     

Variation in diapause and sex ratio in the parasitoidAsobara tabida

Asobara tabida Nees (Hymenoptera: Braconidae) is a widespread parasitoid, attacking larvae ofDrosophila (Diptera: Drosophilidae) species in fermenting substrates. In this species, geographic variation is found in the percentage of parasitoids entering diapause and in the sex ratio of emerging parasitoids. Percentage diapause appears to be influenced by host species (more parasitoids enter diapause inD. melanogaster Meigen than inD. subobscura Collin) and temperature. It is not correlated with any of the abiotic factors investigated, but is correlated with survival probability inD. melanogaster larvae and with the time of year in which the experiment was conducted (even though none of the parasitoids experienced natural day light). Sex ratio was only found to correlate with percentage diapause, suggesting that males enter diapause more frequently than females. It is concluded thatA. tabida uses diapause to survive both unfavourable abiotic and biotic circumstances.     

A histological and immunohistochemical study of the effects of N-acetyl cysteine on retinopathy of prematurity by modifying insulin-like growth factor-1

Retinopathy of prematurity (ROP) is a vasoproliferative disorder that occurs in premature infants and may lead to permanent visual impairment. We investigated both the possible protective role of N-acetyl cysteine (NAC) for preventing ROP and the role of IGF-1 in the disorder. Forty-five newborn rats were divided into three groups. Group 1 was raised in room air as controls. Group 2 was exposed to 60% oxygen for 14 days after birth, then transferred to room air. Group 3 was exposed to the same conditions as group 2, but received intraperitoneal injections of NAC on postnatal days 7–17. After 35 days, both eyes of all rats were processed for histology. Some sections were stained with hematoxylin and eosin to assess structural changes and other sections were immunostained to determine the location of IGF-1. Frozen sections also were prepared and stained for adenosine triphosphatase to detect retinal blood vessels. Compared to the controls, more blood vessels, many of which were abnormal, and increased IGF-1 expression were observed in group 2. In group 3, abnormal blood vessels and IGF-1 expression were less evident. NAC appeared to be an effective vascular-protective agent for ROP by decreasing IGF-1 expression.     

Chemokines CCL3/MIP1α, CCL5/RANTES and CCL18/PARC are Independent Risk Predictors of Short-Term Mortality in Patients with Acute Coronary Syndromes

Cytokines play an important role in ischemic injury and repair. However, little is known about their prognostic value in cardiovascular disease. The aim of this study was to investigate the prognostic importance of chemokines CCL3/MIP-1α, CCL5/RANTES and CCL18/PARC for the risk of future cardiovascular events in patients with acute coronary syndromes (ACS). Baseline levels of CCL3/MIP-1α, CCL5/RANTES and CCL18/PARC were determined in ACS patients from the Bad Nauheim ACS II registry (n = 609). During the following 200 days, patients were monitored for the occurrence of fatal and non-fatal cardiovascular events. Patients with CCL3/MIP1α, CCL5/RANTES and CCL18/PARC concentrations in the highest tertile were associated with an increased risk of a fatal event during follow-up (HR: 2.19, 95%CI: 1.04–4.61 for CCL3/MIP1α, HR: 3.45, 95%CI: 1.54–7.72 for CCL5/RANTES and HR: 3.14, 95%CI: 1.33–7.46 for CCL18/PARC). This risk was highest for patients with all three biomarkers concentrations in the upper tertile (HR: 2.52, 95%CI: 1.11–5.65). Together with known risk predictors of cardiovascular events, CCL3/MIP-1α, CCL5/RANTES and CCL18/PARC combined improved the c-statistics from 0.74 to 0.81 (p = 0.007). In conclusion, CCL3/MIP-1α, CCL5/RANTES and CCL18/PARC are independently associated with the risk of short-term mortality in ACS patients. Combining all three biomarkers further increased their prognostic value.     

Conserved sequences in enzymes of the UDP-GlcNAc/MurNAc family are essential in hamster UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase

The UDP-GlcNAc/MurNAc family of eukaryotic and prokaryotic enzymes use UDP-GlcNAc or UDP-MurNAc-pentapeptide as donors, dolichol-P or polyprenol-P as acceptors, and generate sugar-P-P-polyisoprenols. A series of six conserved sequences, designated A through F and ranging from 5 to 13 amino acid residues, has been identified in this family. To determine whether these conserved sequences are required for enzyme function, various mutations were examined in hamster UDP- GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT). Scramble mutations of sequences B-F, generated by scrambling the residues within each sequence, demonstrated that each is important in GPT. While E and F scrambles appeared to prevent stable expression of GPT, scrambling of B- D resulted in GPT mutants that could be stably expressed and bound tunicamycin, but lacked enzymatic activity. Further, the C and D scramble mutants had an unexpected sorting defect. Replacement of sequences B-F with prokaryotic counterparts from either the B.subtilis mraY or E.coli rfe genes also affected GPT by preventing expression of the mutant protein (B, F) or inhibiting its enzymatic activity (C-E). For the C-E replacements, no acquisition of acceptor activity for polyprenol-P, the fully unsaturated natural bacterial acceptor, was detected. These studies show that the conserved sequences of the UDP- GlcNAc/MurNAc family are important, and that the eukaryotic and prokaryotic counterparts are not freely interchangeable. Since several mutants were efficiently expressed and bound tunicamycin, yet lacked enzymatic activity, the data are consistent with these sequences having a direct role in product formation.      

Quantification of angiogenesis in estrogen receptor-positive and negative breast carcinoma

Background

The objective of this study was to evaluate angiogenesis according to CD34 antigen expression in estrogen receptor (ER)-positive and negative breast carcinomas.

Methods

This study comprised 64 cases of infiltrating ductal carcinoma in postmenopausal women divided into two groups: Group A: ER-positive, n = 35; and Group B: ER-negative, n = 29. The anti-CD34 monoclonal antibody was used as a marker for endothelial cells. Microvessel count was carried out in 10 fields per slide using a 40× objective lens (magnification 400×). Statistical analysis of the data was performed using Student's t-test (p < 0.05).

Results

The mean number of vessels stained with the anti-CD34 antibody in the estrogen receptor-positive and negative tumors was 23.51 ± 1.15 and 40.24 ± 0.42, respectively. The number of microvessels was significantly greater in the estrogen receptor-negative tumors (p < 0.001).

Conclusion

ER-negative tumors have significantly greater CD34 antigen expression compared to ER-positive tumors.

     

Can Simpson's paradox explain co-operation in Pseudomonas aeruginosa biofilms?

Co-operative behaviours, such as the production of public goods, are commonly displayed by bacteria in biofilms and can enhance their ability to survive in environmental or clinical settings. Non-co-operative cheats commonly arise and should, theoretically, disrupt co-operative behaviour. Its stability therefore requires explanation, but no mechanisms to suppress cheating within biofilms have yet been demonstrated experimentally. Theoretically, repeated aggregation into groups, interleaved with dispersal and remixing, can increase co-operation via a 'Simpson's paradox'. That is, an increase in the global proportion of co-operators despite a decrease in within-group proportions, via differential growth of groups. We investigate the hypothesis that microcolony formation and dispersal produces a Simpson's paradox that explains bacterial co-operation in biofilms. Using the production of siderophores in Pseudomonas aeruginosa as our model system for co-operation, we use well-documented co-operator and siderophore-deficient cheat strains to measure the frequency of co-operating and cheating individuals, in-situ within-microcolony structures. We detected significant within-type negative density-dependant effects that vary over microcolony development. However, we find no evidence of Simpson's paradox. Instead, we see clear within-microcolony spatial structure (cheats occupying the interior portions of microcolonies) that may violate the assumption required for Simpson's paradox that group members share equally in the public good.