Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus

Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co‐inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within‐lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others.     

Genetic evidence for prevalence of alloparental care in a socially monogamous biparental cichlid fish,Perissodus microlepis,from Lake Tanganyika supports the “selfish shepherd effect” hypothesis

Alloparental care – care for unrelated young – is rare in animals, and its ecological or evolutionary advantages or, alternative maladaptive nature, remain unclear. We investigate alloparental care in the socially monogamous cichlid fish Perissodus microlepis from Lake Tanganyika that exhibits bi‐parental care. In a genetic parentage analysis, we discovered a surprisingly high percentage of alloparental care represented by brood mixing, extra‐pair paternity and extra‐pair maternity in all broods that we investigated. The percentage of nondescendant juveniles of other parents, i.e., brood mixing, ranged from 5% to 57% (mean = 28%). The distribution of genetic parentage also suggests that this socially monogamous species has, in fact, polygamous mating system. The prevalence of genetically mixed broods can be best explained by two, not mutually exclusive hypotheses on farming‐out and fostering behaviors. In the majority of broods, the sizes of the parents’ own (descendant) offspring were significantly larger than those of the adopted (nondescendant) juveniles, supporting the ‘selfish shepherd effect’ hypothesis, i.e., that foster parents preferentially accept unrelated “smaller or not larger” young since this would tend to lower the predation risks for their own larger offspring. There was also a tendency for larger parents particularly mothers, more so than smaller parents, to care predominantly for their own offspring. Larger parents might be better at defending against cuckoldry and having foreign young dumped into their broods through farming‐out behavior. This result might argue for maladaptive effects of allopatric care for the foster parents that only larger and possibly more experienced pairs can guard against. It needs to be determined why, apparently, the ability to recognize one's own young has not evolved in this species.     

Metabolic Tumour Burden Measured by 18F-FDG PET/CT Predicts Malignant Transformation in Patients with Neurofibromatosis Type-1

Background

To investigate the diagnostic and prognostic performances of ¹⁸F-FDG PET/CT measures of metabolic tumour burden in patients with neurofibromatosis type-1 (NF1), suspect of malignant transformation.

Methods

This retrospective study included 49 patients (15–60 years old, 30 women) with a diagnosis of NF1, followed in our Reference Centre for Rare Neuromuscular Diseases, who presented clinical signs of tumour progression (pain, neurological deficit, tumour growth). Quantitative metabolic parameters were measured on 149 tumoral targets, using semi-automatic software and the best cut off values to predict transformation was assessed by Receiver Operating Characteristics (ROC) analysis. Prognostic value of PET/CT metabolic parameters was assessed by Kaplan-Meier estimates of overall survival.

Results

Lesions were histologically documented in 40 patients: a sarcomatous transformation was found in 16, a dysplastic neurofibroma (NF) in 7, and a benign NF in 17; in the remaining 9 patients, a minimal follow-up of 12 mo (median 59 mo) confirmed the absence of transformation. The optimal cut off values for detection of malignant transformation were, in decreasing order of area under the ROC curves, a tumour-to-liver (T/L) ratio >2.5, SUV_max > 4.5, total lesion glycolysis (TLG) > 377, total metabolic tumour volume (TMTV) > 88 cm³, and heterogeneity index (HI_suv) > 1.69. The best prognostic marker was the TLG: the 4-y estimates of survival were 97% [95% CI, 90% - 100%] in patients with TLG ≤ 377 vs. 27% [95% CI, 5% - 49%] in patients with TLG > 377 (P < 0.0001; χ² 27.85; hazard ratio 13.27 [95% CI, 3.72–47.35]). T/L ratio, SUV_max and TMTV demonstrated slightly lower performance to predict survival, with χ² ranging 14.41–19.12. The HI_suv index was not predictive of survival.

Conclusion

Our study demonstrates that TLG and TMTV, as PET/CT measures of metabolic tumour burden, may be used clinically to identify sarcomatous transformation in patients with NF1 and predict overall survival, with a higher specificity for the TLG. Conventional measures such as the SUV_max, and T/L ratio also demonstrate high prognostic value.     

In-Situ Observation of Membrane Protein Folding during Cell-Free Expression

Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando) at molecular resolution.     

Efficacy,Safety and Cost of Insecticide Treated Wall Lining,Insecticide Treated Bed Nets and Indoor Wall Wash with Lime for Visceral Leishmaniasis Vector Control in the Indian Sub-continent: A Multi-country Cluster Randomized Controlled Trial

BackgroundWe investigated the efficacy, safety and cost of lime wash of household walls plus treatment of sand fly breeding places with bleach (i.e. environmental management or EM), insecticide impregnated durable wall lining (DWL), and bed net impregnation with slow release insecticide (ITN) for sand fly control in the Indian sub-continent.MethodsThis multi-country cluster randomized controlled trial had 24 clusters in each three sites with eight clusters per high, medium or low sand fly density stratum. Every cluster included 45–50 households. Five households from each cluster were randomly selected for entomological measurements including sand fly density and mortality at one, three, nine and twelve months post intervention. Household interviews were conducted for socioeconomic information and intervention acceptability assessment. Cost for each intervention was calculated. There was a control group without intervention.FindingsSand fly mortality [mean and 95%CI] ranged from 84% (81%-87%) at one month to 74% (71%-78%) at 12 months for DWL, 75% (71%-79%) at one month to 49% (43%-55%) at twelve months for ITN, and 44% (34%-53%) at one month to 22% (14%-29%) at twelve months for EM. Adjusted intervention effect on sand fly density measured by incidence rate ratio ranged from 0.28 (0.23–0.34) at one month to 0.62 (0.51–0.75) at 12 months for DWL; 0.72 (0.62–0.85) at one month to 1.02 (0.86–1.22) at 12 months for ITN; and 0.89 (0.76–1.03) at one months to 1.49 (1.26–1.74) at 12 months for EM. Household acceptance of EM was 74% compared to 94% for both DWL and ITN. Operational cost per household in USD was about 5, 8, and 2 for EM, DWL and ITN, respectively. Minimal adverse reactions were reported for EM and ITN while 36% of households with DWL reported transient itching.InterpretationDWL is the most effective, durable and acceptable control method followed by ITN. The Visceral Leishmaniasis (VL) Elimination Program in the Indian sub-continent should consider DWL and ITN for sand fly control in addition to IRS.     

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

Hierarchical shotgun sequencing remains the method of choice for assembling high‐quality reference sequences of complex plant genomes. The efficient exploitation of current high‐throughput technologies and powerful computational facilities for large‐insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole‐genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high‐quality assemblies of a large number of clones to assemble map‐based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.     

Blimp-1-Dependent IL-10 Production by Tr1 Cells Regulates TNF-Mediated Tissue Pathology

Tumor necrosis factor (TNF) is critical for controlling many intracellular infections, but can also contribute to inflammation. It can promote the destruction of important cell populations and trigger dramatic tissue remodeling following establishment of chronic disease. Therefore, a better understanding of TNF regulation is needed to allow pathogen control without causing or exacerbating disease. IL-10 is an important regulatory cytokine with broad activities, including the suppression of inflammation. IL-10 is produced by different immune cells; however, its regulation and function appears to be cell-specific and context-dependent. Recently, IL-10 produced by Th1 (Tr1) cells was shown to protect host tissues from inflammation induced following infection. Here, we identify a novel pathway of TNF regulation by IL-10 from Tr1 cells during parasitic infection. We report elevated Blimp-1 mRNA levels in CD4⁺ T cells from visceral leishmaniasis (VL) patients, and demonstrate IL-12 was essential for Blimp-1 expression and Tr1 cell development in experimental VL. Critically, we show Blimp-1-dependent IL-10 production by Tr1 cells prevents tissue damage caused by IFNγ-dependent TNF production. Therefore, we identify Blimp-1-dependent IL-10 produced by Tr1 cells as a key regulator of TNF-mediated pathology and identify Tr1 cells as potential therapeutic tools to control inflammation.