Divergence across diet,time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.     

Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum

Background

The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in high-throughput chemical screening campaigns against Plasmodium falciparum.

Results

Here we show that tiling microarrays can detect de novo a large proportion of the genetic changes that differentiate one genome from another. We show that we detect most single nucleotide polymorphisms or small insertion deletion events and all known copy number variations that distinguish three laboratory isolates using readily accessible methods. We used the approach to discover mutations that occur during the selection process after transfection. We also elucidated a mechanism by which parasites acquire resistance to the antimalarial fosmidomycin, which targets the parasite isoprenoid synthesis pathway. Our microarray-based approach allowed us to attribute in vitro derived fosmidomycin resistance to a copy number variation event in the pfdxr gene, which enables the parasite to overcome fosmidomycin-mediated inhibition of isoprenoid biosynthesis.

Conclusions

We show that newly emerged single nucleotide polymorphisms can readily be detected and that malaria parasites can rapidly acquire gene amplifications in response to in vitro drug pressure. The ability to define comprehensively genetic variability in P. falciparum with a single overnight hybridization creates new opportunities to study parasite evolution and improve the treatment and control of malaria.     

Effects of light on cyanide‐resistant respiration and alternative oxidase function in Arabidopsis seedlings

Mitochondrial alternative oxidase (AOX), the unique respiratory terminal oxidase in plants, catalyzes the energy wasteful cyanide (CN)‐resistant respiration and plays a role in optimizing photosynthesis. Although it has been demonstrated that leaf AOX is upregulated after illumination, the in vivo mechanism of AOX upregulation by light and its physiological significance are still unknown. In this report, red light and blue light‐induced AOX (especially AOX1a) expressions were characterized. Phytochromes, phototropins and cryptochromes, all these photoreceptors mediate the light‐response of AOX1a gene. When aox1a mutant seedlings were grown under a high‐light (HL) condition, photobleaching was more evident in the mutant than the wild‐type plants. More reactive oxygen species (ROS) accumulation and inefficient dissipation of chloroplast reducing‐equivalents in aox1a mutant may account for its worse adaptation to HL stress. When etiolated seedlings were exposed to illumination for 4 h, chlorophyll accumulation was largely delayed in aox1a plants. We first suggest that more reduction of the photosynthetic electron transport chain and more accumulation of reducing‐equivalents in the mutant during de‐etiolation might be the main reasons.     

Preparative resolution of 1-aminoindan-1,5-dicarboxylic acid (AIDA) by chiral ligand-exchange chromatography

Chiral ligand-exchange chromatography has been shown to be effective in the resolution and semipreparative separation of 1-aminoindan-1,5-dicarboxylic acid (AIDA) enantiomers. In functional activity experiments, only (S)-AIDA was a potent and mGluR1 subtype selective antagonist.     

Investigation of the electronic term scheme of deoxygenated human haemoglobin by a least squares fit procedure using simultaneously magnetic susceptibility and M?ssbauer data.

The calculation of the magnetic susceptibility from a published term scheme for the ferrous iron in deoxygenated human haemoglobin is discussed and a procedure for the simultaneous least squares fit of susceptibility and M?ssbauer data is presented. The application of this procedure to the appropriate measurements on human haemoglobin leads to a rearrangement of the low lying electronic levels of the iron. The term schemes received as results of two different sets of susceptibility data used in combination with one set of M?ssbauer data overlap with their error bars. The obtained level scheme of the Fe is correlated with the distance of the iron atom from the haem plane and the distance Fe-HIS F8, and some biological implications of these correlations are discussed.     

Significance of Over-Mature and Decaying Trees for Carbon Stocks in a Central European Natural Spruce Forest

Old-growth forests are important stores for carbon as they may accumulate C for centuries. The alteration of biomass and soil carbon pools across the development stages of a forest dynamics cycle has rarely been quantified. We studied the above- and belowground C stocks in the five forest development stages (regeneration to decay stage) of a montane spruce (Picea abies) forest of the northern German Harz Mountains, one of Central Europe’s few forests where the natural forest dynamics have not been disturbed by man for several centuries. The over-mature and decay stages had the largest total (up to 480 Mg C ha^?1) and aboveground biomass carbon pools (200 Mg C ha^?1) with biomass C stored in dead wood in the decay stage. The soil C pool (220–275 Mg C ha^?1, 0–60 cm) was two to three times larger than in temperate lowland spruce forests and remained invariant across the forest dynamics cycle. On the landscape level, taking into account the frequency of the five forest development stages, the total carbon pool was approximately 420 Mg C ha^?1. The results evidence the high significance of over-mature and decaying stages of temperate mountain forests not only for conserving specialized forest organisms but also for their large carbon storage potential.     

New species of the genus Plesiolacerta (Squamata: Lacertidae) from the upper Oligocene (MP28) of Southern Germany and a revision of the type species Plesiolacerta lydekkeri

Abstract: The lacertid material from the locality of Herrlingen 8 (upper Oligocene, MP28) is described as a new species of the genus Plesiolacerta. The material is disarticulated and comprises isolated elements including parietal, frontal, maxilla and dentary. It can be assigned to a single species on the basis of the external surface ornamentation. This morphology is typical for the genus Plesiolacerta, but the material differs in detail from the type species P. lydekkeri. The most significant feature of the new species is that the occipital scute of the parietal bone is narrow, rectangular in shape and anteroposteriorly short. Hitherto, the last occurrence of this genus was in the lower Oligocene. This material represents the first evidence of the existence of this genus in the upper Oligocene. Therefore, our knowledge of its evolution is expanded by providing new data on its spatial and temporal ranges and morphology. This taxon has a much longer history than we thought. In addition, the Eocene species, P. lydekkeri, is reviewed here. P. lydekkeri shares the most lacertid synapomorphies and, given our present knowledge, Plesiolacerta is a taxon very close to or possibly within crown Lacertidae. The frontal and postorbitofrontal of Plesiolacerta are described for the first time. In view of the primitive morphology and early occurrence of Plesiolacerta, it seems that the feature of a longer anterior region of the frontal could be considered as a plesiomorphic feature within lacertid lizards, and the condition in Timon (approximately the same length) as derived.     

A genetic technique to identify the diet of cownose rays,Rhinoptera bonasus: analysis of shellfish prey items from North Carolina and Virginia

Cownose rays are implicated in the consumption of commercially important shellfish on the U.S. East Coast. We tested this assumption by developing a molecular technique for species identification from cownose ray gut contents. Digestive tracts sampled from 33 rays in Pamlico Sound, NC and Chesapeake Bay, VA contained pieces of partially-digested tissue, well-digested tissue, fluid, and minute shell fragments which made visual identification to the species level nearly impossible. We sequenced the cytochrome oxidase subunit I (COI) for seven locally acquired bivalve species, chosen for their commercial and ecological importance in NC and VA. Sequences were used to design species-specific primers for each bivalve species to amplify polymerase chain reaction (PCR) products. We designed primers such that PCR products were sufficiently different in size to be distinguishable from one another when resolved on an agarose gel, and multiplexing of several species in one reaction was possible. Digestive tract sample testing revealed that cownose rays in Chesapeake Bay ate stout tagelus and soft shell clams. There was no evidence of the rays in the study consuming commercially important oysters, hard clams, and bay scallops. Further sampling over an extended period of time and additional locations is required to confirm these results. Our diagnostic tests could easily be expanded to elucidate the impact of cownose ray predation on prey populations.     

Low Serum 25-Hydroxyvitamin D Concentrations Are Associated with Increased Risk for Melanoma and Unfavourable Prognosis

Background

Low vitamin D status (serum 25(OH)D concentration) is associated with increased incidence and unfavourable outcome of various types of cancer. However, there are limited data on influence of serum 25(OH)D on risk and prognosis of malignant melanoma.

Methods

Basal serum 25(OH)D concentrations were retrospectively analyzed in a cohort of melanoma patients (n = 324) and healthy controls (n = 141). We tested the hypothesis that serum 25(OH)D concentrations are predictive of melanoma risk, thickness of primary melanomas, and overall survival (OS).

Results

Median serum 25(OH)D concentrations were significantly lower (p = 0.004) in melanoma patients (median = 13.6 ng/ml) as compared to controls (median = 15.6 ng/ml). Primary tumors of patients with low serum 25(OH)D concentrations (<10 ng/ml) had significantly (p = 0.006) greater Breslow thickness (median: 1.9 mm) as compared to patients with higher levels (>20 ng/ml; median: 1.00 mm). Patients with 25(OH)D serum concentrations in the lowest quartile had inferior overall survival (median: 80 months) comparing with the highest quartile (median: 195 months; p = 0.049).

Conclusions

Our data support the concept that serum 25(OH)D concentrations are associated with risk and prognosis of melanoma. Whether normalizing serum 25(OH)D concentrations in these patients improves outcomes will require testing in future clinical trials.