Phylogenetic relationships of the algae scraping cyprinid genus Capoeta (Teleostei: Cyprinidae)

We reconstructed the matrilineal phylogeny of Asian algae-eating fishes of the genus Capoeta based on complete mitochondrial gene for cytochrome b sequences obtained from 20 species sampled from the majority of the range and 44 species of closely related barbs of the genera Barbus s. str. and Luciobarbus. The results of this study show that Capoeta forms a strongly supported monophyletic subclade nested within the Luciobarbus clade, suggesting that specialized scraping morphology appeared once in the evolutionary history of the genus. We detected three main groups of Capoeta: the Mesopotamian group, which includes three species from the Tigris-Euphrates system and adjacent water bodies, the Anatolian-Iranian group, which has the most diversified structure and encompasses many species distributed throughout Anatolian and Iranian inland waters, and the Aralo-Caspian group, which consists of species distributed in basins of the Caspian and Aral Seas, including many dead-end rivers in Central Asia and Northern Iran. The most probable origination pathway of the genus Capoeta is hypothesized to occur as a result of allopolyploidization. The origin of Capoeta was found around the Langhian-Serravallian boundary according to our molecular clock. The diversification within the genus occurred along Middle Miocene-Late Pliocene periods.     

Species identification of the Northern shrimp (Pandalus borealis) by polymerase chain reaction-restriction fragment length polymorphism and proteomic analysis

Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belong to the superfamily Penaeoidea, which include the families Penaeidae and Solenoceridae, and 11 other crustacean species, including prawns, shrimps, lobsters, and crabs. For this purpose, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was designed based on the amplification of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial regions using the primers 16S-CruF and 16S-CruR. The 966-bp PCR products were produced and cleaved with the restriction enzymes AluI, TaqI, and HinfI, which provided species-specific restriction patterns. In addition, a proteomic approach, based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-ion trap (ESI-IT) mass spectrometry, was used to identify and characterize new P. borealis-specific peptides that could be useful as potential markers of this species in protein-based detection methods. To our knowledge, this is the first time a molecular method has been successfully applied to identify a wide range of prawn and shrimp species, including P. borealis, for either whole individuals or processed products. However, validation of the methods proposed here is required by applying them to a larger sample of individuals from different populations and geographic origins in order to avoid mainly false-negative results.     

RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins

Biomolecular condensates formed via liquid–liquid phase separation (LLPS) play a crucial role in the spatiotemporal organization of the cell material. Nucleic acids can act as critical modulators in the stability of these protein condensates. To unveil the role of RNA length in regulating the stability of RNA binding protein (RBP) condensates, we present a multiscale computational strategy that exploits the advantages of a sequence-dependent coarse-grained representation of proteins and a minimal coarse-grained model wherein proteins are described as patchy colloids. We find that for a constant nucleotide/protein ratio, the protein fused in sarcoma (FUS), which can phase separate on its own—i.e., via homotypic interactions—only exhibits a mild dependency on the RNA strand length. In contrast, the 25-repeat proline-arginine peptide (PR₂₅), which does not undergo LLPS on its own at physiological conditions but instead exhibits complex coacervation with RNA—i.e., via heterotypic interactions—shows a strong dependence on the length of the RNA strands. Our minimal patchy particle simulations suggest that the strikingly different effect of RNA length on homotypic LLPS versus RBP–RNA complex coacervation is general. Phase separation is RNA-length dependent whenever the relative contribution of heterotypic interactions sustaining LLPS is comparable or higher than those stemming from protein homotypic interactions. Taken together, our results contribute to illuminate the intricate physicochemical mechanisms that influence the stability of RBP condensates through RNA inclusion.     

Earlywood vessels of the sub-Mediterranean oak Quercus pyrenaica have greater plasticity and sensitivity than those of the temperate Q. petraea at the Atlantic–Mediterranean boundary

Key message

Earlywood vessel features indicate different adaptations of Quercus petraea and Q. pyrenaica , which are probably related with their corresponding Atlantic and sub-Mediterranean ecological requirements.

Abstract

We studied the climatic signal of the earlywood anatomy of a temperate [Quercus petraea (Mattuschka) Liebl.] and a sub-Mediterranean (Quercus pyrenaica Willd.) oak species growing under similar climatic conditions in a transitional area between the Atlantic and Mediterranean regions of the Iberian Peninsula. We hypothesized that both species react differently in their wood anatomy due to their contrasting ecological requirements, and we test the usefulness of earlywood anatomical features to study the behaviour of these ring-porous oaks upon climate. For this, we measured the earlywood vessels, and obtained annual series of several anatomical variables for the period 1937–2006 using dendrochronological techniques, considering whether the vessels belonged to the first row or not. After optimizing the data set by principal component analysis and progressive filtering of large vessels, we selected maximum vessel area and total number of vessels as they resulted to be the optimal variables to describe vessel size and number, respectively. Vessel size of Q. pyrenaica was dependent on precipitation along the previous growing season, whereas it did not show any clear climatic response for Q. petraea. On the contrary, vessel number was related to winter temperature for both species. These relationships observed between climate and anatomy appeared to be stable through time. The results obtained reinforce the utility of earlywood vessel features as potential climate proxies.     

Gene methylation parallelisms between peripheral blood cells and oral mucosa samples in relation to overweight

Epigenetics has an important role in the regulation of metabolic adaptation to environmental modifications. In this sense, the determination of epigenetic changes in non-invasive samples during the development of metabolic diseases could play an important role in the procedures in primary healthcare practice. To help translate the knowledge of epigenetics to public health practice, the present study aims to explore the parallelism of methylation levels between white blood cells and buccal samples in relation to obesity and associated disorders. Blood and buccal swap samples were collected from a subsample of the Spanish cohort of the Food4Me study. Infinium HumanMethylation450 DNA Analysis was carried out for the determination of methylation levels. Standard deviation for β values method and concordance correlation analysis were used to select those CpG which showed best parallelism between samples. A total of 277 CpGs met the criteria and were selected for an enrichment analysis and a correlation analysis with anthropometrical and clinical parameters. From those selected CpGs, four presented high associations with BMI (cg01055691 in GAP43; r = ?0.92 and rho = ?0.84 for blood; r = ?0.89 and rho = ?0.83 for buccal sample), HOMA-IR (cg00095677 in ATP2A3; r = 0.82 and rho = ?0.84 for blood; r = ?0.8 and rho = ?0.83 for buccal sample) and leptin (cg14464133 in ADARB2; r = ?0.9182 and rho = ?0.94 for blood; r = ?0.893 and rho = ?0.79 for buccal sample). These findings demonstrate the potential application of non-invasive buccal samples in the identification of surrogate epigenetic biomarkers and identify methylation sites in GAP43, ATP2A3 and ADARB2 genes as potential targets in relation to overweight management and insulin sensibility.     

Different environmental temperatures affect amino acid metabolism in the eurytherm teleost Senegalese sole (Solea senegalensis Kaup, 1858) as indicated by changes in plasma metabolites

Senegalese sole (Solea senegalensis) is a eurytherm teleost that under natural conditions can be exposed to annual water temperature fluctuations between 12 and 26°C. This study assessed the effects of temperature on sole metabolic status, in particular in what concerns plasma free amino acid changes during thermal acclimation. Senegalese sole maintained at 18°C were acclimated to either cold (12°C) or warm (26°C) environmental temperatures for 21?days. Fish maintained at 18°C served as control. Plasma concentrations of cortisol, glucose, lactate, triglycerides, proteins, and free amino acids were assessed. Cold acclimation influenced interrenal responses of sole by increasing cortisol release. Moreover, plasma glucose and lactate concentrations increased linearly with temperature, presumably reflecting a higher metabolic activity of sole acclimated to 26°C. Acclimation temperature affected more drastically plasma concentrations of dispensable than that of indispensable amino acids, and different acclimation temperatures induced different responses. Asparagine, glutamine and ornithine seem to be of particular importance for ammonia detoxification mechanisms, synthesis of triglycerides that may be used during homeoviscous adaptation and, to a lesser extent, as energetic substrates in specimens acclimated to 12°C. When sole is acclimated to 26°C taurine, glutamate, GABA and glycine increased, which may suggest important roles as antioxidant defences, in osmoregulatory processes and/or for energetic purposes at this thermal regimen. In conclusion, acclimation to different environmental temperatures induces several metabolic changes in Senegalese sole, suggesting that amino acids may be important for thermal acclimation.     

Evolution of Linear Motifs within the Papillomavirus E7 Oncoprotein

Many protein functions can be traced to linear sequence motifs of less than five residues, which are often found within intrinsically disordered domains. In spite of their prevalence, their role in protein evolution is only beginning to be understood. The study of papillomaviruses has provided many insights on the evolution of protein structure and function. We have chosen the papillomavirus E7 oncoprotein as a model system for the evolution of functional linear motifs. The multiple functions of E7 proteins from paradigmatic papillomavirus types can be explained to a large extent in terms of five linear motifs within the intrinsically disordered N-terminal domain and two linear motifs within the globular homodimeric C-terminal domain. We examined the motif inventory of E7 proteins from over 200 known papillomavirus types and found that the motifs reported for paradigmatic papillomavirus types are absent from many uncharacterized E7 proteins. Several motif pairs occur more often than expected, suggesting that linear motifs may evolve and function in a cooperative manner. The E7 linear motifs have appeared or disappeared multiple times during papillomavirus evolution, confirming the evolutionary plasticity of short functional sequences. Four of the motifs appeared several times during papillomavirus evolution, providing direct evidence for convergent evolution. Interestingly, the evolution pattern of a motif is independent of its location in a globular or disordered domain. The correlation between the presence of some motifs and virus host specificity and tissue tropism suggests that linear motifs play a role in the adaptive evolution of papillomaviruses.     

Heterogeneity of terrestrial bromeliad colonies and regeneration of Acacia praecox (Fabaceae) in a humid-subtropical-Chaco forest, Argentina

In several tropical and subtropical forests, plants of the understorey act as an ecological filter that differentially affects woody species regeneration. In convex sectors of the Schinopsis balansae (Anacardiaceae) forests of the Southeastern Chaco there are dense colonies of terrestrial bromeliads. These may influence forest regeneration by intercepting rain water and propagules in their tanks. Within colonies, the spatial distribution of bromeliads is clumped because their clonal growth leaves numerous internal gaps. In this study we describe the internal heterogeneity of three bromeliad colonies (plots) and analyze how this heterogeneity affects Acacia praecox regeneration (i.e. seedling recruitment and survival). In January 1996, we randomly placed three transects with 150 contiguous quadrats of 100 cm(2) in each plot. For each quadrat we recorded the type of floor cover (i.e. bromeliads, herbs, litter, or bare soil) and the presence of A. praecox seeds or seedlings. In July 1996 we relocated the transects and recorded seedling survival. Bromeliad colonies showed a high internal heterogeneity. Almost half of the 450 quadrats were covered by two terrestrial bromeliads. Aechmea distichantha was recorded in 81% of all quadrats with bromeliads, and Bromelia serra in the others. All quadrats with bromeliads were covered by litter. Half of them were occupied by the bases of bromeliads and the others were covered by their leaves. In contrast, where bromeliads were not present, soil surface was covered by litter in 83% and by herbaceous vegetation in 11% of the quadrats; very few quadrats were covered by bare soil. In January 1996, we recorded 127 seeds and 176 seedlings of A. praecox. Seed and seedling densities of A. praecox were similar in quadrats with and without bromeliads, but variability in seedling density of A. praecox was higher within than among plots. Seed density was higher in quadrats covered by bromeliad leaves than inside the tanks. Seedling survival of A. praecox was slightly higher in quadrats with bromeliads in only one of the three plots. No seedling survived inside the bromeliad tanks. Apparently. bromeliad colonies have no effect on seedling regeneration of A. praecox.