Developmental differences in genome replication program and origin activation

To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.     

An interplay between forest and non‐forest South American avifaunas suggested by a phylogeny of lepidocolaptes woodcreepers (dendrocolaptinae)

Very few South American avian superspecies or species groups are composed of both forest and non‐forest taxa. The genus Lepidocolaptes comprises 8–9 species of woodcreepers, most of which are forest birds, but two species, L. angustirostris and L. souleyetii, inhabit open vegetations. Therefore, this genus should play an important role in the discussion about the relationships between forest and non‐forest South American avifaunas. Nucleotide sequences from two mitochondrial genes, cytochrome b and ND2, suggest that: (i) L. fuscus should be removed from the genus since its association with other members of this genus is poorly supported. This view has been pointed out also by morphological and behavioural data; (ii) the phylogenetic position of the open‐vegetation species within the Lepidocolaptes radiation indicate that the split between forest and non‐forest elements within this genus took place as recently as two million years ago. This result suggests that the evolutionary relationships between forest and non‐forest biotas in South America may have been more dynamic than previously thought.     

Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean

Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2^UC) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning.     

Microbial Community Compositional Shifts in Bleached Colonies of the Brazilian Reef-Building Coral Siderastrea stellata

The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes.     

Effects of Agomelatine on Oxidative Stress in the Brain of Mice After Chemically Induced Seizures

Agomelatine is a novel antidepressant drug with melatonin receptor agonist and 5-HT(2C) receptor antagonist properties. We analyzed whether agomelatine has antioxidant properties. Antioxidant activity of agomelatine (25, 50, or 75 mg/kg, i.p.) or melatonin (50 mg/kg) was investigated by measuring lipid peroxidation levels, nitrite content, and catalase activities in the prefrontal cortex, striatum, and hippocampus of Swiss mice pentylenetetrazole (PTZ) (85 mg/kg, i.p.), pilocarpine (400 mg/kg, i.p.), picrotoxin (PTX) (7 mg/kg, i.p.), or strychnine (75 mg/kg, i.p.) induced seizure models. In the pilocarpine-induced seizure model, all dosages of agomelatine or melatonin showed a significant decrease in TBARS levels and nitrite content in all brain areas when compared to controls. In the strychnine-induced seizure model, all dosages of agomelatine and melatonin decreased TBARS levels in all brain areas, and agomelatine at low doses (25 or 50 mg/kg) and melatonin decreased nitrite contents, but only agomelatine at 25 or 50 mg/kg showed a significant increase in catalase activity in three brain areas when compared to controls. Neither melatonin nor agomelatine at any dose have shown no antioxidant effects on parameters of oxidative stress produced by PTX- or PTZ-induced seizure models when compared to controls. Our results suggest that agomelatine has antioxidant activity as shown in strychnine- or pilocarpine-induced seizure models.     

Psychophysical measure of visual luminance contrast during a daily rhythm

ABSTRACT

This study evaluated visual sensitivity to luminance contrast during a daily period. Twenty-eight young male adults (M = 24.85; SD = 2.4) with normal color vision and 20/20 visual acuity participated in this study. The circadian pattern was assessed using the Karolinska Sleepiness Scale (KSS), the Pittsburgh Sleep Quality Index (PSQI), and a sleep diary. To measure the luminance contrast, we used version 11.0 of the Metropsis software with sine-element frequency stimuli for spatial frequencies of 0.2, 0.6, 1, 3.1, 6.1, 8.8, 13.2, and 15.6 cycles per degree of visual angle (cpd). The stimuli were presented on a 19-inch color cathode ray tube (CRT) video monitor with a resolution of 1024 × 786 pixels, an update rate of 100 Hz, and a photopic luminance of 39.6 cd/m2. There was a significant difference in KSS on the weekdays [χ2₍₂₎ = 20.27; p = .001] and in the luminance contrast for frequencies of 13.2 cpd [χ2₍₂₎ = 8.27; p = .001] and 15.6 cpd [χ2₍₂₎ = 13.72; p = .041]. The results showed greater stability of the measurement during the afternoon and a reduction in the visual sensitivity in the high spatial frequencies during the night.     

Genomic data reveal international lineages of critical priority Escherichia coli harbouring wide resistome in Andean condors (Vultur gryphus Linnaeus, 1758)

Critical priority pathogens have globally disseminated beyond clinical settings, thereby threatening wildlife. Andean Condors (Vultur gryphus) are essential for ecosystem health and functioning, but their populations are globally near threatened and declining due to anthropogenic activities. During a microbiological and genomic surveillance study of critical priority antibiotic‐resistant pathogens, we identified pandemic lineages of multidrug‐resistant extended‐spectrum β‐lactamase (ESBL)‐producing Escherichia coli colonizing Andean Condors admitted at two wildlife rehabilitation centres in South America. Genomic analysis revealed the presence of genes encoding resistance to hospital and healthcare agents among international E. coli clones belonging to sequence types (STs) ST162, ST602, ST1196 and ST1485. In this regard, the resistome included genes conferring resistance to clinically important cephalosporins (i.e., CTX‐M‐14, CTX‐M‐55 and CTX‐M‐65 ESBL genes), heavy metals (arsenic, mercury, lead, cadmium, copper, silver), pesticides (glyphosate) and domestic/hospital disinfectants, suggesting a link with anthropogenic environmental pollution. On the other hand, the presence of virulence factors, including the astA gene associated with outbreak of childhood diarrhoea and extra‐intestinal disease in animals, was identified, whereas virulent behaviour was confirmed using the Galleria mellonella infection model. E. coli ST162, ST602, ST1196 and ST1485 have been previously identified in humans and food‐producing animals worldwide, indicating that a wide resistome could contribute to rapid adaptation and dissemination of these clones at the human–animal–environment interface. Therefore, these results highlight that Andean Condors have been colonized by critical priority pathogens, becoming potential environmental reservoirs and/or vectors for dissemination of virulent and antimicrobial‐resistant bacteria and/or their genes, in associated ecosystems and wildlife.     

Small-scale manjuba fishery around Cardoso Island State Park, SP, Brazil.

This work was carried out in the Enseada da Baleia and Vila Rápida communities. Data was provided by the Co-Management Committee of the Cardoso Island State Park (PEIC) on manjuba fishery management, technique and strategies used by the fishermen, as well as locally accumulated knowledge. Based on the results, social, ecological, and economic aspects of this type of fishing were analyzed. The importance of the accumulated knowledge and experience of this community, as well as the limitations imposed by local fishing gear, was concluded to be essential in conserving manjuba fishery conditions in the area. Industrial fishing, relevant state legislation, and market conditions were found to be the main obstacles to local fishery. Various proposals are suggested for manjuba fishery management, with emphasis on the need for fishing community participation in whatever measures are ultimately implemented.     

Biogeographical relationships among tropical forests in north-eastern Brazil

Aim To use parsimony analysis of endemicity and cladistic analysis of distributions and endemism to evaluate two hypotheses addressing biogeographical relationships among Amazonia, the Caatinga forest enclaves, Pernambuco Centre and the southern Atlantic Forest. Location North‐eastern Brazil, South America. Methods To find the most parsimonious areagram we analysed a matrix composed of the presence (1) or absence (0) of 745 taxa (i.e. 293 genera and 452 species of woody plants) within 16 localities belonging to the four large regions addressed in this study. Results One most parsimonious areagram was found and it shows a basal separation between the southern Atlantic Forest and all other regions. This break is followed by a separation between all Caatinga forest enclaves (except Baturité) from a cluster composed of Baturité, the Pernambuco Centre and Amazonia. In this cluster, the most basal separation isolates Baturité from the cluster formed by localities from Amazonia and the Pernambuco Centre. The biogeographical relationships among sites could not be explained by either a random distribution of species among sites or by the geographical distance between sites. Main conclusions We found strong cladistic signal within the raw distribution and phylogenetic data used in our analysis, indicating structured species assemblages in the surveyed localities. They have resulted from the fragmentation of an ancestral biota that was once widely distributed in the region. Our results also support the hypothesis that Atlantic Forest is not a biogeographically natural area, because the Pernambuco Centre is more closely related to Amazonia than to the southern Atlantic Forest. Finally, our data do not support the notion that Caatinga forest enclaves comprise a single biogeographical region, because one Caatinga forest enclave (Baturité) is much more closely related to the cluster formed by Amazonia and the Pernambuco Centre than to other sites. These relationships suggest the occurrence of forest connections between Amazonia and the Atlantic Forests across Caatinga during several periods of the Tertiary and Quaternary. However, palaeoecological data currently available for the Caatinga region are still scarce and do not have either the spatial or temporal resolution required to reconstruct the history of connections among the forests in north‐eastern Brazil.     

ESIPT-exhibiting protein probes: a sensitive method for rice proteins detection during starch extraction.

The 2-(4'-isothiocyanate-2'-hydroxyphenyl)benzoxazole dye was successfully applied as label of rice proteins during the alkaline extraction of starch. Direct fluorescence measurements were used to observe the presence of proteins labelled in different steps of rice starch extraction. The results were compared to those obtained with the well-known biuret colorimetric test. Whereas the colorimetric test indicates the absence of protein after the third extraction step, the fluorescence emission of the conjugate could be observed in all extraction steps. The separation of different rice proteins could also be observed.