The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective

The SAR11 clade of Alphaproteobacteria is the most abundant group of planktonic cells in the near-surface epipelagic waters of the ocean, but the mechanisms underlying its exceptional success have not been fully elucidated. Here, we applied a metagenomic approach to explore microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations as well as homologous recombination in populations of SAR11 from different aquatic habitats (marine epipelagic, bathypelagic, and surface freshwater). The patterns of mutation accumulation and recombination were compared to those of other groups of representative marine microbes with multiple ecological strategies that share the same marine habitat, namely, Cyanobacteria (Prochlorococcus and Synechococcus), Archaea (“Candidatus Nitrosopelagicus” and Marine Group II Thalassoarchaea), and some heterotrophic marine bacteria (Alteromonas and Erythrobacter). SAR11 populations showed widespread recombination among distantly related members, preventing divergence leading to a genetically stable population. Moreover, their high intrapopulation sequence diversity with an enrichment in synonymous replacements supports the idea of a very ancient divergence and the coexistence of multiple different clones. However, other microbes analyzed seem to follow different evolutionary dynamics where processes of diversification driven by geographic and ecological instability produce a higher number of nonsynonymous replacements and lower intrapopulation sequence diversity. Together, these data shed light on some of the evolutionary and ecological processes that lead to the large genomic diversity in SAR11. Furthermore, this approach can be applied to other similar microbes that are difficult to culture in the laboratory, but abundant in nature, to investigate the underlying dynamics of their genomic evolution.This work was supported by grants VIREVO CGL2016-76273-P (AEI/FEDER, EU) (cofunded with FEDER funds) from the Spanish Ministerio de Economía, Industria, y Competitividad and HIDRAS3 PROMETEU/2019/009 from the Generalitat Valenciana to F.R.-V. and by grants CGL2013-40564-R and SAF2013-49267-EXP from the Spanish Ministerio de Economía, Industria, y Competitividad; grant ACIF/2015/332 from the Generalitat Valenciana; and grant 5334 from the Betty Moore Foundation to M.M.-G. F.R.-V. was also a beneficiary of the 5top100-program of the Ministry for Science and Education of Russia. J.M.H.-M. was supported by a Ph.D. fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). F.H.C. was supported by a postdoctoral fellowship from the Generalitat Valenciana (APOSTD/2018/186). M.L.-P. was supported by a postdoctoral fellowship from the Spanish Ministerio de Economía, Industria, y Competitividad (IJCI-2017-34002)

Real-time monitoring of PtaHMGB activity in poplar transactivation assays

Precise control of gene expression is essential to synchronize plant development with the environment. In perennial plants, transcriptional regulation remains poorly understood, mainly due to the long time required to perform functional studies. Transcriptional reporters based on luciferase have been useful to study circadian and diurnal regulation of gene expression, both by transcription factors and chromatin remodelers. The high mobility group proteins are considered transcriptional chaperones that also modify the chromatin architecture. They have been found in several species, presenting in some cases a circadian expression of their mRNA or protein. Results: Transactivation experiments have been shown as a powerful and fast method to obtain information about the potential role of transcription factors upon a certain reporter. We designed and validated a luciferase transcriptional reporter using the 5? sequence upstream ATG of Populus tremula × alba LHY2 gene. We showed the robustness of this reporter line under long day and continuous light conditions. Moreover, we confirmed that pPtaLHY2::LUC activity reproduces the accumulation of PtaLHY2 mRNA. We performed transactivation studies by transient expression, using the reporter line as a genetic background, unraveling a new function of a high mobility group protein in poplar, which can activate the PtaLHY2 promoter in a gate-dependent manner. We also showed PtaHMGB2/3 needs darkness to produce that activation and exhibits an active degradation after dawn, mediated by the 26S proteasome. Conclusions: We generated a stable luciferase reporter poplar line based on the circadian clock gene PtaLHY2, which can be used to investigate transcriptional regulation and signal transduction pathway. Using this reporter line as a genetic background, we established a methodology to rapidly assess potential regulators of diurnal and circadian rhythms. This tool allowed us to demonstrate that PtaHMGB2/3 promotes the transcriptional activation of our reporter in a gate-dependent manner. Moreover, we added new information about the PtaHMGB2/3 protein regulation along the day. This methodology can be easily adapted to other transcription factors and reporters

Effects of organic chromium supplementation to finishing lambs diet on growth performance, carcass characteristics and meat quality

The objective of this study was to evaluate supplemental organic chromium (Cr) to finishing lambs on growth performance, carcass characteristics, and meat quality. Eighteen Suffolk lambs (age (4.5±0.2) mon; (25.8±3.6) kg body weight (BW)) were randomly assigned to three levels of supplemental organic Cr (0.0, 0.2 and 0.4 mg kg–1 dry matter (DM)) in a complete random design. Growth performance was evaluated for 70 d, and then lambs were slaughtered to study carcass characteristics and chemical composition of meat. Orthogonal contrasts were performed (contrast one-average level 0.2 ppm Cr vs. average level 0.4 ppm Cr; contrast two-level 0 vs. average levels (0.2+0.4) ppm Cr). Orthogonal polynomials were used to estimate the linear and quadratic effects of Cr concentrations. Growth and carcass performance were not affected by supplemental organic Cr. Muscle conformation and leg perimeter linearly increased (P<0.05) as organic Cr level increased in the diet. Kidney fat decreased linearly (P<0.05) as supplemental Cr increased. In Longissimus dorsi (LD), the ash content decreased linearly, and shear force (kg cm–2) increased (P<0.05) as organic Cr level increased in the diet. It is concluded that organic Cr did not affect growth performance, but it improved positively the muscle conformation, reduced kidney fat, whereas in LD there was an increment in shear force in finishing carcass lambs

Multi-instrumental observations of the 2014 Ursid meteor outburst

The Ursid meteor shower is an annual shower that usually shows little activity. However, its Zenith hourly rate sometimes increases, usually either when its parent comet, 8P/Tuttle, is close to its perihelion or its aphelion. Outbursts when the comet is away from perihelion are not common and outbursts when the comet is close to aphelion are extremely rare. The most likely explanation offered to date is based on the orbital mean motion resonances. The study of the aphelion outburst of 2000 December provided a means of testing that hypothesis. A new aphelion outburst was predicted for 2014 December. The SPanish Meteor Network, in collaboration with the French Fireball Recovery and InterPlanetary Observation Network, set up a campaign to monitor this outburst and eventually retrieve orbital data that expand and confirm previous preliminary results and predictions. Despite unfavourable weather conditions over the south of Europe over the relevant time period, precise trajectories from multistation meteor data recorded over Spain were obtained, as well as orbital and radiant information for four Ursid meteors. The membership of these four meteors to the expected dust trails that were to provoke the outburst is discussed, and we characterize the origin of the outburst in the dust trail produced by the comet in the year AD 1392.Peer reviewe

Novel winter-associated regulators of the circadian clock in poplar

Background Winter dormancy is an adaptive mechanism that allows trees from temperate and cold regions to survive the harsh conditions of this season. Critical steps of this process are strongly influenced by environmental cues, mainly daylength and temperature. The mechanism that integrates these signals is the circadian clock. Despite the importance of the correct functioning of the clock for the healthy state of the plant [1], low temperatures cause the disruption of the circadian clock in trees, which consists in a transcriptional activation followed by an arrhythmic expression [2-5]. In this work we uncover winter-associated regulators of the circadian clock in poplar. Methods Firstly, we made a transcriptional fusion with the promoter of LHY2, a circadian clock gene, and the luciferase gene. This construct was used to generate transgenic poplars (717-1B4, INRA clone). With these events we characterized the expression of this promoter under different conditions of photoperiod and temperature. To this aim we have set up a circadian luminiscence assay registering luciferase activity from leaf discs with a luminometer. Then we carried out a Yeast One Hybrid (Y1H) screening with a library enriched in winter-associated factors and using this promoter as bait. Candidate regulators are tested in vivo using Golden Braid technology [6] and transient assays in poplar, by which we overexpressed and silenced the candidate genes. Results and Conclusions Here we present the characterization of the Populus tremula x alba LHY2 promoter under three different photoperiod conditions. Our results indicate the selected promoter region contains the circadian elements as well as the luciferase activity shows the expected expression under both long and short days. In the Y1H screening, we found several candidates that are classified either as transcription factors or chromatin remodelers. We will discuss the possible role of these proteins as regulators of the poplar circadian clock

The graphene oxide species induce a different biological response in SN4741 Parkinson cell line

Introduction: Graphene Oxide (GO)has recently emerged as a reliable material to create scaffolds for the neural tissue because of its biocompatibility, electroconductive and physicochemical properties. Graphene is a 2-dimensional material consisting of rings of carbon atoms with an excellent electrical conductivity originating in the sp2 hybridized carbons network. Nevertheless, there is not a consensus which kind of graphene oxide is most useful of benefit.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

The involvement of 5-methyl cytosine DNA Demethylases in the dormant-growth transition in poplar

Background Woody species are highly adapted to their habitats. In response to environmental cues woody perennials trigger self-protective developmental programmes, in which signal transduction, transcriptional reprogramming and epigenetic regulation could participate in defining the winter dormancy state. Winter dormancy is the mechanism used by perennial plants to survive the harsh conditions of winter in temperate and cold regions and determines the geographical distribution of tree species (Chuine and Beaubien 2001; Horvath et al. 2003; Allona et al. 2008). Epigenetic control of winter dormancy in woody plants is barely known. Among the important epigenetic marks, 5-methyl cytosine (5mC) regulates gene expression in animals and plants. Global changes in 5mC DNA methylation have been shown in the transition of developmental stages in plants such as chestnut bud set and burst, flowering in azalea, aging in pine trees among other. However, the mechanism and the enzymes involved in the modification of the methylome and its control over those development processes remain to be identified. Our previous results showed higher DNA methylation and less acetylated Lys 8 of histone H4 global levels in poplar stem during winter dormancy compared to active growing season (Conde et al. 2013). In this study we focus in the understanding of the molecular mechanism behind these changes in DNA methylation profile and their role in the control of winter dormancy. Methods Analysis of the 5-methyl cytosine levels by the application of the immunofluorescence-based method set up in our lab, in stem vibratome sections cut from hybrid poplar (Populus tremula x alba) growing in the field at different stages of winter dormancy process. To develop a protocol for buds paraffin wax embedding to analyze the level of 5-methyl cytosine by applying our immunofluorescence-based method in poplar apex microtome sections in diferents stages of winter dormancy. RT-PCR analysis to determine the profile of gene expresion at diferent stages of winter dormancy involved in modification of DNA methylation profile. Hybrid poplar transformation to obtain transgenic lines with modified expression of a demethylase and phenological experiments with selected lines. Results and Conclusions The immunolocalization assays performed in poplar stem sections showed that DNA methylation leves fall suddenly when trees coming from the dormant state are near to restore the growing season. We have determined the spatial distribution of DNA methylation changes in this organ. We have identified two poplar homologs to Arabidopsis DME gene: PtaDML8/PtaDML10. The DME protein promotes global DNA demethylation along the genome during endosperm development. Our RT-PCR analyses indicate that the expression of PtaDML8/PtaDML10 genes increases significantly when trees are near to restart growing after winter dormancy. The phenologycal assays showed that PtaDML8/PtaDML10 knockdown plants have a delayed in resuming of growth after dormancy. Taken together, we hypothesize that an active control of the 5mC DNA methylation might play a key role in winter dormancy and that 5mC demethylases would be crucial in this process

Towards understanding RAV1 transcriptional network during the growth-dormancy cycle in poplar

As plants are sessile organisms, the decision to grow or to stop growing is fundamental for their survival. To survive to the harsh condition of the winter, temperate and boreal trees undergo a self-protective developmental reprograming known as winter dormancy. Its mechanism involves an intricate interplay between endogenous growth regulators and the winter external signal, such as shortening of photoperiod and cold temperatures. Currently, only few factors including circadian and developmental transcription factors and hormonal signaling molecules have been shown to modulate the extension of the dormancy period in woody plants. In our laboratory, the circadian controlled transcription factor RAV promotes sylleptic branching and reduces dormancy length when RAV is ectopic overexpressed in poplar (1). Comparative mRNA profiling of RAV overexpressing versus wild type revealed a transcriptional rearrangement happens as effect of constitutive high level of RAV, giving rise to phenology. However, to define RAV mode of action as a transcriptional regulator and how RAV activity trigger a modification of dormancy-growth cycle, its primary targets genes should be investigated. At this particular, the translational fusion of a given transcription factor to the rat glucorticoid receptor domain (GR) have been widely used in Arabidopsis and recently in poplar (2). In this work we show the standardization of a methodology required to identify primary target genes for a transcription factor in poplar. This will be useful to future exploration of RAV1 gene network and its mode of action in spatio-temporal studies at tissue level during growth-dormancy cycle in poplar

Breast Cancer Detection by Means of Artificial Neural Networks

Breast cancer is a fatal disease causing high mortality in women. Constant efforts are being made for creating more efficient techniques for early and accurate diagnosis. Classical methods require oncologists to examine the breast lesions for detection and classification of various stages of cancer. Such manual attempts are time consuming and inefficient in many cases. Hence, there is a need for efficient methods that diagnoses the cancerous cells without human involvement with high accuracies. In this research, image processing techniques were used to develop imaging biomarkers through mammography analysis and based on artificial intelligence technology aiming to detect breast cancer in early stages to support diagnosis and prioritization of high-risk patients. For automatic classification of breast cancer on mammograms, a generalized regression artificial neural network was trained and tested to separate malignant and benign tumors reaching an accuracy of 95.83%. With the biomarker and trained neural net, a computer-aided diagnosis system is being designed. The results obtained show that generalized regression artificial neural network is a promising and robust system for breast cancer detection. The Laboratorio de Innovacion y Desarrollo Tecnologico en Inteligencia Artificial is seeking collaboration with research groups interested in validating the technology being developed