PlantFuncSSR: Integrating first and next generation transcriptomics for mining of SSR-functional domains markers

© 2016 Sablok, Pérez-Pulido, Do, Seong, Casimiro-Soriguer, La Porta, Ralph, Squartini, Muñoz-Merida and Harikrishna. Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intrageneric differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www. bioinfocabd.upo.es/plantssr

Land- and water-based exercise intervention in women with fibromyalgia: the al-andalus physical activity randomised controlled trial

Background The al-Andalus physical activity intervention study is a randomised control trial to investigate the effectiveness of a land- and water-based exercise intervention for reducing the overall impact of fibromyalgia (primary outcome), and for improving tenderness and pain-related measures, body composition, functional capacity, physical activity and sedentary behaviour, fatigue, sleep quality, health-related quality of life, and cognitive function (secondary outcomes) in women with fibromyalgia. Methods/Design One hundred eighty women with fibromyalgia (age range: 35-65 years) will be recruited from local associations of fibromyalgia patients in Andalucía (Southern Spain). Patients will be randomly assigned to a usual care (control) group (n = 60), a water-based exercise intervention group (n = 60) or a land-based exercise intervention group (n = 60). Participants in the usual care group will receive general physical activity guidelines and participants allocated in the intervention groups will attend three non-consecutive training sessions (60 min each) per week during 24 weeks. Both exercise interventions will consist of aerobic, muscular strength and flexibility exercises. We will also study the effect of a detraining period (i.e., 12 weeks with no exercise intervention) on the studied variables. Discussion Our study attempts to reduce the impact of fibromyalgia and improve patients' health status by implementing two types of exercise interventions. Results from this study will help to assess the efficacy of exercise interventions for the treatment of fibromyalgia. If the interventions would be effective, this study will provide low-cost and feasible alternatives for health professionals in the management of fibromyalgia. Results from the al-Andalus physical activity intervention will help to better understand the potential of regular physical activity for improving the well-being of women with fibromyalgia.This study was supported by the Consejeria de Turismo, Comercio y Deporte (CTCD-201000019242-TRA), the Spanish Ministry of Science and Innovation (I + D + I DEP2010-15639, grants: BES-2009-013442, BES-2011-047133, RYC-2010-05957, RYC-2011-09011), the Swedish Heart-Lung Foundation (20090635), the Spanish Ministry of Education (AP-2009-3173), Granada Research of Excelence Initiative on Biohealth (GREIB), Campus BioTic, University of Granada, Spain and European University of Madrid. Escuela de Estudios Universitarios Real Madrid. 2010/04RM

Early Life Events Carry Over to Influence Pre-Migratory Condition in a Free-Living Songbird

Conditions experienced during development can have long-term consequences for individual success. In migratory songbirds, the proximate mechanisms linking early life events and survival are not well understood because tracking individuals across stages of the annual cycle can be extremely challenging. In this paper, we first use a 13 year dataset to demonstrate a positive relationship between 1st year survival and nestling mass in migratory Savannah sparrows (Passerculus sandwichensis). We also use a brood manipulation experiment to show that nestlings from smaller broods have higher mass in the nest relative to individuals from larger broods. Having established these relationships, we then use three years of field data involving multiple captures of individuals throughout the pre-migratory period and a multi-level path model to examine the hypothesis that conditions during development limit survival during migration by affecting an individual's ability to accumulate sufficient lean tissue and fat mass prior to migration. We found a positive relationship between fat mass during the pre-migratory period (Sept–Oct) and nestling mass and a negative indirect relationship between pre-migratory fat mass and fledging date. Our results provide the first evidence that conditions during development limit survival during migration through their effect on fat stores. These results are particularly important given recent evidence showing that body condition of songbirds at fledging is affected by climate change and anthropogenic changes to landscape structure

Snowmass2021 - Letter of interest cosmology intertwined IV: the age of the universe and its curvature

A precise measurement of the curvature of the Universe is of prime importance for cosmology since it could not only confirm the paradigm of primordial inflation but also help in discriminating between different early-Universe scenarios. Recent observations, while broadly consistent with a spatially flat standard Cold Dark Matter (CDM) model, show tensions that still allow (and, in some cases, even suggest) a few percent deviations from a flat universe. In particular, the Planck Cosmic Microwave Background power spectra, assuming the nominal likelihood, prefer a closed universe at more than 99% confidence level. While new physics could be at play, this anomaly may be the result of an unresolved systematic error or just a statistical fluctuation. However, since positive curvature allows a larger age of the Universe, an accurate determination of the age of the oldest objects provides a smoking gun in confirming or falsifying the current flat CDM model

Snowmass2021 - Letter of interest cosmology intertwined I: Perspectives for the next decade

The standard Cold Dark Matter cosmological model provides an amazing description of a wide range of astrophysical and astronomical data. However, there are a few big open questions, that make the standard model look like a first-order approximation to a more realistic scenario that still needs to be fully understood. In this Letter of Interest we will list a few important goals that need to be addressed in the next decade, also taking into account the current discordances present between the different cosmological probes, as the Hubble constant value, the tension, and the anomalies present in the Planck results. Finally, we will give an overview of upgraded experiments and next-generation space-missions and facilities on Earth that will be of crucial importance to address all these questions

Cosmology intertwined III: fσ8 and S8

The standard Cold Dark Matter cosmological model provides a wonderful fit to current cosmological data, but a few statistically significant tensions and anomalies were found in the latest data analyses. While these anomalies could be due to the presence of systematic errors in the experiments, they could also indicate the need for new physics beyond the standard model. In this Letter of Interest we focus on the tension between Planck data and weak lensing measurements and redshift surveys, in the value of the matter energy density and the amplitude (or the growth rate ) of cosmic structure. We list a few promising models for solving this tension, and discuss the importance of trying to fit multiple cosmological datasets with complete physical models, rather than fitting individual datasets with a few handpicked theoretical parameters

Snowmass2021 - Letter of interest cosmology intertwined II: the hubble constant tension

The current cosmological probes have provided a fantastic confirmation of the standard Cold Dark Matter cosmological model, which has been constrained with unprecedented accuracy. However, with the increase of the experimental sensitivity, a few statistically significant tensions between different independent cosmological datasets emerged. While these tensions can be in part the result of systematic errors, the persistence after several years of accurate analysis strongly hints at cracks in the standard cosmological scenario and the need for new physics. In this Letter of Interest we will focus on the tension between the Planck estimate of the Hubble constant and the SH0ES collaboration measurements. After showing the evaluations made from different teams using different methods and geometric calibrations, we will list a few interesting models of new physics that could solve this tension and discuss how the next decade’s experiments will be crucial

The comparative effectiveness of rodents and dung beetles as local seed dispersers in Mediterranean oak forests

The process of seed dispersal of many animal-dispersed plants is frequently mediated by a small set of biotic agents. However, the contribution that each of these dispersers makes to the overall recruitment may differ largely, with important ecological and management implications for the population viability and dynamics of the species implied in these interactions. In this paper, we compared the relative contribution of two local guilds of scatter-hoarding animals with contrasting metabolic requirements and foraging behaviours (rodents and dung beetles) to the overall recruitment of two Quercus species co-occurring in the forests of southern Spain. For this purpose, we considered not only the quantity of dispersed seeds but also the quality of the seed dispersal process. The suitability for recruitment of the microhabitats where the seeds were deposited was evaluated in a multi-stage demographic approach. The highest rates of seed handling and predation occurred in those microhabitats located under shrubs, mostly due to the foraging activity of rodents. However, the probability of a seed being successfully cached was higher in microhabitats located beneath a tree canopy as a result of the feeding behaviour of beetles. Rodents and beetles showed remarkable differences in their effectiveness as local acorn dispersers. Quantitatively, rodents were much more important than beetles because they dispersed the vast majority of acorns. However, they were qualitatively less effective because they consumed a high proportion of them (over 95%), and seeds were mostly dispersed under shrubs, a less suitable microhabitat for short-term recruitment of the two oak species. Our findings demonstrate that certain species of dung beetles (such as Thorectes lusitanicus), despite being quantitatively less important than rodents, can act as effective local seed dispersers of Mediterranean oak species. Changes in the abundance of beetle populations could thus have profound implications for oak recruitment and community dynamics.This study was supported by a postdoctoral contract of the Andalusian Government to IMPR, by the Projects of the Ministry of Education and Science entitled “Thorbellota” (“Análisis ecológico y fisiológico de la interacción entre el coleóptero coprófago Thorectes lusitanicus y las bellotas de Quercus suber y Q. canariensis: implicaciones evolutivas y aplicadas”; CGL2008/03878/BOS) and “InTerDist” (“Influencia del nicho térmico en la distribución geográfica de las especies”; CGL2011-25544), and the Andalusian project “Anasinque” (PE2010-RNM5782)

A framework for the study of genetic variation in migratory behaviour

Evolutionary change results from selection acting on genetic variation. For migration to be successful, many different aspects of an animal’s physiology and behaviour need to function in a co-coordinated way. Changes in one migratory trait are therefore likely to be accompanied by changes in other migratory and life-history traits. At present, we have some knowledge of the pressures that operate at the various stages of migration, but we know very little about the extent of genetic variation in various aspects of the migratory syndrome. As a consequence, our ability to predict which species is capable of what kind of evolutionary change, and at which rate, is limited. Here, we review how our evolutionary understanding of migration may benefit from taking a quantitative-genetic approach and present a framework for studying the causes of phenotypic variation. We review past research, that has mainly studied single migratory traits in captive birds, and discuss how this work could be extended to study genetic variation in the wild and to account for genetic correlations and correlated selection. In the future, reaction-norm approaches may become very important, as they allow the study of genetic and environmental effects on phenotypic expression within a single framework, as well as of their interactions. We advocate making more use of repeated measurements on single individuals to study the causes of among-individual variation in the wild, as they are easier to obtain than data on relatives and can provide valuable information for identifying and selecting traits. This approach will be particularly informative if it involves systematic testing of individuals under different environmental conditions. We propose extending this research agenda by using optimality models to predict levels of variation and covariation among traits and constraints. This may help us to select traits in which we might expect genetic variation, and to identify the most informative environmental axes. We also recommend an expansion of the passerine model, as this model does not apply to birds, like geese, where cultural transmission of spatio-temporal information is an important determinant of migration patterns and their variation