Abstract
To sustain and develop the largest fully open human genomic resources the International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on ...the foundation of the 1000 Genomes Project, which created the largest openly accessible catalogue of human genomic variation developed from samples spanning five continents. IGSR (i) maintains access to 1000 Genomes Project resources, (ii) updates 1000 Genomes Project resources to the GRCh38 human reference assembly, (iii) adds new data generated on 1000 Genomes Project cell lines, (iv) shares data from samples with a similarly open consent to increase the number of samples and populations represented in the resources and (v) provides support to users of these resources. Among recent updates are the release of variation calls from 1000 Genomes Project data calculated directly on GRCh38 and the addition of high coverage sequence data for the 2504 samples in the 1000 Genomes Project phase three panel. The data portal, which facilitates web-based exploration of the IGSR resources, has been updated to include samples which were not part of the 1000 Genomes Project and now presents a unified view of data and samples across almost 5000 samples from multiple studies. All data is fully open and publicly accessible.
The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the ...largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest.
Studying the speciation and mineral-fluid partitioning of the rare earth elements (REE) allows us to delineate the key processes responsible for the formation of economic REE mineral deposits in ...natural systems. Hydrothermal REE-bearing calcite is typically hosted in carbonatites and alkaline rocks, such as the giant Bayan Obo REE deposit in China and potential REE deposits such as Bear Lodge, WY. The compositions of these hydrothermal veins yield valuable information regarding pressure (P), temperature (T), salinity, and other physicochemical conditions under which the REE can be fractionated and concentrated in crustal fluids. This study presents numerical simulation results of the speciation of REE in aqueous NaCl-H2O-CO2-bearing hydrothermal fluids and a new partitioning model between calcite and fluids at different P-T-x conditions. Results show that, in a high CO2 and low salinity system, bicarbonate/carbonate are the main transporting ligands for the REE, but predominance shifts to chloride complexes in systems with high CO2 and high salinity. Hydroxyl REE complexes may be important for the solubility and transport of the REE in alkaline fluids. These numerical predictions allow us to make quantitative interpretations of hydrothermal processes in REE mineral deposits, particularly in carbonatites, and show where future experimental work will be essential in improving our modeling capabilities for these ore-forming processes.
The relatively high and possibly rising incidence of mouth squamous cell carcinoma in nonsmokers, especially women, without obvious cause has been noted by previous authors. Is chronic dental trauma ...and irritation a carcinogen, and what is its importance compared with human papillomavirus (HPV) oropharyngeal cancer in nonsmokers?
To determine whether oral cavity cancers occurred more commonly at sites of dental trauma and how the position of these cancers varied between nonsmokers lacking major identified carcinogens and smokers. If these cancers occurred more frequently at sites of chronic trauma, especially in nonsmokers, it would suggest chronic dental trauma as a possible carcinogen.
A retrospective analysis of 881 patients with oral cavity or oropharyngeal cancers seen through a tertiary referral hospital between 2001 and 2011 was performed.
Patient medical records were analyzed to determine the location of the tumor within the oral cavity and oropharynx and how it relates to patient demographics, smoking and alcohol histories, and comorbidities. Dental histories were also sought, including use of dentures.
Nonsmokers comprised 87 of 390 patients with mouth cancer (22%) and 48 of 334 patients with oropharyngeal cancer (14%). Female nonsmoking patients included 53 with oral cancer (61%) but only 12 with oropharyngeal squamous cell carcinoma (25%). Oral cancers occurred on the lateral tongue, a potential site of chronic dental trauma, in 57 nonsmokers (66%) compared with 107 smokers/ex-smokers (33%) (P < .001). Gingival and floor of mouth lesions occurred in older patients, possibly from chronic denture rubbing. Twenty-six patients had dental abnormalities recorded in close proximity to where their tumor developed.
Oral cavity cancers occur predominantly at sites of potential dental and denture trauma, especially in nonsmokers without other risk factors. Recognizing teeth irritation as a potential carcinogen would have an impact on prevention and treatment strategies.
As part of our Q&A series, Genome Biology spoke to four scientists about their personal experiences as parents in their careers to highlight the challenges of researchers having children and the ...support they need in this regard. Our participants also included a couple (Kristin Tessmar-Raible and Florian Raible), as we were interested to know whether both parents being active researchers can have an impact. One of our participants wishes to remain anonymous.
Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel ...climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico “resurrection experiments” showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.
Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction ...controls phenology, life history, and population fitness across multiple generations in natural seasonal environments.
To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations.
Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates.
Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations.
Research into schoolteachers' professional development often focuses on its subject and pedagogical content, delivery model and mechanisms for and evaluation of professional learning. However, the ...role of the professional development facilitators who lead, plan and deliver professional development activities is under-researched and their importance is therefore undervalued. To address this, there is a need for a greater understanding of how professional development facilitators learn, practice and develop their roles. This study contributes to the evidence base about professional development facilitators through a small-scale study of the facilitators of a teacher professional development programme in the Further Education and Skills sector in England. Using qualitative data drawn from facilitators and participants we identify three areas of practice used by the facilitators: content, pedagogy and embodiment. We describe the facilitators' choices in relation to these practices and how these choices interact, identifying modelling as an important practice where content and pedagogy overlap. We show how facilitators' choices were supported by previous experience, ongoing learning and feedback from participants. Drawing on this evidence we suggest ways in which professional development facilitators might be supported in their own professional learning by exploring and improving their knowledge and understanding of the three areas of practice.
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