CWRML: representing crop wild relative conservation and use data in XML

Background Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange. Results Crop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate. Conclusion CWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may be valuable, particularly with regard to the representation of population-specific data and utilisation potential. As crop wild relatives are intrinsically no different to other wild plant species there is potential for the inclusion of CWRML data elements in the emerging standards for representation of biodiversity data

Inference of breed structure in farm animals: Empirical comparison between snp and microsatellite performance

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST ), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number

Late Little Ice Age palaeoenvironmental records from the Anzali and Amirkola Lagoons (south Caspian Sea): Vegetation and sea level changes

This is a postprint version of the article. The official published article can be found from the link below - Copyright @ 2011 Elsevier Ltd.Two internationally important Ramsar lagoons on the south coast of the Caspian Sea (CS) have been studied by palynology on short sediment cores for palaeoenvironmental and palaeoclimatic investigations. The sites lie within a small area of very high precipitation in a region that is otherwise dry. Vegetation surveys and geomorphological investigations have been used to provide a background to a multidisciplinary interpretation of the two sequences covering the last four centuries. In the small lagoon of Amirkola, the dense alder forested wetland has been briefly disturbed by fire, followed by the expansion of rice paddies from AD1720 to 1800. On the contrary, the terrestrial vegetation reflecting the diversity of the Hyrcanian vegetation around the lagoon of Anzali remained fairly complacent over time. The dinocyst and non-pollen palynomorph assemblages, revealing changes that have occurred in water salinity and water levels, indicate a high stand during the late Little Ice Age (LIA), from AD < 1620 to 1800–1830. In Amirkola, the lagoon spit remained intact over time, whereas in Anzali it broke into barrier islands during the late LIA, which merged into a spit during the subsequent sea level drop. A high population density and infrastructure prevented renewed breaking up of the spit when sea level reached its maximum (AD1995). Similar to other sites in the region around the southern CS, these two lagoonal investigations indicate that the LIA had a higher sea level as a result of more rainfall in the drainage basin of the CS.The coring and the sedimentological analyses were funded by the Iranian National Institute for Oceanography in the framework of a research project entitled “Investigation of the Holocene sediment along the Iranian coast of Caspian Sea: central Guilan”. The radiocarbon date of core HCGL02 was funded by V. Andrieu (Europôle Méditerranéen de l'Arbois, France) and that of core HCGA04 by Brunel University

Constitutive RB1 mutation in a child conceived by in vitro fertilization: implications for genetic counseling

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to identify mutations associated with bilateral retinoblastoma in a quadruplet conceived by in vitro fertilization, and to trace the parental origin of mutations in the four quadruplets and their father.</p> <p>Methods</p> <p>Mutational screening was carried out by sequencing. Genotyping was carried out for determining quadruplet zygosity.</p> <p>Results</p> <p>The proband was a carrier of a novel <it>RB1</it> constitutive mutation (g.2056C>G) which was not detected in her father or her unaffected sisters, and of two other mutations (g.39606 C>T and g.174351T>A) also present in two monozygotic sisters. The novel mutation probably occurred de novo while the others were of likely maternal origin. The novel mutation, affecting the Kozak consensus at the 5'UTR of <it>RB1</it> and g.174351T>A were likely associated to retinoblastoma in the proband.</p> <p>Conclusion</p> <p>Molecular diagnosis of retinoblastoma requires genotypic data of the family for determining hereditary transmission. In the case of children generated by IVF with oocytes from an anonymous donor which had been stored in a cell repository, this might not be successfully accomplished, making precise diagnosis impracticable for genetic counseling.</p

Drought mildly reduces plant dominance in a temperate prairie ecosystem across years

1. Shifts in dominance and species reordering can occur in response to global change. However, it is not clear how altered precipitation and disturbance regimes interact to affect species composition and dominance. 2. We explored community‐level diversity and compositional similarity responses, both across and within years, to a manipulated precipitation gradient and annual clipping in a mixed‐grass prairie in Oklahoma, USA. We imposed seven precipitation treatments (five water exclusion levels [−20%, −40%, −60%, −80%, and −100%], water addition [+50%], and control [0% change in precipitation]) year‐round from 2016 to 2018 using fixed interception shelters. These treatments were crossed with annual clipping to mimic hay harvest. 3. We found that community‐level responses were influenced by precipitation across time. For instance, plant evenness was enhanced by extreme drought treatments, while plant richness was marginally promoted under increased precipitation. 4. Clipping promoted species gain resulting in greater richness within each experimental year. Across years, clipping effects further reduced the precipitation effects on community‐level responses (richness and evenness) at both extreme drought and added precipitation treatments. 5. Synthesis: Our results highlight the importance of studying interactive drivers of change both within versus across time. For instance, clipping attenuated community‐level responses to a gradient in precipitation, suggesting that management could buffer community‐level responses to drought. However, precipitation effects were mild and likely to accentuate over time to produce further community change.Open Access fees paid for in whole or in part by the University of Oklahoma Libraries. This study was financially supported by NSF Office of Experimental Program to Stimulate Competitive Research (OIA‐1301789) and Office of the Vice President for Research, University of Oklahoma.Ye

Modern pollen rain–vegetation relationships along a forest–steppe transect in the Golestan National Park, NE Iran

Pollen rain-vegetation relationships were studied over a forest-steppe transect in Golestan National Park, NE Iran. The surface pollen percentages were compared to the vegetation composition of the respective vegetation types in 18 sampling points using both descriptive and numerical approaches. Hyrcanian lowland forests are characterized by pollen assemblages dominated by Quercus, Carpinus betulus and low frequencies of Zelkova carpinifolia. Both Parrotia persica and Zelkova carpinifolia show a very low pollen representation in modern surface samples, an under-representation that should be taken into account in the interpretation of past vegetation records. Transitional communities between the forest and steppe including Acer monspessulanum subsp. turcomanicum, Crataegus and Paliurus scrubs, Juniperus excelsa woodlands and shrub-steppe patches are more difficult to distinguish in pollen assemblages, however, they are characterized by higher values of the dominant shrub species. The transitional vegetation communities at the immediate vicinity of the forest show also a substantial amount of grass pollen. Many insect-pollinated taxa are strongly under-represented in the pollen rain including most of the rosaceous trees and shrubs, Rhamnus, Paliurus, Acer and Berberis. Artemisia steppes are characterized by very high values of Artemisia pollen and the near absence of tree pollen

Plant communities as a tool in temporary ponds conservation in SW Portugal

Pond conservationTemporary ponds are seasonal wetlands annually subjected to extreme and unstable ecological conditions, neither truly aquatic nor truly terrestrial. This habitat and its flora have been poorly studied and documented because of the ephemeral character of the flora, the changeable annual weather that has a great effect on the small, herbaceous taxa and the declining abundance of temporary ponds. The objectives of this study are: (a) to define plant community diversity in terms of floristic composition of ephemeral wetlands in SW Portugal, (b) to identify temporary pond types according to their vegetation composition and (c) to identify those ponds that configure the European community priority habitat (3170* – Mediterranean temporary ponds). Vegetation sampling was conducted in 29 ponds, identifying 168 species grouped among 15 plant communities. Soil texture, pH, organic C and N content were measured, but only N and percent of clay appear to be related with the distribution of each community type. The results showed that ephemeral wetlands could be classified into four type: vernal pools, marshlands, deep ponds and disturbed wetlands. Vernal pools correspond to the Mediterranean temporary ponds (3170*), protected as priority habitat under the EU Habitats Directive. Submersed Isoetes species (Isoetes setaceum and Isoetes velatum) represents, together with Eryngium corniculatum, the indicator species for vernal pools. We identify also indicator plant communities of this priority habitat, namely I. setaceum and E. corniculatum– Baldellia ranunculoides plant communities. In this region, the conservation of temporary ponds has so far been compatible with traditional agricultural activities, but today these ponds are endangered by the intensification of agriculture and the loss of traditional land use practices and by the development of touris

Chromosome alterations in human hepatocellular carcinomas correlate with aetiology and histological grade – results of an explorative CGH meta-analysis

All available comparative genomic hybridisation (CGH) analyses (n=31, until 12/2003) of human hepatocellular carcinomas (HCCs; n=785) and premalignant dysplastic nodules (DNs; n=30) were compiled and correlated with clinical and histological parameters. The most prominent amplifications of genomic material were present in 1q (57.1%), 8q (46.6%), 6p (22.3%), and 17q (22.2%), while losses were most prevalent in 8p (38%), 16q (35.9%), 4q (34.3%), 17p (32.1%), and 13q (26.2%). Deletions of 4q, 16q, 13q, and 8p positively correlated with hepatitis B virus aetiology, while losses of 8p were more frequently found in hepatitis C virus-negative cases. In poorly differentiated HCCs, 13q and 4q were significantly under-represented. Moreover, gains of 1q were positively correlated with the occurrence of all other high-frequency alterations in HCCs. In DNs, amplifications were most frequently present in 1q and 8q, while deletions occurred in 8p, 17p, 5p, 13q, 14q, and 16q. In conclusion, aetiology and dedifferentiation correlate with specific genomic alterations in human HCCs. Gains of 1q appear to be rather early events that may predispose to further chromosomal abnormalities. Thus, explorative CGH meta-analysis generates novel and testable hypotheses regarding the cause and functional significance of genomic alterations in human HCCs