Rescue of heavy metal effects on cell physiology of the algal model system Micrasterias by divalent ions

Recent studies have shown that metals such as copper, zinc, aluminum, cadmium, chromium, iron and lead cause severe dose-dependent disturbances in growth, morphogenesis, photosynthetic and respiratory activity as well as on ultrastructure and function of organelles in the algal model system Micrasterias denticulata ( Volland et al., 2011, Volland et al., 2012 and Andosch et al., 2012). In the present investigation we focus on amelioration of these adverse effects of cadmium, chromium and lead by supplying the cells with different antioxidants and essential micronutrients to obtain insight into metal uptake mechanisms and subcellular metal targets. This seems particularly interesting as Micrasterias is adapted to extremely low-concentrated, oligotrophic conditions in its natural bog environment.     

Assessing the effects of architectural variations on light partitioning within virtual wheat–pea mixtures

Background and Aims

Predicting light partitioning in crop mixtures is a critical step in improving the productivity of such complex systems, and light interception has been shown to be closely linked to plant architecture. The aim of the present work was to analyse the relationships between plant architecture and light partitioning within wheat–pea (Triticum aestivum–Pisum sativum) mixtures. An existing model for wheat was utilized and a new model for pea morphogenesis was developed. Both models were then used to assess the effects of architectural variations in light partitioning.

Methods

First, a deterministic model (L-Pea) was developed in order to obtain dynamic reconstructions of pea architecture. The L-Pea model is based on L-systems formalism and consists of modules for ‘vegetative development’ and ‘organ extension’. A tripartite simulator was then built up from pea and wheat models interfaced with a radiative transfer model. Architectural parameters from both plant models, selected on the basis of their contribution to leaf area index (LAI), height and leaf geometry, were then modified in order to generate contrasting architectures of wheat and pea.

Key results

By scaling down the analysis to the organ level, it could be shown that the number of branches/tillers and length of internodes significantly determined the partitioning of light within mixtures. Temporal relationships between light partitioning and the LAI and height of the different species showed that light capture was mainly related to the architectural traits involved in plant LAI during the early stages of development, and in plant height during the onset of interspecific competition.

Conclusions

In silico experiments enabled the study of the intrinsic effects of architectural parameters on the partitioning of light in crop mixtures of wheat and pea. The findings show that plant architecture is an important criterion for the identification/breeding of plant ideotypes, particularly with respect to light partitioning.     

Validating a rapid,real-time,PCR-based direct mutation detection assay for preimplantation genetic diagnosis

Although co-amplification of polymorphic microsatellite markers is the current gold standard for preimplantation genetic diagnosis (PGD) of single-gene disorders (SGD), this approach can be hampered by the lack of availability of informative markers. We recently (2011) devised a novel in-house assay for PGD of aromatic l-amino acid decarboxylase deficiency, based on an amplification refractory mutation system and quantitative PCR (ARMS-qPCR). The objective of the present study was to verify ARMS-qPCR in a cohort of 20 PGD cycles with a diverse group of SGDs (15 couples at risk for 10 SGDs). Day-3 cleavage-stage embryos were subjected to biopsy and genotyping, followed by fresh embryo transfer (FET). The diagnostic rate was 82.9%; unaffected live births were achieved in 9 of 20 FET cycles (45%), with only one false negative (among 54 transferred embryos). Overall, the ARMS-qPCR had frequent allele-dropout (ADO), rendering it inappropriate as the sole diagnostic method (despite a favorable live-birth rate). Regardless, it has the potential to complement the current gold-standard methodology, especially when trophectoderm biopsy becomes a preferred option and genotyping needs to be timely enough to enable FET.     

Genotype-based databases for variants causing rare diseases

Inherited diseases are the result of DNA sequence changes. In recessive diseases, the clinical phenotype results from the combined functional effects of variants in both copies of the gene. In some diseases there is often considerable variability of clinical presentation or disease severity, which may be predicted by the genotype. Additional effects may be triggered by environmental factors, as well as genetic modifiers which could be nucleotide polymorphisms in related genes, e.g. maternal ApoE or ABCA1 genotypes which may have an influence on the phenotype of SLOS individuals. Here we report the establishment of genotype variation databases for various rare diseases which provide individual clinical phenotypes associated with genotypes and include data about possible genetic modifiers. These databases aim to be an easy public access to information on rare and private variants with clinical data, which will facilitate the interpretation of genetic variants.     

Endometrial stromal cells and decidualized stromal cells: Origins,transformation and functions

Decidualization of endometrium, which is characterized by endometrial stromal cell (ESC) decidualization, vascular reconstruction, immune cell recruitment, and plentiful molecule production, is a crucial step for uterus to become receptive for embryo. When implantation takes place, ESCs surround and directly interact with embryo. Decidualized stromal cells (DSCs) are of great importance in endometrial decidualization, having a broad function in regulating immune activity and vascular remodeling of uterus. DSCs are shown to have a higher metabolic level and looser cytoskeleton than ESCs. What's the origin of ESCs and how ESCs successfully transform into DSCs had puzzled scientists in the last decades. Breakthrough had been achieved recently, and many studies had elucidated some of the characters and functions of DSCs. However, several questions still remain unclear. This paper reviews current understanding of where ESCs come from and how ESCs differentiate into DSCs, summarizes some characters and functions of DSCs, analyzes current studies and their limitations and points out research areas that need further investigation.     

Rehabilitating Seagrass by Facilitating Recruitment: Improving Chances for Success

Attempts to arrest seagrass loss through numerous rehabilitation methods have traditionally produced inconsistent results. On Australia's southern coast, hessian bags made from biodegradable jute fibers show promise for rehabilitating Amphibolis antarctica by facilitating recruitment of seedlings in situ. Testing ways to improve the performance of bags (i.e. increasing seagrass recruitment and establishment) showed that bags with a coarse outer weave of hessian facilitated greater seedling densities (approximately 1700 individuals/m²) than bags with a fine outer weave, but the content of bags (sand vs. sand and rubble mixture) had little effect. Isolated bags facilitated greater longer term densities than bags grouped together, while similar densities were sampled up to 80 m away from a natural meadow. Lastly, bags that had spent less time in situ initially facilitated more recruits than older bags, but longer term (21–32 months) retention was similar among bag ages. Collectively, the results suggest hessian bags can be a relatively simple, cost‐effective, and environmentally friendly method for rehabilitating Amphibolis seagrass, with few considerations in their use other than their physical architecture and arrangement (e.g. isolated coarse‐weave bags).     

Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.     

Forests on thawing permafrost: fragmentation,edge effects,and net forest loss

Much of the world's boreal forest occurs on permafrost (perennially cryotic ground). As such, changes in permafrost conditions have implications for forest function and, within the zone of discontinuous permafrost (30–80% permafrost in areal extent), distribution. Here, forested peat plateaus underlain by permafrost are elevated above the surrounding permafrost‐free wetlands; as permafrost thaws, ground surface subsidence leads to waterlogging at forest margins. Within the North American subarctic, recent warming has produced rapid, widespread permafrost thaw and corresponding forest loss. Although permafrost thaw‐induced forest loss provides a natural analogue to deforestation occurring in more southerly locations, we know little about how fragmentation relates to subsequent permafrost thaw and forest loss or the role of changing conditions at the edges of forested plateaus. We address these knowledge gaps by (i) examining the relationship of forest loss to the degree of fragmentation in a boreal peatland in the Northwest Territories, Canada; and (ii) quantifying associated biotic and abiotic changes occurring across forest‐wetland transitions and extending into the forested plateaus (i.e., edge effects). We demonstrate that the rate of forest loss correlates positively with the degree of fragmentation as quantified by perimeter to area ratio of peat plateaus (edge : area). Changes in depth of seasonal thaw, soil moisture, and effective leaf area index (LAI_e) penetrated the plateau forests by 3–15 m. Water uptake by trees was sevenfold greater in the plateau interior than at the edges with direct implications for tree radial growth. A negative relationship existed between LAI_e and soil moisture, suggesting that changes in vegetation physiological function may contribute to changing edge conditions while simultaneously being affected by these changes. Enhancing our understanding of mechanisms contributing to differential rates of permafrost thaw and associated forest loss is critical for predicting future interactions between the land surface processes and the climate system in high‐latitude regions.     

Urban expansion dynamics and natural habitat loss in China: a multiscale landscape perspective

China's extensive urbanization has resulted in a massive loss of natural habitat, which is threatening the nation's biodiversity and socioeconomic sustainability. A timely and accurate understanding of natural habitat loss caused by urban expansion will allow more informed and effective measures to be taken for the conservation of biodiversity. However, the impact of urban expansion on natural habitats is not well‐understood, primarily due to the lack of accurate spatial information regarding urban expansion across China. In this study, we proposed an approach that can be used to accurately summarize the dynamics of urban expansion in China over two recent decades (1992–2012), by integrating data on nighttime light levels, a vegetation index, and land surface temperature. The natural habitat loss during the time period was evaluated at the national, ecoregional, and local scales. The results revealed that China had experienced extremely rapid urban growth from 1992 to 2012 with an average annual growth rate of 8.74%, in contrast with the global average of 3.20%. The massive urban expansion has resulted in significant natural habitat loss in some areas in China. Special attention needs to be paid to the Pearl River Delta, where 25.79% or 1518 km² of the natural habitat and 41.99% or 760 km² of the local wetlands were lost during 1992–2012. This raises serious concerns about species viability and biodiversity. Effective policies and regulations must be implemented and enforced to sustain regional and national development in the context of rapid urbanization.