Long-lasting Imprint of Former Glassworks on Vegetation Pattern in an Extremely Species-rich Grassland: A Battle of Species Pools on Mesic Soils

Increasing evidence suggests that past human activities have irreversibly changed soil properties and biodiversity patterns. In the White Carpathian Mts (Central-Eastern Europe), a mosaic of hyper-species-rich and species-rich patches have developed in a regularly mown dry grassland in the area of a glassworks abandoned in the eighteenth century. We tested whether and how anthropogenically changed soils affected the distribution of extraordinary species richness. Using magnetometry we detected former furnaces, workspace, waste deposit and unaffected surrounding grasslands and compared their vegetation and environmental conditions. Archaeological features, especially furnaces and waste deposits, showed a higher pH, higher soil concentrations of exchangeable phosphorus, manganese, lead and calcium, and higher productivity. Surrounding grassland showed higher iron and sodium concentrations in the soil, higher N:P ratio in the biomass and higher species richness. Moisture was uniformly lower in soils on archaeological features, where non-trivially a more ‘mesic’ vegetation in terms of European habitat classification occurred. Plant compositional variation was best explained by water-extractable phosphorus. Because nutrient-richer patches were not moister as common elsewhere, and because species richness was only poorly accounted for by productivity, the occurrence of a species-poor ‘mesic’ vegetation on archaeological features was evidently caused by a long-lasting phosphorus oversupply which favours a comparatively small species pool of rather recently arriving species. On the contrary, surrounding phosphorus-poorer grasslands still contain the ancient species pool whose extraordinary size determines the exceptional species richness of grasslands in the study region. Its maintenance or restoration demands a persistent phosphorus deficiency.     

Linking Above- and Belowground Responses to 16 Years of Fertilization,Mowing, and Removal of the Dominant Species in a Temperate Grassland

Species-rich oligotrophic meadows are affected by a wide range of management interventions that influence their functioning and capacity to deliver ecosystem services, but long-term studies on the above- and belowground adaptations to different management tools are still scarce. We focused on the interactive effects of NPK fertilization, mowing, and removal of the initially dominant species (Molinia caerulea) on plant, soil, and microbial responses in wet oligotrophic grassland in a 16-year full-factorial manipulative experiment. Changes in vegetation composition, soil pH, and nutrient availability were accompanied by altered microbial phospholipid fatty acid (PLFA) composition, whereas treatment effects on soil microbial biomass and carbon (C) mineralization were mainly related to changes in soil organic matter (SOM) content and nutrient availability. Fertilization decreased plant species richness aboveground and lowered SOM storage and microbial activity belowground. Mowing preserved high plant diversity and led to more efficient recycling of N within the grassland, whereas Molinia removal significantly affected only plant community composition. Mowing combined with fertilization maintained high species richness only in the short term. Belowground, mowing reduced N leaching from the fertilized system but did not prevent SOM depletion, soil acidification, and concomitant adverse effects on soil microbes. We conclude that annual mowing is the appropriate type of extensive management for oligotrophic species-rich meadows, but the concomitant nutrient depletion should not be compensated for by regular NPK fertilization due to its adverse effects on soil quality.     

Rational confederation of genes and diseases: NGS interpretation via GeneCards,MalaCards and VarElect

Background

A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient’s disease phenotypes. This necessitates bioinformatics tools linked to comprehensive knowledgebases. The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards utility for NGS interpretation as well as for large scale bioinformatic analyses.

Results

VarElect, our NGS interpretation tool, leverages the broad information in the GeneCards suite databases. MalaCards algorithms unify disease-related terms and annotations from 69 sources. Further, MalaCards defines hierarchical relatedness—aliases, disease families, a related diseases network, categories and ontological classifications. GeneCards and MalaCards delineate and share a multi-tiered, scored gene-disease network, with stringency levels, including the definition of elite status—high quality gene-disease pairs, coming from manually curated trustworthy sources, that includes 4500 genes for 8000 diseases. This unique resource is key to NGS interpretation by VarElect. VarElect, a comprehensive search tool that helps infer both direct and indirect links between genes and user-supplied disease/phenotype terms, is robustly strengthened by the information found in MalaCards. The indirect mode benefits from GeneCards’ diverse gene-to-gene relationships, including SuperPaths—integrated biological pathways from 12 information sources. We are currently adding an important information layer in the form of “disease SuperPaths”, generated from the gene-disease matrix by an algorithm similar to that previously employed for biological pathway unification. This allows the discovery of novel gene-disease and disease–disease relationships. The advent of whole genome sequencing necessitates capacities to go beyond protein coding genes. GeneCards is highly useful in this respect, as it also addresses 101,976 non-protein-coding RNA genes. In a more recent development, we are currently adding an inclusive map of regulatory elements and their inferred target genes, generated by integration from 4 resources.

Conclusions

MalaCards provides a rich big-data scaffold for in silico biomedical discovery within the gene-disease universe. VarElect, which depends significantly on both GeneCards and MalaCards power, is a potent tool for supporting the interpretation of wet-lab experiments, notably NGS analyses of disease. The GeneCards suite has thus transcended its 2-decade role in biomedical research, maturing into a key player in clinical investigation.

     

Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3′-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII_170–755, as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.     

Iron-induced lipid peroxidation and protein modification in endoplasmic reticulum membranes. Protection by stobadine

Treatment with FeSO(4)/EDTA (0.2 micromol Fe(II) per mg of protein) was used to study the effect of oxidative stress on lipid peroxidation and structural properties of endoplasmic reticulum (ER) membranes isolated from rabbit brain. Oxidative stress resulted in conjugated diene formation and a decrease of 1-anilino-8-naphthalenesulfonate (ANS) fluorescence in a time-dependent manner. In contrast, fluorescence anisotropy of 1, 6-diphenyl-1,3,5-hexatriene was increased early after the initiation of lipid peroxidation and no further increase was observed after 1, 2 and 3 h of peroxidation. FeSO(4)/EDTA treatment was accompanied by formation of conjugates of lipid peroxidation products with membrane proteins, as detected by the increase in fluorescence excitation (350-360 nm) and emission (440-450 nm) maximum. Oxidative stress also induced a marked decrease of the intrinsic fluorescence of aromatic amino acids, suggesting modification or changes in the environment of these amino acid residue(s). The lipid antioxidant, stobadine, completely prevented the changes of ANS fluorescence and production of peroxidized lipid-protein conjugates whereas tryptophan fluorescence was only partially protected. These results suggest that Fe(II) induces both lipid-mediated- and lipid peroxidation independent-modification of ER membrane proteins. The study also demonstrates that stobadine is a potent inhibitor of Fe(II)-induced protein modification.     

Soil chemical properties affect the concentration of elements (N,P, K,Ca, Mg,As, Cd,Cr, Cu,Fe, Mn,Ni, Pb,and Zn) and their distribution between organs of Rumex obtusifolius

Background and aims

The ionome (elemental composition) of grassland species has rarely been studied at the level of individual organs and little is known about effects of soil chemical properties on the ionome. Using the model oxalate plant Rumex obtusifolius, we asked how its biomass production and the distribution of elements between its organs is affected by soil chemical properties.

Methods

We established a pot experiment with R. obtusifolius planted in acidic non-contaminated control and in slightly acidic and alkaline soils anthropogenically contaminated by the risk elements As, Cd, Pb, and Zn. Both contaminated soils were untreated and treated by lime and superphosphate. We determined biomass production and the concentrations of elements in its organs.

Results

Biomass production was negatively related to the mobility of micro- and risk elements. Restricted transport of micro- and risk elements from belowground organs into leaves was recorded in untreated contaminated soils. In both lime-treated soils and in superphosphate-treated alkaline soil, elevated transport of micro- and risk elements from belowground organs into leaves was recorded in comparison to untreated contaminated soils. The lowest concentrations of micro- and risk elements were recorded in stems and seeds, followed by belowground organs and leaves.

Conclusions

R. obtusifolius is an As-, Cd-, Pb-, and Zn-excluder and is sensitive to high availability of micro- and risk elements in the soil. Soil chemical properties affect the distribution of essential elements within the plant greatly.     

Cadmium uptake,localization and stress-induced morphogenic response in the fern Pteris vittata

Cadmium uptake, tissue localization and structural changes induced at cellular level are essential to understand Cd tolerance in plants. In this study we have exposed plants of Pteris vittata to different concentrations of CdCl₂ (0, 30, 60, 100 μM) to evaluate the tolerance of the fern to cadmium. Cadmium content determination and its histochemical localization showed that P. vittata not only takes up, but also transports and accumulates cadmium in the aboveground tissues, delocalizing it mainly in the less bioactive tissues of the frond, the trichomes and the scales. Cadmium tolerance in P. vittata was strictly related to morphogenic response induced by the metal itself in the root system. Adaptive response regarded changes of the root apex size, the developmental pattern of root hairs, the differentiation of xylem elements and endodermal suberin lamellae. All the considered parameters suggest that, in our experimental conditions, 60 μM of Cd may represent the highest concentration that P. vittata can tolerate; indeed this Cd level even improves the absorbance features of the root and allows good transport and accumulation of the metal in the fronds. The results of this study can provide useful information for phytoremediation strategies of soils contaminated by Cd, exploiting the established ability of P. vittata to transport, delocalize in the aboveground biomass and accumulate polluting metals.     

Mutations in DNAJC5, encoding cysteine-string protein alpha, cause autosomal-dominant adult-onset neuronal ceroid lipofuscinosis

Autosomal-dominant adult-onset neuronal ceroid lipofuscinosis (ANCL) is characterized by accumulation of autofluorescent storage material in neural tissues and neurodegeneration and has an age of onset in the third decade of life or later. The genetic and molecular basis of the disease has remained unknown for many years. We carried out linkage mapping, gene-expression analysis, exome sequencing, and candidate-gene sequencing in affected individuals from 20 families and/or individuals with simplex cases; we identified in five individuals one of two disease-causing mutations, c.346_348delCTC and c.344T>G, in DNAJC5 encoding cysteine-string protein alpha (CSPα). These mutations-causing a deletion, p.Leu116del, and an amino acid exchange, p.Leu115Arg, respectively-are located within the cysteine-string domain of the protein and affect both palmitoylation-dependent sorting and the amount of CSPα in neuronal cells. The resulting depletion of functional CSPα might cause in parallel the presynaptic dysfunction and the progressive neurodegeneration observed in affected individuals and lysosomal accumulation of misfolded and proteolysis-resistant proteins in the form of characteristic ceroid deposits in neurons. Our work represents an important step in the genetic dissection of a genetically heterogeneous group of ANCLs. It also confirms a neuroprotective role for CSPα in humans and demonstrates the need for detailed investigation of CSPα in the neuronal ceroid lipofuscinoses and other neurodegenerative diseases presenting with neuronal protein aggregation.     

Population history of the Red Sea--genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup

Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.