Composition and structure of the centromeric region of rice chromosome 8

Understanding the organization of eukaryotic centromeres has both fundamental and applied importance because of their roles in chromosome segregation, karyotypic stability, and artificial chromosome-based cloning and expression vectors. Using clone-by-clone sequencing methodology, we obtained the complete genomic sequence of the centromeric region of rice (Oryza sativa) chromosome 8. Analysis of 1.97 Mb of contiguous nucleotide sequence revealed three large clusters of CentO satellite repeats (68.5 kb of 155-bp repeats) and >220 transposable element (TE)-related sequences; together, these account for approximately 60% of this centromeric region. The 155-bp repeats were tandemly arrayed head to tail within the clusters, which had different orientations and were interrupted by TE-related sequences. The individual 155-bp CentO satellite repeats showed frequent transitions and transversions at eight nucleotide positions. The 40 TE elements with highly conserved sequences were mostly gypsy-type retrotransposons. Furthermore, 48 genes, showing high BLAST homology to known proteins or to rice full-length cDNAs, were predicted within the region; some were close to the CentO clusters. We then performed a genome-wide survey of the sequences and organization of CentO and RIRE7 families. Our study provides the complete sequence of a centromeric region from either plants or animals and likely will provide insight into the evolutionary and functional analysis of plant centromeres.     

Genes involved in systemic and arterial bed dependent atherosclerosis--Tampere Vascular study

Background

Atherosclerosis is a complex disease with hundreds of genes influencing its progression. In addition, the phenotype of the disease varies significantly depending on the arterial bed.

Methodology/Principal Findings

We characterized the genes generally involved in human advanced atherosclerotic (AHA type V–VI) plaques in carotid and femoral arteries as well as aortas from 24 subjects of Tampere Vascular study and compared the results to non-atherosclerotic internal thoracic arteries (n=6) using genome-wide expression array and QRT-PCR. In addition we determined genes that were typical for each arterial plaque studied. To gain a comprehensive insight into the pathologic processes in the plaques we also analyzed pathways and gene sets dysregulated in this disease using gene set enrichment analysis (GSEA). According to the selection criteria used (>3.0 fold change and p-value <0.05), 235 genes were up-regulated and 68 genes down-regulated in the carotid plaques, 242 genes up-regulated and 116 down-regulated in the femoral plaques and 256 genes up-regulated and 49 genes down-regulated in the aortic plaques. Nine genes were found to be specifically induced predominantly in aortic plaques, e.g., lactoferrin, and three genes in femoral plaques, e.g., chondroadherin, whereas no gene was found to be specific for carotid plaques. In pathway analysis, a total of 28 pathways or gene sets were found to be significantly dysregulated in atherosclerotic plaques (false discovery rate [FDR] <0.25).

Conclusions

This study describes comprehensively the gene expression changes that generally prevail in human atherosclerotic plaques. In addition, site specific genes induced only in femoral or aortic plaques were found, reflecting that atherosclerotic process has unique features in different vascular beds.     

Fish Oil Supplementation Alters the Plasma Lipidomic Profile and Increases Long-Chain PUFAs of Phospholipids and Triglycerides in Healthy Subjects

Background

While beneficial health effects of fish and fish oil consumption are well documented, the incorporation of n-3 polyunsaturated fatty acids in plasma lipid classes is not completely understood. The aim of this study was to investigate the effect of fish oil supplementation on the plasma lipidomic profile in healthy subjects.

Methodology/Principal Findings

In a double-blinded randomized controlled parallel-group study, healthy subjects received capsules containing either 8 g/d of fish oil (FO) (1.6 g/d EPA+DHA) (n = 16) or 8 g/d of high oleic sunflower oil (HOSO) (n = 17) for seven weeks. During the first three weeks of intervention, the subjects completed a fully controlled diet period. BMI and total serum triglycerides, total-, LDL- and HDL-cholesterol were unchanged during the intervention period. Lipidomic analyses were performed using Ultra Performance Liquid Chromatography (UPLC) coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (QTOFMS), where 568 lipids were detected and 260 identified. Both t-tests and Multi-Block Partial Least Square Regression (MBPLSR) analysis were performed for analysing differences between the intervention groups. The intervention groups were well separated by the lipidomic data after three weeks of intervention. Several lipid classes such as phosphatidylcholine, phosphatidylethanolamine, lysophosphatidylcholine, sphingomyelin, phosphatidylserine, phosphatidylglycerol, and triglycerides contributed strongly to this separation. Twenty-three lipids were significantly decreased (FDR<0.05) in the FO group after three weeks compared with the HOSO group, whereas fifty-one were increased including selected phospholipids and triglycerides of long-chain polyunsaturated fatty acids. After seven weeks of intervention the two intervention groups showed similar grouping.

Conclusions/Significance

In healthy subjects, fish oil supplementation alters lipid metabolism and increases the proportion of phospholipids and triglycerides containing long-chain polyunsaturated fatty acids. Whether the beneficial effects of fish oil supplementation may be explained by a remodeling of the plasma lipids into phospholipids and triglycerides of long-chain polyunsaturated fatty acids needs to be further investigated.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01034423","term_id":"NCT01034423"}}NCT01034423     

Widely distributed native and alien plant species differ in arbuscular mycorrhizal associations and related functional trait interactions

It is debated whether alien plants in new environments benefit from being mycorrhizal and whether widely distributed natives and aliens differ in their associations with mycorrhizal fungi. Here, we compared whether species differing in their origin status, i.e. natives, archaeophytes (alien species introduced before the year 1500) and neophytes (introduced after the year 1500), and arbuscular mycorrhizal (AM) status (obligate, facultative, non‐mycorrhizal) differ in their area of occupancy in Germany (i.e. number of occupied grid cells, each ~130 km²). We used generalized linear models, incorporating main effects and up to three‐way interactions combining AM status, origin status and plant functional traits. The latter were chosen to describe the possible trade‐off in carbon allocation either towards the symbiosis or to other plant structures, such as storage organs (significant interactions involving traits were assumed to indicate the existence of such trade‐offs). AM status significantly explained the area of occupancy of natives and neophytes – with facultative mycorrhizal species occupying the largest area in both groups – but was less pronounced among archaeophytes. Archaeophytes may have reduced dependency on AM fungi, as they are generally agricultural weeds and the symbiosis potentially becomes obsolete for plants growing in habitats providing a steady provision of nutrients. Trait interactions between AM status and other functional traits were almost exclusively detected for neophytes. While facultative mycorrhizal neophytes benefit from trade‐offs with other traits related to high C cost in terms of area of occupancy, such trade‐offs were almost absent among natives. This indicates that natives and neophytes benefit differently from the symbiosis and suggests that native AM fungal partners might be less important for neophytic than for native plant species or that more time is required to establish similar relationships between neophytes and native fungal symbionts.     

Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes

Various microbial activities determine the effectiveness of bioremediation processes. In this work, we evaluated the feasibility of gene array hybridization for monitoring the efficiency of biodegradation processes. Biodegradation of ¹⁴C-labelled naphthalene and toluene by the aromatic hydrocarbon-degrading Pseudomonas putida F1, P. putida mt-2 and P. putida G7 was followed in mixed liquid culture microcosm by a preliminary, nylon membrane-based gene array. In the beginning of the study, toluene was degraded rapidly and increased amount of toluene degradation genes was detected by the preliminary gene array developed for the study. After toluene was degraded, naphthalene mineralization started and the amount of naphthalene degradation genes increased as biodegradation proceeded. The amount of toluene degradation genes decreased towards the end of the study. The hybridization signal intensities determined by preliminary gene array were in good agreement with mineralization of naphthalene and toluene and with the amount of naphthalene dioxygenase and toluene dioxygenase genes quantified by dot blot hybridization. The clear correlation between the results obtained by the preliminary array and the biodegradation process suggests that gene array methods can be considered as a promising tool for monitoring the efficiency of biodegradation processes.     

Cellular concentrations of DDB2 regulate dynamic binding of DDB1 at UV-induced DNA damage

Nucleotide excision repair (NER) is the principal pathway for counteracting cytotoxic and mutagenic effects of UV irradiation. To provide insight into the in vivo regulation of the DNA damage recognition step of global genome NER (GG-NER), we constructed cell lines expressing fluorescently tagged damaged DNA binding protein 1 (DDB1). DDB1 is a core subunit of a number of cullin 4-RING ubiquitin ligase complexes. UV-activated DDB1-DDB2-CUL4A-ROC1 ubiquitin ligase participates in the initiation of GG-NER and triggers the UV-dependent degradation of its subunit DDB2. We found that DDB1 rapidly accumulates on DNA damage sites. However, its binding to damaged DNA is not static, since DDB1 constantly dissociates from and binds to DNA lesions. DDB2, but not CUL4A, was indispensable for binding of DDB1 to DNA damage sites. The residence time of DDB1 on the damage site is independent of the main damage-recognizing protein of GG-NER, XPC, as well as of UV-induced proteolysis of DDB2. The amount of DDB1 that is temporally immobilized on damaged DNA critically depends on DDB2 levels in the cell. We propose a model in which UV-dependent degradation of DDB2 is important for the release of DDB1 from continuous association to unrepaired DNA and makes DDB1 available for its other DNA damage response functions.     

Peptidase activities of the 20/26S proteasome and a novel protease in human brain

Many neurodegenerative diseases are characterized by ubiquitin-positive protein aggregates or inclusion bodies. Ubiquitin-conjugated proteins are degraded by the 20/26S proteasome, and reduced proteasome peptidase activities in brain homogenates have been reported in pathologic lesions of Parkinson's and Alzheimer's diseases. However, it is unknown whether crude extracts of human brain contain other proteases having peptidase activities. We found a novel protease of molecular weight of approximately 105 kDa in normal human brain, which exhibited trypsin-like (T-L) and chymotrypsin-like (ChT-L) activities (corresponding to 52% and 21% of the total activities in crude extracts) but not peptidyl glutamyl peptide hydrolase activity. Both T-L and ChT-L activities of this protease were partially inhibited by proteasome inhibitors (MG132, lactacystin) and, in contrast to those of the proteasome, also by sodium dodecyl sulfate. A simple method to obtain a brain fraction specific to the 20/26S proteasome was developed. Our human brain data suggest that T-L and ChT-L activity levels of the proteasome reported previously may include those of the 105 kDa protease, an enzyme of as yet unknown biological significance, and that it is necessary to separate the proteasome from this protease to evaluate the actual status of the ubiquitin-proteasome system in neurodegenerative disorders.     

AM fungal communities inhabiting the roots of submerged aquatic plant <Emphasis Type="Italic">Lobelia dortmanna</Emphasis> are diverse and include a high proportion of novel taxa

While the arbuscular mycorrhizal (AM) symbiosis is known to be widespread in terrestrial ecosystems, there is growing evidence that aquatic plants also form the symbiosis. It has been suggested that symbiosis with AM fungi may represent an important adaptation for isoëtid plants growing on nutrient-poor sediments in oligotrophic lakes. In this study, we address AM fungal root colonization intensity, richness and community composition (based on small subunit (SSU) ribosomal RNA (rRNA) gene sequencing) in five populations of the isoëtid plant species Lobelia dortmanna inhabiting oligotrophic lakes in Southern Sweden. We found that the roots of L. dortmanna hosted rich AM fungal communities and about 15 % of the detected molecular taxa were previously unrecorded. AM fungal root colonization intensity and taxon richness varied along an environmental gradient, being higher in oligotrophic and lower in mesotrophic lakes. The overall phylogenetic structure of this aquatic fungal community differed from that described in terrestrial systems: The roots of L. dortmanna hosted more Archaeosporaceae and fewer Glomeraceae taxa than would be expected based on global data from terrestrial AM fungal communities.     

Seasonal physiological responses of Argania spinosa tree from Mediterranean to semi-arid climate

Argania spinosa (the argan tree) is a slow-growing tree endemic of Morocco, growing on semi-arid areas where no other tree species can live. With the aim of predicting temporal changes in A. spinosa woodlands under a probable increase in aridity, we set off to investigate these questions: how do A. spinosa physiological attributes respond to variations in climatic conditions and seasonality, and which is the set of attributes that most affects tree response to environmental conditions? In three study sites, Beni Snassen (North), High-Atlas (Mountain) and Admine Forest in Agadir (Coastal), gas exchange measurements, photochemical efficiency, leaf water potential and different leaf attributes were monitored in February, July and November of 2006. The Mountain site presents the most continental climate. Trees in this site were the most stressed in summer, having the lowest midday leaf water potential values, photochemical efficiency and assimilation rates. We found a Ψ_md threshold around -4 MPa, below which stomatal conductance responds linearly to Ψ_md. Plants from the North area never reached this threshold during the study period. Although leaf pigments presented a clear seasonal pattern, leaves from Coastal trees exhibit the highest content for each season. The three study sites were separated by two discriminate functions obtained by canonical discriminant analysis. In summer, the Mountain population is separated from the other sites mainly by assimilation rate and F_v/F_m, while in winter transpiration rates and chlorophyll content are the main discriminant variables. Our study shows that A. spinosa trees adjust their physiological status and leaf attributes to environmental conditions allowing plants to thrive under a dry climate. Under a scenario of global change, the distribution of the argan tree likely shifts to milder areas.