ALBERT

Description: We present spectroscopic and photometric solutions for three spotted systems with red giant components. Absolute physical and orbital parameters for these double-lined detached eclipsing binary stars are presented for the first time. These were derived from the V -, and I -band ASAS and WASP photometry, and new radial velocities calculated from high quality optical spectra we obtained with a wide range of spectrographs and using the two-dimensional cross-correlation technique (TODCOR). All of the investigated systems (ASAS J184949-1518.7, BQ Aqr, and V1207 Cen) show the differential evolutionary phase of their components consisting of a main-sequence star or a subgiant and a red giant, and thus constitute very informative objects in terms of testing stellar evolution models. Additionally, the systems show significant chromospheric activity of both components. They can be also classified as classical RS CVn-type stars. Besides the standard analysis of radial velocities and photometry, we applied spectral disentangling to obtain separate spectra for both components of each analysed system which allowed for a more detailed spectroscopic study. We also compared the properties of red giant stars in binaries that show spots, with those that do not, and found that the activity phenomenon is substantially suppressed for stars with Rossby number higher than ~1 and radii larger than ~20 R .

Description: In this work, we investigate the statistical computation of the Boltzmann entropy of statistical samples. For this purpose, we use both histogram and kernel function to estimate the probability density function of statistical samples. We find that, due to coarse-graining, the entropy is a monotonic increasing function of the bin width for histogram or bandwidth for kernel estimation, which seems to be difficult to select an optimal bin width/bandwidth for computing the entropy. Fortunately, we notice that there exists a minimum of the first derivative of entropy for both histogram and kernel estimation, and this minimum point of the first derivative asymptotically points to the optimal bin width or bandwidth. We have verified these findings by large amounts of numerical experiments. Hence, we suggest that the minimum of the first derivative of entropy be used as a selector for the optimal bin width or bandwidth of density estimation. Moreover, the optimal bandwidth selected by the minimum of the first derivative of entropy is purely data-based, independent of the unknown underlying probability density distribution, which is obviously superior to the existing estimators. Our results are not restricted to one-dimensional, but can also be extended to multivariate cases. It should be emphasized, however, that we do not provide a robust mathematical proof of these findings, and we leave these issues with those who are interested in them.

Description: Aims Legumes and non-legumes usually differ in using soil water and nutrients. Both water and nutrients are scarce in the semi-arid Mu Us Sandland where legume and/or non-legume shrubs coexist/dominate. Here, we addressed the responses of legume versus non-legume shrubs to different soil water and nutrient conditions. Methods We conducted an experiment in which a legume ( Hedysarum laeve ) and a non-legume ( Artemisia ordosica ) were used, both of which are dominant species in the Mu Us Sandland. Seedlings of these two species were subjected to three water levels (45.0, 67.5 and 90.0 ml every 3 days) and three nutrient treatments (0, 0.1% and 0.2% nutrient solution every week) during the experiment. Important Findings Interactions between water and nutrients on total biomass, root weight ratio and rain use efficiency (RUE) were detected in A. ordosica but not in H. laeve , suggesting that water effects on A. ordosica but not on H. laeve are dependent on soil nutrients. Nutrient addition alleviated drought stress and increased RUE in A. ordosica . The interspecific differences in response to soil water and nutrients may be linked to the ability of plants to fix nitrogen. In addition, under low-soil water or nutrient conditions, H. laeve produced more biomass than A. ordosica , and the opposite was the case under high-soil resources. The relationship between relative growth rate (RGR) and RUE [or nutrient use efficiency (NUE)] varied with two species. RGR of A. ordosica was positively correlated with both RUE and NUE while RGR of H. laeve was negatively correlated with NUE. The different responses may be linked to the trade-off between high-growth rate and low-resource use efficiency.

Description: This paper explores efficient ways to use flash memory to store online analytical processing (OLAP) data. The particular type of queries considered are range queries using the aggregate functions SUM, COUNT and AVG. The asymmetric cost of reads and writes for flash memory gives higher importance to how updates are handled in a flash memory environment. A popular data structure used for answering OLAP range-sum queries is the prefix sum cube. It allows the range-sum query to be answered in constant time. However, updating the prefix sum cube is very expensive. To overcome this, the -tree was proposed by Chun et al . (Dynamic update cube for range-sum queries. Proc. Int. Conf. Very Large Data Bases, San Francisco, CA, USA, 2001, pp. 521–530. Morgan Kaufmann Publisher). The -tree stores all updates to the prefix sum cube in a separate r-tree. This approach worked well for the hard disk where in-place updates are relatively cheap. However, for flash memory where in-place updates are very expensive, the -tree performs very poorly. We take a four-pronged approach to overcome the problem of expensive in-place updates. The first is efficient caching of updates in RAM. The second is writing out whole trees from RAM to flash memory instead of incrementally updating a disk resident tree. The third is we allow users to trade bounded amounts of accuracy for less updates via lossy compression. Finally, we use a quadtree index structure instead of the R-tree. We prove that the quadtree compression problem is NP-complete. A greedy heuristic is proposed to find near optimal solutions in polynomial time. Various experiments were conducted to compare the proposed algorithms against the existing -tree. The results show that our algorithms consistently outperformed -tree by factors of between 10 and 100. This demonstrates the importance of designing flash memory customized algorithms for OLAP range queries. In addition, among our algorithms, the error bound solutions with a small error bound setting significantly outperform the accurate solution in terms of performance for a variety of parameter settings. This indicates that the error bound algorithms offer users an effective trade-off between execution time and accuracy.

Description: The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we characterized the molecular evolution and expressional diversification of DA1 -like genes. Surveying 354 sequenced genomes revealed 142 DA1 -like genes only in plants, indicating plant-specificity of these genes. The DA1-like protein modular structure was composed of two UIMs (ubiquitin interaction motifs), one LIM-domain (from lin-11 , isl-1 , and mec-3 ), and a conserved C-terminal, and was distinguishable from the already defined three groups of LIM-domain proteins. We further found that the DA1 -like genes diverged into Classes I and II at the ancestor of seed plants and acquired 13 clade-specific residues during their evolutionary history. Moreover, diverse intron size evolution was noted following the transition from size-expandable introns to minimal ones, accompanying the emergence and diversification of angiosperms. Functional diversification as it relates to gene expression was further investigated in soybean. Glycine max DA1 genes showed diverse tissues expression patterns during development and had substantially varied abiotic stress response expression. Thus, variations in the coding regions, intron size, and gene expression contributed to the functional diversification of this gene family. Our data suggest that the evolution of the DA1 -like genes facilitated the development of diverse molecular and functional diversification patterns to accompany the successful radiation of plants into diverse environments during evolution.

Description: Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp . japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.

Description: Ten Eleven Translocation (TET) protein-catalyzed 5mC oxidation not only creates novel DNA modifications, such as 5hmC, but also initiates active or passive DNA demethylation. TETs’ role in the crosstalk with specific histone modifications, however, is largely elusive. Here, we show that TET2-mediated DNA demethylation plays a primary role in the de novo establishment and maintenance of H3K4me3/H3K27me3 bivalent domains underlying methylated DNA CpG islands (CGIs). Overexpression of wild type (WT), but not catalytic inactive mutant (Mut), TET2 in low-TET-expressing cells results in an increase in the level of 5hmC with accompanying DNA demethylation at a subset of CGIs. Most importantly, this alteration is sufficient in making de novo bivalent domains at these loci. Genome-wide analysis reveals that these de novo synthesized bivalent domains are largely associated with a subset of essential developmental gene promoters, which are located within CGIs and are previously silenced due to DNA methylation. On the other hand, deletion of Tet1 and Tet2 in mouse embryonic stem (ES) cells results in an apparent loss of H3K27me3 at bivalent domains, which are associated with a particular set of key developmental gene promoters. Collectively, this study demonstrates the critical role of TET proteins in regulating the crosstalk between two key epigenetic mechanisms, DNA methylation and histone methylation (H3K4me3 and H3K27me3), particularly at CGIs associated with developmental genes.

Description: Recent genome-wide association studies indicate that a simple alteration of Leucine-rich repeat kinase 2 ( LRRK2 ) gene expression may contribute to the etiology of sporadic Parkinson's disease (PD). However, the expression and regulation of LRRK2 protein in the sporadic PD brains remain to be determined. Here, we found that the expression of LRRK2 protein was enhanced in the sporadic PD patients using the frontal cortex tissue from a set of 16 PD patients and 7 control samples. In contrast, no significant difference was detected in the level of LRRK2 mRNA expression between the control and PD cases, suggesting a potential post-transcriptional modification of the LRRK2 protein expression in the sporadic PD brains. Indeed, it was identified that microRNA-205 (miR-205) suppressed the expression of LRRK2 protein through a conserved-binding site at the 3'-untranslated region (UTR) of LRRK2 gene. Interestingly, miR-205 expression was significantly downregulated in the brains of patients with sporadic PD, showing the enhanced LRRK2 protein levels. Also, in vitro studies in the cell lines and primary neuron cultures further established the role of miR-205 in modulating the expression of LRRK2 protein. In addition, introduction of miR-205 prevented the neurite outgrowth defects in the neurons expressing a PD-related LRRK2 R1441G mutant. Together, these findings suggest that downregulation of miR-205 may contribute to the potential pathogenic elevation of LRRK2 protein in the brains of patients with sporadic PD, while overexpression of miR-205 may provide an applicable therapeutic strategy to suppress the abnormal upregulation of LRRK2 protein in PD.

Description: In mitochondria, carbamoyl-phosphate synthetase 1 activity produces carbamoyl phosphate for urea synthesis, and deficiency results in hyperammonemia. Cytoplasmic carbamoyl-phosphate synthetase 2, however, is part of a tri-functional enzyme encoded by CAD ; no human disease has been attributed to this gene. The tri-functional enzyme contains carbamoyl-phosphate synthetase 2 (CPS2), aspartate transcarbamylase (ATCase) and dihydroorotase (DHOase) activities, which comprise the first three of six reactions required for de novo pyrimidine biosynthesis. Here we characterize an individual who is compound heterozygous for mutations in different domains of CAD. One mutation , c.1843-1G〉A, results in an in-frame deletion of exon 13. The other, c.6071G〉A, causes a missense mutation (p.Arg2024Gln) in a highly conserved residue that is essential for carbamoyl-phosphate binding. Metabolic flux studies showed impaired aspartate incorporation into RNA and DNA through the de novo synthesis pathway. In addition, CTP, UTP and nearly all UDP-activated sugars that serve as donors for glycosylation were decreased. Uridine supplementation rescued these abnormalities, suggesting a potential therapy for this new glycosylation disorder.

Description: Coordinated regulation of gene expression that involves activation of lineage specific genes and repression of pluripotency genes drives differentiation of embryonic stem cells (ESC). For complete repression of pluripotency genes during ESC differentiation, chromatin at their enhancers is silenced by the activity of the Lsd1-Mi2/NuRD complex. The mechanism/s that regulate DNA methylation at these enhancers are largely unknown. Here, we investigated the affect of the Lsd1-Mi2/NuRD complex on the dynamic regulatory switch that induces the local interaction of histone tails with the Dnmt3 ATRX-DNMT3-DNMT3L (ADD) domain, thus promoting DNA methylation at the enhancers of a subset of pluripotency genes. This is supported by previous structural studies showing a specific interaction between Dnmt3-ADD domain with H3K4 unmethylated histone tails that is disrupted by histone H3K4 methylation and histone acetylation. Our data suggest that Dnmt3a activity is triggered by Lsd1-Mi2/NuRD-mediated histone deacetylation and demethylation at these pluripotency gene enhancers when they are inactivated during mouse ESC differentiation. Using Dnmt3 knockout ESCs and the inhibitors of Lsd1 and p300 histone modifying enzymes during differentiation of E14Tg2A and ZHBTc4 ESCs, our study systematically reveals this mechanism and establishes that Dnmt3a is both reader and effector of the epigenetic state at these target sites.