Integral D-Finite Functions

We propose a differential analog of the notion of integral closure of algebraic function fields. We present an algorithm for computing the integral closure of the algebra defined by a linear differential operator. Our algorithm is a direct analog of van Hoeij's algorithm for computing integral bases of algebraic function fields

(—)-3-(1-Phenylpropyl)-4-hydroxycoumarin

The title compound [generic name: (—)-phenprocoumon], C18H16O3, monoclinic, P21. Z = 4 with two molecules/asymmetric unit, a= 7·171 (1), b = 17·751 (5), c = 11·752 (2) Å, β = 92·58 (2)°, V = 1494 Å3, Dc = 1·28, d0 = 1·30 (2) g cm-3 is pseudoisostructural with the crystalline racemate as suggested by a similarity in cell constants and symmetry. Structural differences involve small translations and where the racemate crystal contains layers of (—) and layers of (+) enantiomers, the (—) crystal contains one layer nearly identical with the (—) layer in the racemate while the 01olecules in the other layer adopt a different conformation so that packing is similar to that in the (+) layer of the racemate. Already high thermal motion in the racemate is dramatically increased in the enantiomeric structure which has a larger cell volume. Hydrogen bonding occurs along the a direction with O···O distances of 2·617 (5) and 2·587 (6) Å. The final R is 0·094 on 3060 counter-collected data

The Crystal and Molecular Structure and Absolute Configuration of (—)-(\u3ci\u3eS\u3c/i\u3e)-Warfarin

The crystal and molecular structure and the absolute configuration of (—)-(S)-warfarin, C19H1604, have been determined by X-ray crystallographic techniques. Crystals of (—)-(S)-warfarin are orthorhombic, space group P212121, with a=10·883 (3), b=9·562 (3), and c=14·902 (5) Å. Solution of the structure was by direct methods, and refinement by least-squares calculations led to a conventional R of 0·053 (Mo Kα data). The molecule crystallizes as the intramolecular hemiketal and thus may be described as (2S,4S)-2,3H-2-methyl-4-phenyl-5-oxobenzopyrano[3,4-e]dihydropyran-2-ol. The absolute configuration was confirmed by recollecting with Cu Kα radiation a group of reflect ions predicted to have the greatest observable Bijvoet differences based on the anomalous scattering of oxygen and the parameters from the refinement with Mo Kα data. A group of 51 Friedel pairs, 86% of which indicate the S enantiomer, gave a 17% decrease in the residual over the R enantiomer. Refinement of the imaginary part of the anomalous dispersion of oxygen gave a value of 0·037 for Δf

Elemental Abundances in the X-Ray Gas of Early-Type Galaxies with XMM and Chandra Observations

The source of hot gas in elliptical galaxies is thought to be due to stellar mass loss, with contributions from supernova events and possibly from infall from a surrounding environment. This picture predicts supersolar values for the metallicity of the gas toward the inner part of the galaxy, which can be tested by measuring the gas phase abundances. We use high-quality data for 10 nearby early-type galaxy from XMM-Newton, featuring both the EPIC and the Reflection Grating Spectrometer, where the strongest emission lines are detected with little blending; some Chandra data are also used. We find excellent consistency in the elemental abundances between the different XMM instruments and good consistency with Chandra. Differences in abundances with aperture size and model complexity are examined, but large differences rarely occur. For a two-temperature thermal model plus a point source contribution, the median Fe and O abundances are 0.86 and 0.44 of the Solar value, while Si and Mg abundances are similar to that for Fe. This is similar to stellar abundances for these galaxies but supernovae were expected to enhance the gas phase abundances considerably, which is not observed.Comment: 35 pages, 10 figures, accepted for publication in Astrophysical Journa

Identifying and Quantifying Genotypes in Polyclonal Infections due to Single Species

The combination of real-time PCR and capillary electrophoresis permits the rapid identification and quantification of pathogen genotypes

Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)

One of the major virulence factors of the malaria causing parasite is the Plasmodium falciparum encoded erythrocyte membrane protein 1 (PfEMP1). It is translocated to It the membrane of infected erythrocytes and expressed from approximately 60 var genes in a mutually exclusive manner. Switching of var genes allows the parasite to alter functional and antigenic properties of infected erythrocytes, to escape the immune defense and to establish chronic infections. We have developed an efficient method for isolating VAR genes from telomeric and other genome locations by adapting transformation-associated recombination (TAR) cloning, which can then be analyzed and sequenced. For this purpose, three plasmids each containing a homologous sequence representing the upstream regions of the group A, B, and C var genes and a sequence homologous to the conserved acidic terminal segment (ATS) of var genes were generated. Co-transfection with P. falciparum strain ITG2F6 genomic DNA in yeast cells yielded 200 TAR clones. The relative frequencies of clones from each group were not biased. Clones were screened by PCR, as well as Southern blotting, which revealed clones missed by PCR due to sequence mismatches with the primers. Selected clones were transformed into E. coli and further analyzed by RFLP and end sequencing. Physical analysis of 36 clones revealed 27 distinct types potentially representing 50% of the var gene repertoire. Three clones were selected for sequencing and assembled into single var gene containing contigs. This study demonstrates that it is possible to rapidly obtain the repertoire of var genes from P. falciparum within a single set of cloning experiments. This technique can be applied to individual isolates which will provide a detailed picture of the diversity of var genes in the field. This is a powerful tool to overcome the obstacles with cloning and assembly of multi-gene families by simultaneously cloning each member

Platelets Alter Gene Expression Profile in Human Brain Endothelial Cells in an In Vitro Model of Cerebral Malaria

Platelet adhesion to the brain microvasculature has been associated with cerebral malaria (CM) in humans, suggesting that platelets play a role in the pathogenesis of this syndrome. In vitro co-cultures have shown that platelets can act as a bridge between Plasmodium falciparum-infected red blood cells (pRBC) and human brain microvascular endothelial cells (HBEC) and potentiate HBEC apoptosis. Using cDNA microarray technology, we analyzed transcriptional changes of HBEC in response to platelets in the presence or the absence of tumor necrosis factor (TNF) and pRBC, which have been reported to alter gene expression in endothelial cells. Using a rigorous statistical approach with multiple test corrections, we showed a significant effect of platelets on gene expression in HBEC. We also detected a strong effect of TNF, whereas there was no transcriptional change induced specifically by pRBC. Nevertheless, a global ANOVA and a two-way ANOVA suggested that pRBC acted in interaction with platelets and TNF to alter gene expression in HBEC. The expression of selected genes was validated by RT-qPCR. The analysis of gene functional annotation indicated that platelets induce the expression of genes involved in inflammation and apoptosis, such as genes involved in chemokine-, TREM1-, cytokine-, IL10-, TGFβ-, death-receptor-, and apoptosis-signaling. Overall, our results support the hypothesis that platelets play a pathogenic role in CM

Evolutionary Patterning: A Novel Approach to the Identification of Potential Drug Target Sites in Plasmodium falciparum

Malaria continues to be the most lethal protozoan disease of humans. Drug development programs exhibit a high attrition rate and parasite resistance to chemotherapeutic drugs exacerbates the problem. Strategies that limit the development of resistance and minimize host side-effects are therefore of major importance. In this study, a novel approach, termed evolutionary patterning (EP), was used to identify suitable drug target sites that would minimize the emergence of parasite resistance. EP uses the ratio of non-synonymous to synonymous substitutions (ω) to assess the patterns of evolutionary change at individual codons in a gene and to identify codons under the most intense purifying selection (ω≤0.1). The extreme evolutionary pressure to maintain these residues implies that resistance mutations are highly unlikely to develop, which makes them attractive chemotherapeutic targets. Method validation included a demonstration that none of the residues providing pyrimethamine resistance in the Plasmodium falciparum dihydrofolate reductase enzyme were under extreme purifying selection. To illustrate the EP approach, the putative P. falciparum glycerol kinase (PfGK) was used as an example. The gene was cloned and the recombinant protein was active in vitro, verifying the database annotation. Parasite and human GK gene sequences were analyzed separately as part of protozoan and metazoan clades, respectively, and key differences in the evolutionary patterns of the two molecules were identified. Potential drug target sites containing residues under extreme evolutionary constraints were selected. Structural modeling was used to evaluate the functional importance and drug accessibility of these sites, which narrowed down the number of candidates. The strategy of evolutionary patterning and refinement with structural modeling addresses the problem of targeting sites to minimize the development of drug resistance. This represents a significant advance for drug discovery programs in malaria and other infectious diseases

Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63–0.75], p = 1.86×10−18), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21–1.43], p = 3.87×10−11). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50–0.67], p = 1.17×10−12) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53–0.72], p = 8.88×10−10). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41–0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54–1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma