geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome

Genetic variation, gene expression and DNA methylation influence each other in a complex way. To study the impact of sequence variation and DNA methylation on gene expression, we generated geno⁵mC, a database that contains statistically significant SNP-CpG associations that are biologically classified either through co-localization with known regulatory regions (promoters and enhancers), or through known correlations with the expression levels of nearby genes. The SNP rs727563 can be used to illustrate the usefulness of this approach. This SNP has been associated with inflammatory bowel disease through GWAS, but it is not located near any gene related to this phenotype. However, geno⁵mC reveals that rs727563 is associated with the methylation state of several CpGs located in promoter regions of genes reported to be involved in inflammatory processes. This case exemplifies how geno⁵mC can be used to infer relevant and previously unknown interactions between described disease-associated SNPs and their functional targets.

Putting patients at the center of kidney care transitions: PREPARE NOW, a cluster randomized controlled trial

Care for patients transitioning from chronic kidney disease to kidney failure often falls short of meeting patients' needs. The PREPARE NOW study is a cluster randomized controlled trial studying the effectiveness of a pragmatic health system intervention, 'Patient Centered Kidney Transition Care,' a multi-component health system intervention designed to improve patients' preparation for kidney failure treatment. Patient-Centered Kidney Transition Care provides a suite of new electronic health information tools (including a disease registry and risk prediction tools) to help providers recognize patients in need of Kidney Transitions Care and focus their attention on patients' values and treatment preferences. Patient-Centered Kidney Transition Care also adds a 'Kidney Transitions Specialist' to the nephrology health care team to facilitate patients' self-management empowerment, shared-decision making, psychosocial support, care navigation, and health care team communication. The PREPARE NOW study is conducted among eight [8] outpatient nephrology clinics at Geisinger, a large integrated health system in rural Pennsylvania. Four randomly selected nephrology clinics employ the Patient Centered Kidney Transitions Care intervention while four clinics employ usual nephrology care. To assess intervention effectiveness, patient reported, biomedical, and health system outcomes are collected annually over a period of 36 months via telephone questionnaires and electronic health records. The PREPARE NOW Study may provide needed evidence on the effectiveness of patient-centered health system interventions to improve nephrology patients' experiences, capabilities, and clinical outcomes, and it will guide the implementation of similar interventions elsewhere.

TRIAL REGISTRATION

NCT02722382.

On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica

Liver flukes represent a paraphyletic group of endoparasitic flatworms that significantly affect man either indirectly due to economic damage on livestock or directly as pathogens. A range of studies have focussed on how these macroscopic organisms can evade the immune system and live inside a hostile environment such as the mammalian liver and bile ducts. Recently, microRNAs, a class of short noncoding gene regulators, have been proposed as likely candidates to play roles in this scenario. MicroRNAs (miRNAs) are key players in development and pathogenicity and are highly conserved between metazoans: identical miRNAs can be found in flatworms and mammalians. Interestingly, miRNAs are enriched in extracellular vesicles (EVs) which are secreted by most cells. EVs constitute an important mode of parasite/host interaction, and recent data illustrate that miRNAs play a vital part. We have demonstrated the presence of miRNAs in the EVs of the trematode species Dicrocoelium dendriticum and Fasciola hepatica (Fhe) and identified potential immune-regulatory miRNAs with targets in the host. After our initial identification of miRNAs expressed by F. hepatica, an assembled genome and additional miRNA data became available. This has enabled us to update the known complement of miRNAs in EVs and speculate on potential immune-regulatory functions that we review here.

Anomalous impurity segregation and local bonding fluctuation in l-Si

Anomalous impurity redistribution after a laser irradiation process in group-IV elements has been reported in numerous papers. In this Letter, we correlate this still unexplained behavior with the peculiar bonding character of the liquid state of group-IV semiconductors. Analyzing the B-Si system in a wide range of experimental conditions we demonstrate that this phenomenon derives from the non-Fickian diffusion transport of B in l-Si. The proposed diffusion model relies on the balance between two impurity states in different bonding configurations: one migrating at higher diffusivity than the other. This microscopic mechanism explains the anomalous B segregation, whereas accurate comparisons between experimental chemical profiles and simulation results validate the model.

Segmentation of time series with long-range fractal correlations

Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nonstationarities. To avoid this oversegmentation, we present a segmentation algorithm which takes as a reference for homogeneity, instead of a random i.i.d. series, a correlated series modeled by a fractional noise with the same degree of correlations as the series to be segmented. We apply our algorithm to artificial series with long-range correlations and show that it systematically detects only the change-points produced by real nonstationarities and not those created by the correlations of the signal. Further, we apply the method to the sequence of the long arm of human chromosome 21, which is known to have long-range fractal correlations. We obtain only three segments that clearly correspond to the three regions of different G + C composition revealed by means of a multi-scale wavelet plot. Similar results have been obtained when segmenting all human chromosome sequences, showing the existence of previously unknown huge compositional superstructures in the human genome.

High-level organization of isochores into gigantic superstructures in the human genome

Human DNA shows a complex structure with compositional features at many scales; the isochores--long DNA segments (~10⁵ bp) of relatively homogeneous guanine-cytosine (G + C) content--are the largest well-documented and well-analyzed compositional structures. However, we report here on the existence of a high-level compositional organization of isochores in the human genome. By using a segmentation algorithm incorporating the long-range correlations existing in human DNA, we find that every chromosome is composed of a few huge segments (~ 10⁷ bp) of relatively homogeneous G + C content, which become the largest compositional organization of the genome. Finally, we show evidence of the biological relevance of these superstructures, pointing to a large-scale functional organization of the human genome.

Level statistics of words: finding keywords in literary texts and symbolic sequences

Using a generalization of the level statistics analysis of quantum disordered systems, we present an approach able to extract automatically keywords in literary texts. Our approach takes into account not only the frequencies of the words present in the text but also their spatial distribution along the text, and is based on the fact that relevant words are significantly clustered (i.e., they self-attract each other), while irrelevant words are distributed randomly in the text. Since a reference corpus is not needed, our approach is especially suitable for single documents for which no a priori information is available. In addition, we show that our method works also in generic symbolic sequences (continuous texts without spaces), thus suggesting its general applicability.

Identifying characteristic scales in the human genome

The scale-free, long-range correlations detected in DNA sequences contrast with characteristic lengths of genomic elements, being particularly incompatible with the isochores (long, homogeneous DNA segments). By computing the local behavior of the scaling exponent alpha of detrended fluctuation analysis (DFA), we discriminate between sequences with and without true scaling, and we find that no single scaling exists in the human genome. Instead, human chromosomes show a common compositional structure with two characteristic scales, the large one corresponding to the isochores and the other to small and medium scale genomic elements.

The progesterone antagonist onapristone increases the effectiveness of oxytocin to produce delivery without changing the myometrial oxytocin receptor concentrations

The progesterone antagonist onapristone was used in guinea pigs during late pregnancy (43 +/- 2 days after coitus) and before term (day 61 after coitus) to investigate the role of progesterone on uterine reactivity to exogenous oxytocin, concentration of oxytocin receptors, and gap junctions in the myometrium. Onapristone priming increased the ability of oxytocin to induce delivery during late pregnancy and before term by factors of greater than or equal to 30 and approximately 10, respectively. The intrauterine pressure recording on day 43 after coitus revealed phasic, laborlike contractions in response to oxytocin in onapristone-treated animals, in contrast to tonic reactions in controls. The increase in the oxytocin response in onapristone-treated animals was not associated with an increase in myometrial oxytocin receptor concentrations either during late pregnancy or before term. By contrast, treatment with onapristone significantly decreased the input resistance of myometrial cells in guinea pigs in late pregnancy (43 +/- 1 day after coitus) to the level of animals at term. This was associated with a marked increase in myometrial gap junctions stained with antibodies against connexin 43. These results indicate that progesterone may control myometrial reactivity to oxytocin in pregnant guinea pigs by effects on postreceptor events mainly by suppressing the gap junctions.

Identification and enzymatic deglycosylation of the myometrial oxytocin receptor using a radioiodinated photoreactive antagonist

To identify and characterize oxytocin receptors, a 125I-labeled photoreactive oxytocin antagonist was synthesized. The specific oxytocin antagonist [1-(beta-mercapto-beta,beta- cyclopentamethylenepropionic acid), 2-O-methyltyrosine,4-threonine,8- ornithine,9-tyrosylamide]oxytocin ([Mca,Tyr(O-Me)2,Thr4,Orn8,Tyr9-NH2]oxytocin) described by Elands et al. (Elands, J., Barberis, C., Jard, S., Tribollet, E., Dreifuss, J.-J., Bankowski, K., Manning, M., and Sawyer, W. H. (1987) Eur. J. Pharmacol. 147, 192-207) bound to the guinea pig uterine oxytocin receptor with high affinity (apparent Kd = 0.74 nM). The introduction of a 4-azidophenylamidino group at Orn8 resulted in the photoreactive ligand [Mca1,Tyr(O-Me)2,Thr4,Orn(4-azidophenylamidino)8,Tyr9- NH2]oxytocin, which retained the high binding affinity (Kd = 0.69 nM) of the parent compound. The photoreactive antagonist monoiodinated at Tyr9 had approximately double (Kd = 0.39 nM) the affinity of the photoreactive antagonist and several times that of oxytocin (Kd = 2.6 nM) for the guinea pig uterine oxytocin receptor. In photo-affinity labeling experiments using myometrial membranes obtained from guinea pigs during late pregnancy, the 125I-labeled photoreactive antagonist specifically labeled a protein with an apparent molecular mass of between 68 and 80 kDa: the labeling of this protein was completely suppressed by a 100-fold molar excess of oxytocin and oxytocin receptor-specific agonists, but not by vasopressin analogues specific for V1 or V2 receptors or by other peptide hormones. The ability of oxytocin to suppress labeling was decreased in the presence of guanosine 5'-O-(thiotriphosphate) or in the absence of Mn2+. Digestion of the photolabeled oxytocin receptor with endoglycosidase F gave rise to a protein with an apparent molecular mass of 38 +/- 2 kDa. The endoglycosidase F effect and the lack of endoglycosidase H action show that the myometrial oxytocin receptor is highly glycosylated with asparagine-linked complex oligosaccharide chains. Our results suggest that the radioiodinated photoreactive oxytocin antagonist could be a helpful tool in the isolation and further characterization of the oxytocin receptor.

Identification of a myometrial oxytocin-receptor protein

The specific binding of [3H]oxytoxin to uterine membrane preparations derived from different species at late pregnancy was examined. The highest receptor density (bmax value) was found in membranes derived from the myometria of guinea pigs between day 60 post-conception (bmax = 3.6 +/- 0.1 pmol/mg) and day 65 (bmax = 4.4 +/- 0.1 pmol/mg). The similarity of Kd values for oxytocin binding (Kd = 2.6 +/- 0.2 nM) and for vasopressin binding (Kd = 2.1 +/- 0.4 nM) to the same membranes derived from a guinea pig myometrium indicate a homogeneous population of high-affinity binding sites which do not discriminate between these two hormones. Competitive binding experiments with specific oxytocin agonists containing either sarcosine or N-methylalanine in the place of Pro7 demonstrated that these myometrial receptors have the pharmacological properties of oxytocin receptors. The analogue of 1-deamino-[8-lysine]vasopressin containing a photoreactive azidophenylamidino group at the sidechain of Lys8 retained roughly the same receptor affinity as oxytocin. In photoaffinity labelling experiments with the tritium-labelled analogue a membrane protein from guinea pig myometrium with an apparent relative molecular mass Mr of 78,000 +/- 5000 (n = 13) was preferentially labelled. The labelling of this protein was completely suppressed by a 100-fold molar excess of either oxytocin, or [Sar7]oxytocin or [Thr4, Sar7]oxytocin, but not by other peptide hormones. These results provide evidence that the labelled 78,000-Mr protein is a myometrial oxytocin-receptor protein.