Analysis of Kinase Effects on Viral Replication of the Papillomavirus

Papillomaviruses are a genera of small tumor viruses in the Papovaviridae family, whose lifecycle and replication ability is directed by epithelial differentiation. During latency, papillomavirus DNA replication occurs synchronously with the host cell\u27s replication by the activation of the El protein. To elucidate the effects upon viral replication, this study utilized chemical inhibition of several kinases predicted to phosphorylate, and subsequently modify the activity of, the papillomavirus\u27 E1 protein. The amount of DNA replicated was observed via autoradiography following DNA extraction and southern blotting of BPV-transformed C127 cells. Sample extracts from cells exposed to specific chemical inhibitors of PKC, CDK, and DNAPK showed a consistent and significant decrease in viral DNA when compared to the DNA abundance of a control set of extracts. Extracts of cells subjected to inhibition of CK2 displayed an observable increase in replicated viral DNA. To ensure that the kinase modification was not effecting the growth or viability of the cells, a neutral red assay was performed and found no significant difference between control and chemically treated samples in cell viability or overall cell number. These findings, in conjunction with the differential viral DNA abundance, implicate that kinases PKC, CDK, CK2, and DNAPK, have a role in viral genome replication

De-novo design of complementary (antisense) peptide mini-receptor inhibitor of interleukin 18 (IL-18).

Complementary (antisense) peptide mini-receptor inhibitors are complementary peptides designed to be receptor-surrogates that act by binding to selected surface features of biologically important proteins thereby inhibiting protein-cognate receptor interactions and subsequent biological effects. Previously, we described a complementary peptide mini-receptor inhibitor of interleukin-1beta (IL-1beta) that was designed to bind to an external surface loop (beta-bulge) of IL-1beta (Boraschi loop) clearly identified in the X-ray crystal structure of this cytokine. Here, we report the de-novo design and rational development of a complementary peptide mini-receptor inhibitor of cytokine interleukin-18 (IL-18), a protein for which there is no known X-ray crystal structure. Using sequence homology comparisons with IL-1beta, putative IL-18 surface loops are identified and used as a starting point for design, including a loop region 1 thought to be equivalent with the Boraschi loop of IL-1beta. Only loop region 1 complementary peptides are found to be promising leads as mini-receptor inhibitors of IL-18 but these are prevented from being properly successful owing to solubility problems. The application of "M-I pair mutagenesis" and inclusion of a C-terminal arginine residue are then sufficient to solve this problem and convert one lead peptide into a functional complementary peptide mini-receptor inhibitor of IL-18. This suggests that the biophysical and biological properties of complementary peptides can be improved in a rational and logical manner where appropriate, further strengthening the potential importance of complementary peptides as inhibitors of protein-protein interactions, even when X-ray crystal structural information is not readily available

A phosphorylation map of the bovine papillomavirus E1 helicase

BACKGROUND: Papillomaviruses undergo a complex life cycle requiring regulated DNA replication. The papillomavirus E1 helicase is essential for viral DNA replication and plays a key role in controlling viral genome copy number. The E1 helicase is regulated at least in part by protein phosphorylation, however no systematic approach to phosphate site mapping has been attempted. We have utilized mass spectrometry of purified bovine papillomavirus E1 protein to identify and characterize new sites of phosphorylation. RESULTS: Mass spectrometry and in silico sequence analysis were used to identify phosphate sites on the BPV E1 protein and kinases that may recognize these sites. Five new and two previously known phosphorylation sites were identified. A phosphate site map was created and used to develop a general model for the role of phosphorylation in E1 function. CONCLUSION: Mass spectrometric analysis identified seven phosphorylated amino acids on the BPV E1 protein. Taken with three previously identified sites, there are at least ten phosphoamino acids on BPV E1. A number of kinases were identified by sequence analysis that could potentially phosphorylate E1 at the identified positions. Several of these kinases have known roles in regulating cell cycle progression. A BPV E1 phosphate map and a discussion of the possible role of phosphorylation in E1 function are presented

A systematic review of community participation measures for people with intellectual disabilities

Background: Community participation is considered a fundamental aspect of quality of life and one of the essential goals of services for people with intellectual disabilities (ID), yet there is no agreed way of measuring community participation. Method: Two systematic searches were performed across eight electronic databases to identify measures of community participation and identify validation studies for each measure. Measures were included if they were developed for adults with ID, measured extent of participation and had published information regarding content and psychometric properties. Each measure was evaluated on the basis of psychometric properties and in relation to coverage of nine domains of community participation from the International Classification of Functioning, Disability and Health (ICF). Results: Eleven measures were selected with the quality rating scores varying substantially ranging from 2-11 of a possible 16. Conclusions: The majority of measures were not sufficiently psychometrically tested. Findings suggest a need for the development of a psychometrically robust instrument

Ab-initio theory of NMR chemical shifts in solids and liquids

We present a theory for the ab-initio computation of NMR chemical shifts (sigma) in condensed matter systems, using periodic boundary conditions. Our approach can be applied to periodic systems such as crystals, surfaces, or polymers and, with a super-cell technique, to non-periodic systems such as amorphous materials, liquids, or solids with defects. We have computed the hydrogen sigma for a set of free molecules, for an ionic crystal, LiH, and for a H-bonded crystal, HF, using density functional theory in the local density approximation. The results are in excellent agreement with experimental data.Comment: to appear in Physical Review Letter

Serum Amyloid A, C-Reactive Protein, and Retinal Microvascular Changes in Hypertensive Diabetic and Nondiabetic Individuals: An Anglo-Scandinavian Cardiac Outcomes Trial (ASCOT) substudy

To study the association of the inflammatory markers serum amyloid A (SAA) and C-reactive protein (CRP) with retinal microvascular parameters in hypertensive individuals with and without type 2 diabetes

Stillbirth risk prediction using machine learning for a large cohort of births from Western Australia, 1980–2015

Quantification of stillbirth risk has potential to support clinical decision-making. Studies that have attempted to quantify stillbirth risk have been hampered by small event rates, a limited range of predictors that typically exclude obstetric history, lack of validation, and restriction to a single classifier (logistic regression). Consequently, predictive performance remains low, and risk quantification has not been adopted into antenatal practice. The study population consisted of all births to women in Western Australia from 1980 to 2015, excluding terminations. After all exclusions there were 947,025 livebirths and 5,788 stillbirths. Predictive models for stillbirth were developed using multiple machine learning classifiers: regularised logistic regression, decision trees based on classification and regression trees, random forest, extreme gradient boosting (XGBoost), and a multilayer perceptron neural network. We applied 10-fold cross-validation using independent data not used to develop the models. Predictors included maternal socio-demographic characteristics, chronic medical conditions, obstetric complications and family history in both the current and previous pregnancy. In this cohort, 66% of stillbirths were observed for multiparous women. The best performing classifier (XGBoost) predicted 45% (95% CI: 43%, 46%) of stillbirths for all women and 45% (95% CI: 43%, 47%) of stillbirths after the inclusion of previous pregnancy history. Almost half of stillbirths could be potentially identified antenatally based on a combination of current pregnancy complications, congenital anomalies, maternal characteristics, and medical history. Greatest sensitivity is achieved with addition of current pregnancy complications. Ensemble classifiers offered marginal improvement for prediction compared to logistic regression

Stillbirth risk prediction using machine learning for a large cohort of births from Western Australia, 1980–2015

Quantification of stillbirth risk has potential to support clinical decision-making. Studies that have attempted to quantify stillbirth risk have been hampered by small event rates, a limited range of predictors that typically exclude obstetric history, lack of validation, and restriction to a single classifier (logistic regression). Consequently, predictive performance remains low, and risk quantification has not been adopted into antenatal practice. The study population consisted of all births to women in Western Australia from 1980 to 2015, excluding terminations. After all exclusions there were 947,025 livebirths and 5,788 stillbirths. Predictive models for stillbirth were developed using multiple machine learning classifiers: regularised logistic regression, decision trees based on classification and regression trees, random forest, extreme gradient boosting (XGBoost), and a multilayer perceptron neural network. We applied 10-fold cross-validation using independent data not used to develop the models. Predictors included maternal socio-demographic characteristics, chronic medical conditions, obstetric complications and family history in both the current and previous pregnancy. In this cohort, 66% of stillbirths were observed for multiparous women. The best performing classifier (XGBoost) predicted 45% (95% CI: 43%, 46%) of stillbirths for all women and 45% (95% CI: 43%, 47%) of stillbirths after the inclusion of previous pregnancy history. Almost half of stillbirths could be potentially identified antenatally based on a combination of current pregnancy complications, congenital anomalies, maternal characteristics, and medical history. Greatest sensitivity is achieved with addition of current pregnancy complications. Ensemble classifiers offered marginal improvement for prediction compared to logistic regression

Genetic, environmental and stochastic factors in monozygotic twin discordance with a focus on epigenetic differences

PMCID: PMC3566971This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Friendship activities of adults with intellectual disability in supported accommodation in northern England

Background Despite there being considerable evidence to suggest that friendships are central to health and well-being, relatively little attention had been paid to the friendships of people with intellectual disabilities. Methods Friendship activities involving people with and without intellectual disabilities were measured over the preceding month in a sample of 1542 adults with intellectual disabilities receiving supported accommodation in nine geographical localities in Northern England. Results The results of the study indicate: (1) low levels of friendship activities among people with intellectual disabilities in supported accommodation; (2) people with intellectual disabilities are more likely to be involved in activities with friends who also have intel lectual disabilities than with friends who do not have intellectual disabilities; (3) most friendship activities take place in the public domain rather than in more private settings (e.g. at home); (4) the setting in which a person lives is a more significant determinant of the form and content of activities with their friends than the characteristics of participants. Conclusions Further attention needs to be given to research and practice initiatives aimed at increasing the levels of friendship activities of people with intellectual disabilities