X=Y–ZH compounds as potential 1,3-dipoles. Part 64: Synthesis of highly substituted conformationally restricted and spiro nitropyrrolidines via Ag(I) catalysed azomethine ylide cycloadditions

1,3-Dipolar reactions of imines of both acyclic and cyclic α-amino esters with a range of nitroolefins using a combination of AgOAc or Ag2O with NEt3 are described. In most cases the reactions were highly regio- and stereospecific and endo-cycloadducts were obtained in good yield. However, in a few cases the initially formed cycloadducts underwent base catalysed epimerisation. The stereochemistry of the cycloadducts was assigned from NOE data and established unequivocally in several cases by X-ray crystallography

Cosmological models in scalar tensor theories of gravity and observations: a class of general solutions

We consider cosmological models in scalar tensor theories of gravity that describe an accelerating universe, and we study a family of inverse power law potentials, for which exact solutions of the Einstein equations are known. We also compare theoretical predictions of our models with observations. For this we use the following data: the publicly available catalogs of type Ia supernovae and high redshift Gamma Ray Bursts, the parameters of large scale structure determined by the 2-degree Field Galaxy Redshift Survey (2dFGRS), and measurements of cosmological distances based on the Sunyaev-Zel'dovich effect, among others.Comment: 26 pages,23 figures, accepted for publication in A&

Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93 accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak

Sequence-specific recognition of methylated DNA by human zinc-finger proteins

DNA methylation is an essential epigenetic mark. Three classes of mammalian proteins recognize methylated DNA: MBD proteins, SRA proteins and the zinc-finger proteins Kaiso, ZBTB4 and ZBTB38. The last three proteins can bind either methylated DNA or unmethylated consensus sequences; how this is achieved is largely unclear. Here, we report that the human zinc-finger proteins Kaiso, ZBTB4 and ZBTB38 can bind methylated DNA in a sequence-specific manner, and that they may use a mode of binding common to other zinc-finger proteins. This suggests that many other sequence-specific methyl binding proteins may exist

The functional response of a generalist predator

Peer reviewedPublisher PD

Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NF\u3baB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place

An evaluation of Canada's Compassionate Care Benefit from a family caregiver's perspective at end of life

<p>Abstract</p> <p>Background</p> <p>The goal of Canada's Compassionate Care Benefit (CCB) is to enable family members and other loved ones who are employed to take a temporary <it>secured </it>leave to care for a terminally ill individual at end of life. Successful applicants of the CCB can receive up to 55% of their average insured earnings, up to a maximum of CDN$435 per week, over a six week period to provide care for a gravely ill family member at risk of death within a six month period, as evidenced by a medical certificate. The goal of this study is to evaluate the CCB from the perspective of family caregivers providing care to individuals at end of life. There are three specific research objectives. Meeting these objectives will address our study purpose which is to make policy-relevant recommendations informed by the needs of Canadian family caregivers and input from other key stakeholders who shape program uptake. Being the first study that will capture family caregivers' experiences and perceptions of the CCB and gather contextual data with front-line palliative care practitioners, employers, and human resources personnel, we will be in a unique position to provide policy solutions/recommendations that will address concerns raised by numerous individuals and organizations.</p> <p>Methods</p> <p>We will achieve the research goal and objectives through employing utilization-focused evaluation as our methodology, in-depth interviews and focus groups as our techniques of data collection, and constant comparative as our technique of data analysis. Three respondent groups will participate: (1) family caregivers who are providing or who have provided end of life care via phone interview; (2) front-line palliative care practitioners via phone interview; and (3) human resources personnel and employers via focus group. Each of these three groups has a stake in the successful administration of the CCB. A watching brief of policy documents, grey literature, media reports, and other relevant items will also be managed throughout data collection.</p> <p>Discussion</p> <p>We propose to conduct this study over a three year period beginning in October, 2006 and ending in October, 2009.</p

Incorporating background frequency improves entropy-based residue conservation measures

BACKGROUND: Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may correlate with structurally or functionally important residues. However, amino acid background frequencies are usually not taken into account in these entropy-based scoring schemes. RESULTS: We demonstrate that using a relative entropy measure that incorporates amino acid background frequency results in improved performance in identifying functional sites from protein multiple sequence alignments. CONCLUSION: Our results suggest that the application of appropriate background frequency information may lead to more biologically relevant results in many areas of bioinformatics

Predicting Protein Kinase Specificity: Predikin Update and Performance in the DREAM4 Challenge

Predikin is a system for making predictions about protein kinase specificity. It was declared the “best performer” in the protein kinase section of the Peptide Recognition Domain specificity prediction category of the recent DREAM4 challenge (an independent test using unpublished data). In this article we discuss some recent improvements to the Predikin web server — including a more streamlined approach to substrate-to-kinase predictions and whole-proteome predictions — and give an analysis of Predikin's performance in the DREAM4 challenge. We also evaluate these improvements using a data set of yeast kinases that have been experimentally characterised, and we discuss the usefulness of Frobenius distance in assessing the predictive power of position weight matrices