Connection Formulae for Asymptotics of Solutions of the Degenerate Third Painlev\'{e} Equation. I

The degenerate third Painlev\'{e} equation, $u^{\prime \prime} = \frac{(u^{\prime})^{2}}{u} - \frac{u^{\prime}}{\tau} + \frac{1}{\tau}(-8 \epsilon u^{2} + 2ab) + \frac{b^{2}}{u}$, where $\epsilon,b \in \mathbb{R}$, and $a \in \mathbb{C}$, and the associated tau-function are studied via the Isomonodromy Deformation Method. Connection formulae for asymptotics of the general as $\tau \to \pm 0$ and $\pm i0$ solution and general regular as $\tau \to \pm \infty$ and $\pm i \infty$ solution are obtained.Comment: 40 pages, LaTeX2

Leading Order Temporal Asymptotics of the Modified Non-Linear Schrodinger Equation: Solitonless Sector

Using the matrix Riemann-Hilbert factorisation approach for non-linear evolution equations (NLEEs) integrable in the sense of the inverse scattering method, we obtain, in the solitonless sector, the leading-order asymptotics as $t$ tends to plus and minus infinity of the solution to the Cauchy initial-value problem for the modified non-linear Schrodinger equation: also obtained are analogous results for two gauge-equivalent NLEEs; in particular, the derivative non-linear Schrodinger equation.Comment: 29 pages, 5 figures, LaTeX, revised version of the original submission, to be published in Inverse Problem

Genetic Editing of HBV DNA by Monodomain Human APOBEC3 Cytidine Deaminases and the Recombinant Nature of APOBEC3G

Hepatitis B virus (HBV) DNA is vulnerable to editing by human cytidine deaminases of the APOBEC3 (A3A-H) family albeit to much lower levels than HIV cDNA. We have analyzed and compared HBV editing by all seven enzymes in a quail cell line that does not produce any endogenous DNA cytidine deaminase activity. Using 3DPCR it was possible to show that all but A3DE were able to deaminate HBV DNA at levels from 10−2 to 10−5 in vitro, with A3A proving to be the most efficient editor. The amino terminal domain of A3G alone was completely devoid of deaminase activity to within the sensitivity of 3DPCR (∼10−4 to 10−5). Detailed analysis of the dinucleotide editing context showed that only A3G and A3H have strong preferences, notably CpC and TpC. A phylogenic analysis of A3 exons revealed that A3G is in fact a chimera with the first two exons being derived from the A3F gene. This might allow co-expression of the two genes that are able to restrict HIV-1Δvif efficiently

Comparing angular and curved shapes in terms of implicit associations and approach/avoidance responses.

Most people prefer smoothly curved shapes over more angular shapes. We investigated the origin of this effect using abstract shapes and implicit measures of semantic association and preference. In Experiment 1 we used a multidimensional Implicit Association Test (IAT) to verify the strength of the association of curved and angular polygons with danger (safe vs. danger words), valence (positive vs. negative words) and gender (female vs. male names). Results showed that curved polygons were associated with safe and positive concepts and with female names, whereas angular polygons were associated with danger and negative concepts and with male names. Experiment 2 used a different implicit measure, which avoided any need to categorise the stimuli. Using a revised version of the Stimulus Response Compatibility (SRC) task we tested with a stick figure (i.e., the manikin) approach and avoidance reactions to curved and angular polygons. We found that RTs for approaching vs. avoiding angular polygons did not differ, even in the condition where the angles were more pronounced. By contrast participants were faster and more accurate when moving the manikin towards curved shapes. Experiment 2 suggests that preference for curvature cannot derive entirely from an association of angles with threat. We conclude that smoothly curved contours make these abstract shapes more pleasant. Further studies are needed to clarify the nature of such a preference

Extrastriate body area underlies aesthetic evaluation of body stimuli

Humans appear to be the only animals to have developed the practice and culture of art. This practice presumably relies on special processing circuits within the human brain associated with a distinct subjective experience, termed aesthetic experience, and preferentially evoked by artistic stimuli. We assume that positive or negative aesthetic judgments are an important function of neuroaesthetic circuits. The localization of these circuits in the brain remains unclear, though neuroimaging studies have suggested several possible neural correlates of aesthetic preference. We applied repetitive transcranial magnetic stimulation (rTMS) over candidate brain areas to disrupt aesthetic processing while healthy volunteers made aesthetic preference judgments between pairs of dance postures, or control non-body stimuli. Based on evidence from visual body perception studies, we targeted the ventral premotor cortex (vPMC) and extrastriate body area (EBA), in the left and right hemispheres. rTMS over EBA reduced aesthetic sensitivity for body stimuli relative to rTMS over vPMC, while no such difference was found for non-body stimuli. We interpret our results within the framework of dual routes for visual body processing. rTMS over either EBA or vPMC reduced the contributions of the stimulated area to body processing, leaving processing more reliant on the unaffected route. Disruption of EBA reduces the local processing of the stimuli, and reduced observers’ aesthetic sensitivity. Conversely, disruption of the global route via vPMC increased the relative contribution of the local route via EBA, and thus increased aesthetic sensitivity. In this way, we suggest a complementary contribution of both local and global routes to aesthetic processing

Evolution of the Primate APOBEC3A Cytidine Deaminase Gene and Identification of Related Coding Regions

The APOBEC3 gene cluster encodes six cytidine deaminases (A3A-C, A3DE, A3F-H) with single stranded DNA (ssDNA) substrate specificity. For the moment A3A is the only enzyme that can initiate catabolism of both mitochondrial and nuclear DNA. Human A3A expression is initiated from two different methionine codons M1 or M13, both of which are in adequate but sub-optimal Kozak environments. In the present study, we have analyzed the genetic diversity among A3A genes across a wide range of 12 primates including New World monkeys, Old World monkeys and Hominids. Sequence variation was observed in exons 1–4 in all primates with up to 31% overall amino acid variation. Importantly for 3 hominids codon M1 was mutated to a threonine codon or valine codon, while for 5/12 primates strong Kozak M1 or M13 codons were found. Positive selection was apparent along a few branches which differed compared to positive selection in the carboxy-terminal of A3G that clusters with A3A among human cytidine deaminases. In the course of analyses, two novel non-functional A3A-related fragments were identified on chromosome 4 and 8 kb upstream of the A3 locus. This qualitative and quantitative variation among primate A3A genes suggest that subtle differences in function might ensue as more light is shed on this increasingly important enzyme

All-codon scanning identifies p53 cancer rescue mutations

In vitro scanning mutagenesis strategies are valuable tools to identify critical residues in proteins and to generate proteins with modified properties. We describe the fast and simple All-Codon Scanning (ACS) strategy that creates a defined gene library wherein each individual codon within a specific target region is changed into all possible codons with only a single codon change per mutagenesis product. ACS is based on a multiplexed overlapping mutagenesis primer design that saturates only the targeted gene region with single codon changes. We have used ACS to produce single amino-acid changes in small and large regions of the human tumor suppressor protein p53 to identify single amino-acid substitutions that can restore activity to inactive p53 found in human cancers. Single-tube reactions were used to saturate defined 30-nt regions with all possible codon changes. The same technique was used in 20 parallel reactions to scan the 600-bp fragment encoding the entire p53 core domain. Identification of several novel p53 cancer rescue mutations demonstrated the utility of the ACS approach. ACS is a fast, simple and versatile method, which is useful for protein structure–function analyses and protein design or evolution problems

Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

BACKGROUND: Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. METHODOLOGY/PRINCIPAL FINDINGS: Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R(2) methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. CONCLUSIONS: By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study