Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele

Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory—for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft sweeps, as well as on data from well-known sweeps in human populations.     

Significance of Four Methionine Sulfoxide Reductases in Staphylococcus aureus

Staphylococcus aureus is a major human pathogen and emergence of antibiotic resistance in clinical staphylococcal isolates raises concerns about our ability to control these infections. Cell wall-active antibiotics cause elevated synthesis of methionine sulfoxide reductases (Msrs: MsrA1 and MsrB) in S. aureus. MsrA and MsrB enzymes reduce S-epimers and R-epimers of methionine sulfoxide, respectively, that are generated under oxidative stress. In the S. aureus chromosome, there are three msrA genes (msrA1, msrA2 and msrA3) and one msrB gene. To understand the precise physiological roles of Msr proteins in S. aureus, mutations in msrA1, msrA2 and msrA3 and msrB genes were created by site-directed mutagenesis. These mutants were combined to create a triple msrA (msrA1, msrA2 and msrA3) and a quadruple msrAB (msrA1, msrA2, msrA3, msrB) mutant. These mutants were used to determine the roles of Msr proteins in staphylococcal growth, antibiotic resistance, adherence to human lung epithelial cells, pigment production, and survival in mice relative to the wild-type strains. MsrA1-deficient strains were sensitive to oxidative stress conditions, less pigmented and less adherent to human lung epithelial cells, and showed reduced survival in mouse tissues. In contrast, MsrB-deficient strains were resistant to oxidants and were highly pigmented. Lack of MsrA2 and MsrA3 caused no apparent growth defect in S. aureus. In complementation experiments with the triple and quadruple mutants, it was MsrA1 and not MsrB that was determined to be critical for adherence and phagocytic resistance of S. aureus. Overall, the data suggests that MsrA1 may be an important virulence factor and MsrB probably plays a balancing act to counter the effect of MsrA1 in S. aureus.     

Chlorophyll a fluorescence kinetics of mung bean (Vigna radiata L.) grown under artificial continuous light

Continuous light can be used as a tool to understand the diurnal rhythm of plants and it can also be used to increase the plant production. In the present research, we aimed to investigate the photosynthetic performance of V. radiata under continuous light as compared with the plants grown under normal light duration. Chlorophyll a fluorescence transient (OJIP test) technique was used to understand the effect on various stages of photosynthesis and their consequences under continuous light condition. Various Chl a Fluorescence kinetic parameters such as Specific energy fluxes (per Q_A-reducing PSII reaction center (RC)) (ABS /RC; TR₀/RC; ET₀/RC; DI₀/RC), phenomenological fluxes, leaf model, (ABS/CSm; TR/CSm; ETo/CSm), Quantum yields and efficiencies (φPo; φEo; Ψo) and Performance index (PI_abs) was extracted and analysed in our investigation. Conclusively, our study has revealed that continuous light alters the photosynthetic performance of V. radiata at a different point but also improve plant productivity.     

CLEAN: CLustering Enrichment ANalysis

Background  

Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analyses have been used to identify biologically meaningful clusters, compare clustering algorithms and identify biological pathways associated with the biological process under investigation.     

Tropic failure of Phyllactinia corylea contributes to the mildew resistance of mulberry genotypes

Different mulberry genotypes show great variation in their resistance to the powdery mildew Phyllactinia corylea. Conidial germination and hyphal growth of P. corylea on the leaf surface of two susceptible mulberry genotypes, viz., Kanva 2 (K2) and Victory 1 (V1) varieties of Morus indica, and on two resistant species, viz., M. laevigata and M. serrata were studied by scanning electron microscopy. Conidial germination and growth of germ tubes were normal on all the leaves. The hyphae of P. coryleaidentify stomata on host leaves by their topographical features to produce the stomatopodia precisely over them. The holes and/or the grooves of stomata appear to provide the signals for the initiation of stomatopodia and similar structures are erratically developed over many local depressions or grooves on leaf surface. The abaxial surface of K2 leaf is smooth without prominent undulations of epidermal cell surface, and the stomata are flush with the leaf surface. Although successful penetration is also achieved on V1 leaf, its slightly undulated surface occasionally provides inaccurate tropic signals to the hyphae, inducing the development of stomatopodia away from the stomata. The leaf surfaces of M. laevigata and M. serrata are very rough with highly sculptured cuticle and abundant epidermal outgrowths. Stomata mostly remain sunken or hidden amidst the cuticular ornamentations and the hyphae fail to recognise the precise signals from them. As the surface architecture of the leaves provides many immense sources of tropic signals, stomatopodia are often produced over local depressions or grooves. In these cases the fungus fails to penetrate the leaf, does not develop beyond 24 h and penetration is rarely achieved on the leaves of the resistant plants. The study indicates that the stimulatory effect of the leaf surface topography of resistant varieties misleads the pathogen from successful penetration, thus contributing to the plant's resistance.This revised version was published online in October 2005 with corrections to the Cover Date.     

Virmid: accurate detection of somatic mutations with sample impurity inference

Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at http://sourceforge.net/projects/virmid/.     

Agonist Leukadherin-1 Increases CD11b/CD18-Dependent Adhesion Via Membrane Tethers

Integrin CD11b/CD18 is a key adhesion receptor that mediates leukocyte migration and immune functions. Leukadherin-1 (LA1) is a small molecule agonist that enhances CD11b/CD18-dependent cell adhesion to its ligand ICAM-1. Here, we used single-molecule force spectroscopy to investigate the biophysical mechanism by which LA1-activated CD11b/CD18 mediates leukocyte adhesion. Between the two distinct populations of CD11b/CD18:ICAM-1 complex that participate in cell adhesion, the cytoskeleton(CSK)-anchored elastic elements and the membrane tethers, we found that LA1 enhanced binding of CD11b/CD18 on K562 cells to ICAM-1 via the formation of long membrane tethers, whereas Mn²⁺ additionally increased ICAM-1 binding via CSK-anchored bonds. LA1 activated wild-type and LFA1^−/− neutrophils also showed longer detachment distances and time from ICAM-1-coated atomic force microscopy tips, but significantly lower detachment force, as compared to the Mn²⁺-activated cells, confirming that LA1 primarily increased membrane-tether bonds to enhance CD11b/CD18:ICAM-1 binding, whereas Mn²⁺ induced additional CSK-anchored bond formation. The results suggest that the two types of agonists differentially activate integrins and couple them to the cellular machinery, providing what we feel are new insights into signal mechanotransduction by such agents.