Descriptive histograms for the reduced population of 247 sires used for additional genotyping of SNPs within the <i>LAP3</i>, <i>NCAPG</i> and <i>LCORL</i> genes after the GWAS.

<p>Left Panel: histograms of EBVs for direct calving ease distributed in five equally spaced classes. Right panel: histogram of kinship coefficients between sires in five equally spaced classes. In both panels, the number of sires belonging to each class is plotted as a function of classes.</p

SNP name, gene name, region within the gene, significance level (P*) and minor allele effect (βB) for the SNPs selected in the <i>LAP3</i>, <i>NCAPG</i> and <i>LCORL</i> genes and significantly associated to direct calving ease.

<p>Where available, rs number links to NCBI dbSNP page for the relative SNP.</p

Single nucleotide polymorphisms associated to direct calving ease and located on BTA6 in the region comprised between 37 and 39 millions of base pairs sorted according to their position on the Illumina BovineSNP50 panel.

<p>SNP name, position, the gene in which they are located (if any), significance levels both unadjusted (P*) and corrected for multiple testing (Q*), allelic frequencies (fB) and effects of the minor allele (βB).</p

Left Panel: histograms of EBVs for direct calving ease distributed in five equally spaced classes.

<p>Right panel: histogram of kinship coefficients between sires in five equally spaced classes. In both panels, the number of sires belonging to each class is plotted as a function of classes.</p

Upper panel: log significance levels of SNPs association with direct calving ease for the entire filtered dataset before the correction for inflation.

<p>Each autosome is represented with a different colour and position is calculated along the entire genome length. Values above the dot-dashed green line denote a P*<0.05. Lower panel: The chromosomal region spanned by the 13 markers listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050137#pone-0050137-t001" target="_blank">Table 1</a>. The approximate position and size of genes located in the region (blue rectangles) together with the position of each SNP (red numbers and red dashed lines) are shown.</p

Origin of Fluorescence in 11-<i>cis</i> Locked Bovine Rhodopsin

The excited state lifetime of bovine rhodopsin (Rh) increases from ca. 100 fs to 85 ps when the C11C12 bond of its chromophore is locked by a cyclopentene moiety (Rh5). To explain such an increase, we employed <i>ab initio</i> multiconfigurational quantum chemistry to construct computer models of Rh and Rh5 and to investigate the shape of their excited state potential energy surfaces in a comparative way. Our results show that the observed Rh5 fluorescence (λ_max^f = 620 nm) is due to a previously unreported locally excited intermediate whose lifetime is controlled by a small energy barrier. The analysis of the properties and decay path of such an intermediate provides useful information for engineering rhodopsin variants with augmented fluorescence efficiencies

Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors

Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies

Mechanical Forces Alter Conical Intersections Topology

Photoreactivity can be influenced by mechanical forces acting over a reacting chromophore. Nevertheless, the specific effect of the external forces in the photoreaction mechanism remains essentially unknown. Conical intersections are key structures in photochemistry, as they constitute the funnels connecting excited and ground states. These crossing points are well known to provide valuable information on molecular photoreactivity, including crucial aspects as potential photoproducts which may be predicted by just inspection of the branching plane vectors. Here, we outline a general framework for understanding the effect of mechanical forces on conical intersections and their implications on photoreactivity. Benzene S₁/S₀ conical intersection topology can be dramatically altered by applying less than 1 nN force, making the peaked pattern of the intersection become a sloped one, also provoking the transition state in the excited state to disappear. Both effects can be related to an increase in the photostability as the conical intersection becomes more accessible, and its topology in this case favors the recovery of the initial reactant. The results indicate that the presence of external forces acting over a chromophore have to be considered as a potential method for photochemical reactivity control

MOESM1 of Use of canonical discriminant analysis to study signatures of selection in cattle

Additional file 1: Table S1. Matrices of Mahalanobis distances between the five breeds on the 29 autosomes. This table reports the Mahalanobis distance between the centroids of the five cattle populations calculated with the canonical discriminant analysis. The distances are reported for all the 29 autosomes. BRW = Italian Brown Swiss; HOL = Italian Holstein; MAR = Marchigiana; PIE = Piemontese; SIM = Italian Simmental

MOESM2 of Use of canonical discriminant analysis to study signatures of selection in cattle

Additional file 2: Figure S1. Manhattan plot of FST values (light and dark grey dots) and canonical coefficients (red dots) for all ten pairwise comparisons. This plot reports the FST values and the canonical coefficient along the whole genome obtained in the ten pairwise comparisons between all the five breeds considered in this study, evidencing the concordance between the two approaches in the detection of selection signatures. BRW = Italian Brown Swiss; HOL = Italian Holstein; MAR = Marchigiana; PIE = Piemontese; ISIM = Italian Simmental