Directional surface plasmon-coupled emission: application for an immunoassay in whole blood

We present a new approach for performing fluorescence immunoassay in whole blood using fluorescently labeled anti-rabbit immunoglobulin G (IgG) on a silver surface. This approach, which is based on surface plasmon-coupled emission (SPCE), provides increased sensitivity and substantial background reduction due to exclusive selection of the signal from the fluorophores located near a bioaffinity surface. This article describes the effect of an optically dense sample matrix, namely human whole blood and serum, on the intensity of the SPCE. An antigen (rabbit IgG) was adsorbed to a slide covered with a thin silver metal layer, and the SPCE signal from the fluorophore-labeled anti-rabbit antibody, binding to the immobilized antigen, was detected. The effect of the sample matrix (buffer, human serum, or human whole blood) on the end-point immunoassay SPCE signal was studied. It was demonstrated that the kinetics of binding could be monitored directly in whole blood or serum. The results showed that human serum and human whole blood attenuate the SPCE end-point signal and the immunoassay kinetic signal only approximately two- and threefold, respectively, as compared with buffer, resulting in signals that are easily detectable even in whole blood. The high optical absorption of the hemoglobin can be tolerated because only fluorophores within a couple of hundred nanometers from the metallic film contribute to SPCE. Excited fluorophores outside the 200-nm layer do not contribute to SPCE, and their free space emission is not transmitted through the opaque metallic film into the glass substrate. We believe that SPCE has the potential of becoming a powerful approach for performing immunoassays based on surface-bound analytes or antibodies for many biomarkers directly in dense samples such as whole blood with no need for washing steps.     

Two-photon induced fluorescence of Cy5-DNA in buffer solution and on silver island films

We report the observation of a strong two-photon induced fluorescence emission of Cy5-DNA within the tunable range of a Ti:Sapphire laser. The estimated two-photon cross-section for Cy5-DNA of 400GM is about 3.5-fold higher than it was reported for rhodamine B. The fundamental anisotropies of Cy5-DNA are close to the theoretical limits of 2/5 and 4/7 for one- and two-photon excitation, respectively. We also observed an enhanced two-photon induced fluorescence (TPIF) of Cy5-DNA deposited on silver island films (SIFs). In the presence of SIFs, the TPIF is about 100-fold brighter. The brightness increase of Cy5-DNA TPIF near SIFs is mostly due to enhanced local field.     

Conformations of the signal recognition particle protein Ffh from Escherichia coli as determined by FRET

The signal recognition particle (SRP) initiates the co-translational targeting of proteins to the plasma membrane in bacteria by binding to the N-terminal signal sequence emerging from the translating ribosome. SRP in Escherichia coli is composed of one protein, Ffh, and 4.5S RNA. In the present work, we probe the structure of Ffh alone and in the complex with 4.5S RNA by measuring distances between different positions within Ffh and between Ffh and 4.5S RNA by fluorescence resonance energy transfer (FRET). According to the FRET distances, NG and M domains in free Ffh are in close contact, as in the A/A arrangement in the crystal structure of Ffh from Thermus aquaticus, in agreement with the formation of a crosslink between cysteine residues at two critical positions in the G and M domains. Upon Ffh binding to 4.5S RNA or a 61 nucleotide fragment comprising internal loops A-C, the G and M domains move apart to assume a more open conformation, as indicated by changes of FRET distances. The movement is smaller when Ffh binds to a 49 nucleotide fragment of 4.5S RNA comprising only internal loops A and B, i.e. lacking the binding site of the NG domain. The FRET results suggest that in the SRP complex 4.5S RNA is present in a bent, rather than extended, conformation. The domain rearrangement of Ffh that takes place upon formation of the SRP is probably important for subsequent steps of membrane targeting, including interactions with the translating ribosome and the SRP receptor.     

Accuracy of estimated breeding values with genomic information on males,females, or both: an example on broiler chicken

Background

As more and more genotypes become available, accuracy of genomic evaluations can potentially increase. However, the impact of genotype data on accuracy depends on the structure of the genotyped cohort. For populations such as dairy cattle, the greatest benefit has come from genotyping sires with high accuracy, whereas the benefit due to adding genotypes from cows was smaller. In broiler chicken breeding programs, males have less progeny than dairy bulls, females have more progeny than dairy cows, and most production traits are recorded for both sexes. Consequently, genotyping both sexes in broiler chickens may be more advantageous than in dairy cattle.

Methods

We studied the contribution of genotypes from males and females using a real dataset with genotypes on 15 723 broiler chickens. Genomic evaluations used three training sets that included only males (4648), only females (8100), and both sexes (12 748). Realized accuracies of genomic estimated breeding values (GEBV) were used to evaluate the benefit of including genotypes for different training populations on genomic predictions of young genotyped chickens.

Results

Using genotypes on males, the average increase in accuracy of GEBV over pedigree-based EBV for males and females was 12 and 1 percentage points, respectively. Using female genotypes, this increase was 1 and 18 percentage points, respectively. Using genotypes of both sexes increased accuracies by 19 points for males and 20 points for females. For two traits with similar heritabilities and amounts of information, realized accuracies from cross-validation were lower for the trait that was under strong selection.

Conclusions

Overall, genotyping males and females improves predictions of all young genotyped chickens, regardless of sex. Therefore, when males and females both contribute to genetic progress of the population, genotyping both sexes may be the best option.     

Quality Control of Genotypes Using Heritability Estimates of Gene Content at the Marker

Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the number of copies of a particular reference allele in a genotype of an animal (0, 1, or 2). If there is no mutation at the marker, gene content has an additive heritability of 1 by construction. The method uses restricted maximum likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood-ratio test statistic to test for zero error variance in genotyping. As a by-product, estimates of the allele frequencies of markers at the base population are obtained. Using simulated data with 10% permutation error (4% actual error) in genotyping, the method had a specificity of 0.96 (4% of correct markers are rejected) and a sensitivity of 0.99 (1% of wrong markers are accepted) if markers with heritability lower than 0.975 are discarded. Checking of Mendelian errors resulted in a lower sensitivity (0.84) for the same simulation. The proposed method is further illustrated with a real data set with genotypes from 3534 animals genotyped for 50,433 markers from the Illumina PorcineSNP60 chip and a pedigree of 6473 individuals; those markers underwent very little quality control. A total of 4099 markers with P-values lower than 0.01 were discarded based on our method, with associated estimates of heritability as low as 0.12. Contrary to other techniques, our method uses all information in the population simultaneously, can be used in any population with markers and pedigree recordings, and is simple to implement using standard software for REML estimation. Scripts for its use are provided.     

波兰东南部乌灰鹞在雏鸟出羽后期的同窝雏间冲突

通过对波兰东南部的13巢乌灰鹞(Circus pygargus) ,37只雏鸟观察,对同窝雏鸟间的竞争进行了研究。无论是在食物的数量或者生物量上,早孵出的雏鸟占有空中喂养与巢内喂养的食物源的绝对优势。空中学习捕食的食物量占喂养食物量的比例随着雏鸟年龄的增长而增加。雏鸟在空中喂养中的攻击行为通过对空中食物传递进行研究。在370次的食物传递中,由于雏间竞争而引起的落地食物的比例57次(7·8 %)。由于雏间竞争而不能获得亲鸟喂养的幼鸟有时捕食周围的雀形目小鸟。亲鸟很少喂养较小的雏鸟。窝雏数越大,雏鸟间对食物的争斗持续时间越长。空中食物传递中捕食的成功率与雏鸟的空间分布相关。这种建立在雏鸟早期的等级制一直持续到雏鸟的出羽后期,从而保证早出雏具备开始迁徙的良好身体条件[动物学报51 (5) : 790 -796 ,2005]。     

Occurrence of the medicinal leech (Hirudo medicinalis) in birds’ nests

Occurrence and breeding of Hirudo medicinalis were recorded in birds’ nests in the fishing ponds and water bodies used extensively by anglers in south-eastern Poland, in 4 of 11 studied bird species (Circus aeruginosus, Fulica atra, Cygnus olor, Chroicocephalus ridibundus). Factors important for the distribution and density of this leech were: nest height, pH of the water and oxygen concentration in the water inside the nests, the body-length of the nesting birds. Our data show that (1) H. medicinalis chooses nests as habitats that are safe in water bodies rich in predators (particularly fish) and provide stable feeding conditions; (2) fishing ponds and other water bodies used extensively by anglers in a landscape modified by human pressure can be an important secondary habitat for the medicinal leech. As the nesting activity of some aquatic birds apparently favors the occurrence of H. medicinalis, active protection of aquatic birds and creating sites appropriate for their breeding may be an indirect way for the conservation of the leech in such areas.     

Comparison of Orientation and Rotational Motion of Skeletal Muscle Cross-bridges Containing Phosphorylated and Dephosphorylated Myosin Regulatory Light Chain

Calcium binding to thin filaments is a major element controlling active force generation in striated muscles. Recent evidence suggests that processes other than Ca²⁺ binding, such as phosphorylation of myosin regulatory light chain (RLC) also controls contraction of vertebrate striated muscle (Cooke, R. (2011) Biophys. Rev. 3, 33–45). Electron paramagnetic resonance (EPR) studies using nucleotide analog spin label probes showed that dephosphorylated myosin heads are highly ordered in the relaxed fibers and have very low ATPase activity. This ordered structure of myosin cross-bridges disappears with the phosphorylation of RLC (Stewart, M. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 430–435). The slower ATPase activity in the dephosporylated moiety has been defined as a new super-relaxed state (SRX). It can be observed in both skeletal and cardiac muscle fibers (Hooijman, P., Stewart, M. A., and Cooke, R. (2011) Biophys. J. 100, 1969–1976). Given the importance of the finding that suggests a novel pathway of regulation of skeletal muscle, we aim to examine the effects of phosphorylation on cross-bridge orientation and rotational motion. We find that: (i) relaxed cross-bridges, but not active ones, are statistically better ordered in muscle where the RLC is dephosporylated compared with phosphorylated RLC; (ii) relaxed phosphorylated and dephosphorylated cross-bridges rotate equally slowly; and (iii) active phosphorylated cross-bridges rotate considerably faster than dephosphorylated ones during isometric contraction but the duty cycle remained the same, suggesting that both phosphorylated and dephosphorylated muscles develop the same isometric tension at full Ca²⁺ saturation. A simple theory was developed to account for this fact.     

Metal particle-enhanced fluorescent immunoassays on metal mirrors

We present fluoroimmunoassays on plain metal-coated surfaces (metal mirrors) enhanced by metal nanoparticles (silver island films [SIFs]). Metal mirrors (aluminum, gold, or silver protected with a thin silica layer) were coated with SIFs, and an immunoassay (model assay for rabbit immunoglobulin G or myoglobin immunoassay) was performed on this surface using fluorescently labeled antibodies. Our results showed that SIFs alone (on glass surface not coated with metal) enhance the immunoassay signal approximately 3- to 10-fold. Using a metal mirror instead of glass as support for SIFs results in up to 50-fold signal enhancement.