On prediction of optical properties of two- and multiphase nanocomposites for nanomedicine

The theory of optical properties of nanoparticles is considered with the aid of dispersion relations, which are based on the Kramers-Kronig analysis. It is shown that one can utilize rather general dispersion relations, which hold for liquid matrices that contain nanoparticles. Wiener bounds incorporating the Kramers-Kronig analysis are utilized in assessment of the complex permittivity of a nanoparticle.     

Local and average gloss from flat-faced sodium chloride tablets

The purpose of this study was to detect local gloss and surface structure changes of sodium chloride tablets. The changes in surface structure were reflected by gloss variation, which was measured using a diffractive optical element-based gloss-meter (DOG). By scanning a surface area, we constructed a 2-dimensional gloss map that characterized the tablet’s surface structure. The gloss variation results were compared with scanning electron microscopy (SEM) images and average surface roughness values that were measured by conventional diamond stylus profilometry. The profilometry data showed a decrease in tablet surface roughness as a function of compression force. In general, a smoother surface contributes to higher average gloss values. The average gloss values for this material, in contrast, showed a decrease as a function of the compression force. The sequence of particle fragmentation and deformation together with crack formation in sodium chloride particles resulted in a loss of gloss for single sodium chloride particles at the tablet surfaces, which could be detected by the DOG. These results were supported by the SEM images. The results show that detailed information regarding tablets’ surface structure changes can be obtained by detection of local gloss variation and average gloss. Published: January 13, 2006     

Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

Two previously described QTL mapping methods, which combine linkage analysis (LA) and linkage disequilibrium analysis (LD), were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA) gave good results as long as the distance between the QTL was large (> 90 cM). When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA) gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM) the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.     

The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

Background

Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD) test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets.

Methods

The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5^th, 10^th and 50^th highest T_CLD value from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively.

Results

In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001), where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001). In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05), i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position.

Conclusions

The CLD test can provide evidence for a causative SNP, but its power may be low in situations with closely linked markers. In such situations, also functional evidence will be needed to definitely conclude whether the SNP is causative or not.     

On Optical Properties of Dilute Colloidal Gold

Wavelength-dependent complex effective refractive index of dilute colloidal gold, i.e., spherical gold nanoparticles in water was measured using a reflectometer and a spectrophotometer. The spectral data obtained was used for the calculation of the wavelength-dependent complex permittivity of the gold nanoparticle with the aid of the Maxwell Garnett effective medium model for the colloid. It is shown that the wavelength-dependent complex permittivity of gold nanoparticle is different from the complex permittivity of bulk gold. Furthermore, Smakula’s formula is introduced for the calculation of the relative concentration of gold nanoparticles embedded in liquid using absorption data of the colloid.     

From SELDI-TOF MS to protein identification by on-chip elution

SELDI-TOF MS has been demonstrated as a powerful tool for biomarker discovery. However, a major disadvantage of SELDI-TOF MS is the lack of direct identification of the discriminatory peaks discovered. We describe a novel experimental identification strategy where peptides/proteins captured to a weak cation exchange ProteinArray surface (CM10) are eluted, and thereafter identified by utilizing a sensitive LC-MS/MS (i.e. LTQ Orbitrap). A mixture of four known proteins was used to test the novel experimental approach described, and all four proteins were successfully identified. Additionally, a biomarker candidate previously discovered in plasma of Atlantic cod (Gadus morhua) by SELDI-TOF MS was identified. Thus, this study indicated that a combination of on-chip elution and a highly sensitive LC-MS/MS system can be an alternative approach to identify biomarker candidates discovered by use of SELDI-TOF MS.     

Accumulation and Loss of Nitrogen in White Clover (Trifolium repens L.) Plant Organs as Affected by Defoliation Regime on Two Sites in Norway

In order to improve the basis for utilising nitrogen (N) fixed by white clover (Trifolium repens L.) in northern agriculture, we studied how defoliation stress affected the N contents of major plant organs in late autumn, N losses during the winter and N accumulation in the following spring. Plants were established from stolon cuttings and transplanted to pots that were dug into the field at Apelsvoll Research Centre (60°42′ N, 10°51′ E) and at Holt Research Centre (69°40′ N, 18°56′ E) in spring 2001 and 2002. During the first growing season, the plants were totally stripped of leaves down to the stolon basis, cut at 4 cm height or left undisturbed. The plants were sampled destructively in late autumn, early spring the second year and after 6 weeks of new spring growth. The plant material was sorted into leaves, stolons and roots. Defoliation regime did not influence the total amount of leaf N harvested during and at the end of the first growing season. However, for intensively defoliated plants, the repeated leaf removal and subsequent regrowth occurred at the expense of stolon and root development and resulted in a 61–85% reduction in the total plant N present in late autumn and a 21–59% reduction in total accumulation of plant N (plant N present in autumn + previously harvested leaf N). During the winter, the net N loss from leaf tissue (N not recovered in living nor dead leaves in the spring) ranged from 57% to 74% of the N present in living leaves in the autumn, while N stored in stolons and roots was much better conserved. However, the winter loss of stolon N from severely defoliated plants (19%) was significantly larger than from leniently defoliated (12%) and non-defoliated plants (6%). Moreover, the fraction of stolon N determined as dead in the spring was 63% for severely defoliated as compared to 14% for non-defoliated plants. Accumulation in absolute terms of new leaf N during the spring was highly correlated to total plant N in early spring (R² = 0.86), but the growth rates relative to plant N present in early spring were not and, consequently, were similar for all treatments. The amount of inorganic N in the soil after snowmelt and the N uptake in plant root simulator probes (PRS^TM) during the spring were small, suggesting that microbial immobilisation, leaching and gas emissions may have been important pathways for N lost from plant tissue.     

Paedocypris, a new genus of Southeast Asian cyprinid fish with a remarkable sexual dimorphism, comprises the world's smallest vertebrate

Paedocypris is a new genus of paedomorphic cyprinid fish from highly acidic blackwater peat swamps in Southeast Asia. It includes two new species, one of which (Paedocypris progenetica) appears to be the smallest fish and vertebrate known, with the smallest mature female measuring a mere 7.9 mm. Paedocypris has many 'larval' features typically associated with paedomorphic fish (e.g. narrow frontals that leave the brain unprotected dorsally by bone and a precaudal larval-fin-fold), but, uniquely among fishes, males also possess highly modified pelvic fins with hypertrophied muscles and a keratinized pad in front of the pelvic girdle, which, we hypothesize, function together as a clasping or holding device, thereby suggesting an unusual reproductive mode. Unfortunately, habitat destruction jeopardizes the survival of these fishes and thus opportunities for further research.