Incorporation of xenobiotic carboxylic acids into lipids

Over thirty-six different xenobiotic carboxylic acids have been reported to form xenobiotic lipids. The majority form triacylglycerol analogs or cholesterol esters with fewer reports of polar lipids being formed. As yet there is insufficient information to deduce a relationship between the structure of the xenobiotic acid and its activity as a substrate for lipid biosynthesis, although the ability to form a CoA ester appears to be important. The action of monoacylglycerol acyltransferase, diacylglycerol acyltransferase, lecithin cholesterol acyltransferase and a carboxylesterase in synthesizing xenobiotic lipids has been demonstrated. One xenobiotic lipid has been shown to be the cause of granulomatous changes and there are some indications that others may prove to be of toxicological or pharmacological significance. Detailed investigations into several aspects of xenobiotic lipid biochemistry are still required.     

Growth and development of offspring following supplementation of sow diets with oil during mid to late gestation

This study aimed to determine the consequences of altering the fatty acid profile of sow diets during mid-to-late gestation; oils of different fatty acid composition were chosen as energy supplements to provide diets with different fatty acid profiles. Forty-eight multiparous sows were used to evaluate the effects of fat supplementation from day 60 of gestation until parturition. Sows were allocated to either 3 kg/day of commercial sow pellets (control; C) or an experimental diet consisting of 3 kg/day of commercial sow pellets supplemented with 10% extra energy in the form of excess pellets (E), palm oil (P), olive oil (O), sunflower oil (S) or fish oil (F). From days 0 to 60 of gestation, all sows were given 3 kg/day of sow pellets as for the C group. The E diet resulted in the heaviest piglets at birth whereas the offspring of O and S sows were the lightest at birth. The offspring of S sows remained lighter throughout the pre-weaning period, and were also the leanest by 14 days of age. In contrast, pigs born to S sows possessed more fat by the time they reached commercial end point (≈140 days of age). In conclusion, altering the fatty acid profile of the sow diet during the second half of gestation has long-term consequences for the development of their offspring.     

Comparative mapping of sheep chromosome 2q

Sheep chromosome 2q (OAR2q), which is homologous with human chromosome 2q (HSA2q), and cattle chromosome 2 (BTA2), is known to contain several loci contributing to carcass traits. However, the chromosomal rearrangements differentiating these chromosomes among the three species have not yet been determined and thus precise correspondences between the locations of sheep and human genes are not known. Twenty-six genes from HSA2q (2q21.1-->2q36) have been assigned to OAR2q by genetic linkage mapping to refine this area of the sheep genome. Seventy-six genes were initially selected from HSA2q. Sixty-eight percent of the PCR primer sets designed for these genes amplified successfully in sheep, and 34% amplified polymorphic products. Part of the proximal arm of OAR2q was found to be inverted compared with HSA2q. The breakpoint has been localised near the growth differentiation factor 8 gene (GDF8), spanning 380 kb between the positions of the hypothetical protein (FLJ20160) (HSA2:191008944-191075046) and glutaminase (GLS) (HSA2:191453847-191538510) (Build36.1).     

Immune activation in advanced cancer patients treated with recombinant IL-21: multianalyte profiling of serum proteins

Purpose  Recombinant interleukin-21 (rIL-21) is an immune stimulating cytokine recently tested in two Phase 1 trials for immune responsive cancers. A secondary objective of these trials was to characterize pharmacodynamic responses to rIL-21 in patients. Here, we report the effects of systemic rIL-21 on serum markers of immune stimulation. Experimental design  Recombinant IL-21 was administered by intravenous bolus injection at dose levels from 1 to 100 μg/kg using two distinct treatment regimens: thrice weekly (‘3/w’) for 6 weeks; or once daily for five consecutive days followed by nine dose-free days (‘5 + 9’). In the absence of dose limiting toxicity, additional cycles of dosing were initiated immediately following the nine dose-free days. An array of 70 different proteins was profiled in subject serum samples from several time points during the course of the study. Hierarchical clustering analysis was performed on a normalized subset of these data. Results  Systemic administration of rIL-21 affected the serum levels of several cytokines, chemokines, acute-phase proteins and cell adhesion proteins. The magnitude and duration of response were dose dependent for a subset of these biomarkers. The 5 + 9 dosing regimen generally produced cyclic changes that were of greater magnitude, as compared to a more chronic stimulation with the 3/w dosing regimen. Despite these differences, rIL-21 effects on many analytes were similar between regimens when averaged over the time of treatment. Based on similar temporal, between-subject and dose response changes, groups of analytes were identified that exhibited distinct components of the rIL-21-mediated immune activation. Biomarkers indicative of lymphocyte activation (increased IL-16, decreased RANTES), acute phase response (increased CRP, ferritin), myeloid activation (increased MDC, MIP-1 alpha), and leukocyte chemotaxis/trafficking (increased sCAMs, MCP-1) were strongly modulated in subjects treated with rIL-21. Conclusions  Administration of rIL-21 resulted in activation of multiple cell types and immune response pathways. The changes observed in serum proteins were consistent with coincident processes of lymphoid and myeloid cell activation and trafficking, and acute phase response. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Enhanced peptide mass fingerprinting through high mass accuracy: Exclusion of non-peptide signals based on residual mass

Peptide mass fingerprinting (PMF) is among the principle methods of contemporary proteomic analysis. While PMF is routinely practiced in many laboratories, the complexity of protein tryptic digests is such that PMF based on unrefined mass spectrometric peak lists is often inconclusive. A number of data processing strategies have thus been designed to improve the quality of PMF peak lists, and the development of increasingly elaborate tools for PMF data reduction remains an active area of research. In this report, a novel and direct means of PMF peak list enhancement is suggested. Since the monoisotopic mass of a peptide must fall within a predictable range of residual values, PMF peak lists can in principle be relieved of many non-peptide signals solely on the basis of accurately determined monoisotopic mass. The calculations involved are relatively simple, making implementation of this scheme computationally facile. When this procedure for peak list processing was used, the large number of unassigned masses typical of PMF peak lists was considerably attenuated. As a result, protein identifications could be made with greater confidence and improved discrimination as compared to PMF queries submitted with raw peak lists. Importantly, this scheme for removal of non-peptide masses was found to conserve peptides bearing various post-translational and artificial modifications. All PMF experiments discussed here were performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which provided the high mass resolution and high mass accuracy essential for this application. Previously reported equations relating the nominal peptide mass to the permissible range of fractional peptide masses were slightly modified for this application, and these adjustments have been illustrated in detail. The role of mass accuracy in application of this scheme has also been explored.     

Temperature and kairomone induced life history plasticity in coexisting Daphnia

We investigated the life history alterations of coexisting Daphnia species responding to environmental temperature and predator cues. In a laboratory experiment, we measured Daphnia life history plasticity under different predation risk and temperature treatments that simulate changing environmental conditions. Daphnia pulicaria abundance and size at first reproduction (SFR) declined, while ephippia (resting egg) formation increased at high temperatures. Daphnia mendotae abundance and clutch size increased with predation risk at high temperatures, but produced few ephippia. Thus, each species exhibited phenotypic plasticity, but responded in sharply different ways to the same environmental cues. In Glen Elder reservoir, Kansas USA, D. pulicaria dominance shifted to D. mendotae dominance as temperature and predation risk increased from March to June in both 1999 and 2000. Field estimates of life history shifts mirrored the laboratory experiment results, suggesting that similar phenotypic responses to seasonal cues contribute to seasonal Daphnia population trends. These results illustrate species-specific differences in life history plasticity among coexisting zooplankton taxa.     

Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors

Rust fungi, obligate biotrophs that cause disease and yield losses in crops such as cereals and soybean (Glycine max), obtain nutrients from the host through haustoria, which are specialized structures that develop within host cells. Resistance of flax (Linum usitatissimum) to flax rust (Melampsora lini) involves the induction of a hypersensitive cell death response at haustoria formation sites, governed by gene-for-gene recognition between host resistance and pathogen avirulence genes. We identified genes encoding haustorially expressed secreted proteins (HESPs) by screening a flax rust haustorium-specific cDNA library. Among 429 unigenes, 21 HESPs were identified, one corresponding to the AvrL567 gene. Three other HESPs cosegregated with the independent AvrM, AvrP4, and AvrP123 loci. Expression of these genes in flax induced resistance gene-mediated cell death with the appropriate specificity, confirming their avirulence activity. AvrP4 and AvrP123 are Cys-rich proteins, and AvrP123 contains a Kazal Ser protease inhibitor signature, whereas AvrM contains no Cys residues. AvrP4 and AvrM induce cell death when expressed intracellularly, suggesting their translocation into plant cells during infection. However, secreted AvrM and AvrP4 also induce necrotic responses, with secreted AvrP4 more active than intracellular AvrP4, possibly as a result of enhanced formation of endoplasmic reticulum-dependent disulfide bonds. Addition of an endoplasmic reticulum retention signal inhibited AvrM-induced necrosis, suggesting that both AvrM and AvrP4 can reenter the plant cell after secretion in the absence of the pathogen.     

The effect of an imprecise map on interval mapping QTLs

The statistical analysis of quantitative trait locus (QTL) experiments relies on the use of a linkage map of the markers genotyped. Such a map is, at best, a good estimate of the true map. Resources might be diverted into developing better marker maps or improved maps become available after the analysis, raising concerns over the original analysis. It is therefore important to understand the sensitivity of QTL analysis to map inaccuracy. We have used simulation methods to investigate the consequences of an incorrect map on the results of a QTL analysis using interval mapping. Backcross data sets were generated with a particular map and then analysed with both the correct map and incorrect maps. If the incorrect maps maintained the true linkage groups (i.e. no markers were incorrectly assigned to another linkage group), the accuracy of the map had little or no impact on the ability to detect QTLs, the true significance levels of the tests or the relative placement of QTLs. When a marker was incorrectly placed on another linkage group, there was a small increase in the level of the test. After adjusting for this increase, there was a decrease in power to detect a QTL near the misplaced marker. This decrease was of a similar magnitude to that found when using a single-marker analysis compared with interval mapping. These results mean that QTL analyses can proceed without the need for very accurate marker maps, and that estimated QTL positions can be translated onto updated maps without the need for reanalysis.     

Identification and characterization of a novel interaction between pulmonary surfactant protein D and decorin

Surfactant-associated protein D (SP-D) is a collectin that is present in lung surfactant and mucosal surfaces. Although SP-D regulates diverse functions, only a few proteins are known to bind to this collectin. Here we describe the co-purification of decorin, a novel SP-D-binding protein, from amniotic fluid. The human decorin that co-purified with SP-D is a 130-150-kDa proteoglycan, which has a 46-kDa protein core and approximately 90-kDa dermatan sulfate chain. Both native and recombinant decorin can bind to SP-D that is already bound to maltose-agarose matrix, and these SP-D-decorin complexes are dissociated at high salt (0.5-1.0 m NaCl) conditions, releasing the decorin. We further show that SP-D and decorin interact with each other (kd = 4 nm) by two mechanisms. First, the direct binding and competition experiments show that the carbohydrate recognition domain (CRD) of SP-D binds in a calcium dependent-manner to the sulfated N-acetyl galactosamine moiety of the glycosaminoglycan chain. Second, complement component C1q, a complement protein that is known to interact with decorin core protein via its collagen-like region, partially blocks the interaction between decorin and native SP-D. This protein, however, does not block the interaction between decorin and SP-D(n/CRD), a recombinant fragment that lacks the N-terminal and collagen-like regions. Furthermore, the core protein, obtained by chondroitin ABC lyase treatment of decorin, binds SP-D, but not SP-D(n/CRD). These findings suggest that decorin core protein binds the collagen-like region of the SP-D. Concentrations of decorin and SP-D are negatively correlated to each other, in amniotic fluid, implying a functional relevance for SP-D-decorin interaction, in vivo. Collectively, our results show that carbohydrate recognition domains of SP-D interact with the dermatan sulfate moiety of decorin via lectin activity and that the core protein of decorin binds the collagen-like region of SP-D in vitro, and these interactions may be operative in vivo.