T cell epitope definition by differential mass spectrometry: identification of a novel, immunogenic HLA-B8 ligand directly from renal cancer tissue

In this study, we describe a differential mass spectrometric technique for the immuno-proteomic analysis of the major histocompatibility complex (MHC) peptides of a renal cell carcinoma (RCC) biopsy compared with the healthy kidney tissue of the same patient after nephrectomy. Using a stable isotope labeling approach, we could directly compare and relatively quantify 43 MHC-peptide pairs, most of which were present in similar proportions on both normal kidney and tumor. Significantly, two dominant peptides of monoisotopic masses ([M+H](+)) 973.43 u and 967.59 u, respectively, were found exclusively in the tumor sample. One of these was identified as originating from heme oxygenase-1 (HO-1), a protein involved in induction of apoptosis resistance, immuno-suppression and neoangiogenesis and reported to be up-regulated in various cancer types. Moreover, the corresponding synthetic HO-1-derived peptide was shown to be immunogenic in vitro by generation of CD8+ T cell lines with peptide-specific cytolytic activity. Thus, this peptide is an example of a differentially identified T cell epitope that could be considered as a target for immunotherapy.     

Fyn promotes phosphorylation of collapsin response mediator protein 1 at tyrosine 504, a novel,isoform‐specific regulatory site

In vertebrates the collapsin response mediator proteins (CRMPs) are encoded by five highly related genes. CRMPs are cytosolic phosphoproteins abundantly expressed in developing and mature mammalian brains. CRMPs are best understood as effectors of Semaphorin 3A signaling regulating growth cone collapse in migratory neurons. Phosphorylation in the carboxyl‐terminal regulatory domain of CRMPs by several serine/threonine kinases has been described. These phoshorylation events appear to function, at least in part, to disrupt the interaction of CRMPs with tubulin heterodimers. In a large‐scale phosphoproteomic analysis of murine brain, we recently identified a number of in vivo tyrosine phosphorylation sites on CRMP isoforms. Using biochemical approaches and quantitative mass spectrometry we demonstrate that one of these sites, CRMP1 tyrosine 504 (Y504), is a primary target of the Src family of tyrosine kinases (SFKs), specifically Fyn. Y504 is adjacent to CDK5 and GSK‐3β sites that regulate the interaction of CRMPs with tubulin. Although Y504 is highly conserved among vertebrate CRMP1 orthologs, a residue corresponding to Y504 is absent in CRMP isoforms 2–5. This suggests an isoform‐specific regulatory role for CRMP1 Y504 phosphorylation and may help explain the observation that CRMP1‐deficient mice exhibit neuronal migration defects not compensated for by CRMPs 2–5. J. Cell. Biochem. 111: 20–28, 2010. © 2010 Wiley‐Liss, Inc.     

Preparation of 13C-labeled ceramide by acetic acid bacteria and its incorporation in mice

We prepared 2-hydroxypalmitoyl-sphinganine (dihydroceramide) labeled with a stable isotope by culturing acetic acid bacteria with ¹³C-labeled acetic acid. The GC/MS spectrum of the trimethylsilyl derivative of ¹³C-labeled dihydroceramide gave molecular ions with an increased mass of 12–17 Da over that of nonlabeled dihydroceramide. The fragment ions derived from both sphinganine base and 2-hydroxypalmitate were confirmed to be labeled with the stable isotope in the spectrum. Therefore, ¹³C-labeled dihydroceramide can be an extremely useful tool for analyzing sphingolipid metabolism. The purified [¹³C]dihydroceramide was administered orally to mice for 12 days, and the total sphingoid base fractions in various tissues were analyzed by GC/MS. The spectrum patterns specific to ¹³C-labeled sphingoids were detected in the tissues tested. Sphinganine pools in skin epidermis, liver, skeletal muscle, and synapse membrane in brain were replaced by [¹³C]sphinganine at about 4.5, 4.0, 1.0, and 0.3%, respectively. Moreover, about 1.0% of the sphingosine pool in the liver was replaced by [¹³C]sphingosine, implying that exogenous dihydroceramide can be converted to sphingosine. These results clearly indicate that ingested dihydroceramide can be incorporated into various tissues, including brain, and metabolized to other sphingolipids.     

Behavioural responses of invasive American mink Neovison vison to an eradication campaign, revealed by stable isotope analysis

1.  The detrimental impacts of invasive, non-native species on islands are widely acknowledged and it is often best to act rapidly against such species, even where uncertainty exists over the best way to proceed. If management actions are evaluated and refined, using information learnt from the biology of culled animals, this uncertainty can be gradually reduced, increasing the likelihood of a successful outcome.
2.  American mink Neovison vison carcasses were collected as part of an eradication campaign on several islands of the Outer Hebrides, Scotland, and stable isotope analysis was used to describe ecological variation in this invasive non-native predator.
3.  Isotope profiles from individual mink whiskers demonstrated how behaviour at a population level changed markedly over time. As the eradication campaign progressed, mink increased their reliance on marine food sources and focused their activity on the coastline. Stable isotope analyses also demonstrated sex-related changes in foraging and ranging behaviour in relation to food resource availability on the two main island complexes.
4.   Synthesis and applications. Our findings contribute to the refinement of a campaign to extend the successful eradication of mink from Uist and Harris, to the whole of the Outer Hebrides archipelago, UK. They also highlight the potential for stable isotope approaches to provide more detailed postmortem information that can inform adaptive management of wildlife populations for conservation objectives.     

Stable isotope analysis indicates trophic differences among forest floor carabids in Japan

Differences in trophic niches among carabid beetles (Coleoptera: Carabidae) co‐occurring on the forest floors of warm temperate forests in central Japan were studied using carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope analyses. Different carabid species showed similar δ¹⁵N values, which were higher than those of their possible invertebrate prey (herbivores and detritivores) collected from the litter layer, indicating that these species were consumers in the same trophic level. In contrast, δ¹³C values differed among carabid species, indicating interspecific differences in prey animals. The variation in the δ¹³C value was larger in summer than in autumn. In summer, δ¹³C values indicated that some carabids depended highly on either grazing (low δ¹³C values) or detrital sources (high δ¹³C values) within the food chain [Chlaenius posticalis Motschulsky and Haplochlaenius costiger (Chaudoir), respectively], although other species with intermediate δ¹³C values likely depended on both. The latter group of species comprised mostly two dominant genera (Carabus and Synuchus). Although congeners might have similar feeding habits, the stable isotope ratios indicated trophic niche differences between adults of different species and between adults and larvae of the same genus.     

Measuring Brain Uptake and Incorporation into Brain Phosphatidylinositol of Plasma myo-[2H6]Inositol in Unanesthetized Rats: An Approach to Estimate In vivo Brain Phosphatidylinositol Turnover

The in vivo rate of turnover of phosphatidylinositol (PtdIns) in brain is not known. In brain, certain receptor-mediated signal transduction involves metabolism of PtdIns and a method to measure its turnover in awake animals is useful in studying the effect of lithium and other therapeutic agents. In a method described here, rats were infused subcutaneously with myo-[²H₆]inositol (Ins*) using an osmotic pump and, at 1 and 8 weeks, concentrations of free myo-inositol (Ins) and Ins* in plasma and brain were measured by GC-MS (chemical ionization). Also, PtdIns and PtdIns* together in brain were isolated, and Ins and Ins* from their headgroups were released enzymatically and specific activity of incorporated inositol was measured. The specific activity of inositol reached a steady state in plasma within 1 week of infusion, but not in brain even at 8 weeks. However, in brain, the specific activity of phosphatidylinositol was same as that of inositol at both time-points, suggestive of fast turnover of PtdIns. The animal experiment and the analytical methodology described here should be useful for measuring the rate of turnover of brain PtdIns in pathological and drug treatment conditions.     

DIFFERENCES IN FORAGING LOCATION OF MEXICAN AND CALIFORNIA ELEPHANT SEALS: EVIDENCE FROM STABLE ISOTOPES IN PUPS

Female northern elephant seals, Mirounga angustirostris, from Año Nuevo (AN) in central California feed offshore in mid‐latitude waters (40°–55°N). Migratory patterns and foraging locations of seals from Mexico are unknown. Rookeries on San Benitos (SB) islands in Baja California Sur, Mexico, are ～1,170 km south of AN. Although the colonies are similar in size, seals from SB begin breeding earlier and have an earlier breeding birthing peak than seals from AN. To determine if the foraging location of seals from Mexico was similar to that of seals from California, we measured δ¹³C and δ¹⁵N values in the hair of 48 suckling pups at SB and 37 from AN, assuming that their isotopic signatures reflected those of mothers' milk, their exclusive diet. The mean δ¹³C and δ¹⁵N values for SB pups (?16.1‰± 0.9‰ and 17.7‰± 0.9‰, respectively) were significantly higher than those for AN pups (?17.6‰± 0.4‰ and 15.6‰± 1.0‰, respectively). From data on environmental isotope gradients and known behavior of SB and AN populations, we hypothesize that the isotope differences are due to females in the SB colony foraging ～8° south of seals from AN. This hypothesis can be tested by deployment of satellite tags on adult females from the SB colony.     

Computational and Empirical Trans-hydrogen Bond Deuterium Isotope Shifts Suggest that N1–N3 A:U Hydrogen Bonds of RNA are Shorter than those of A:T Hydrogen Bonds of DNA

Density functional theory calculations of isolated Watson–Crick A:U and A:T base pairs predict that adenine ¹³C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, ^2hΔ¹³C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that ^2hΔ¹³C2 is sensitive to hydrogen-bond strength. Calculated ^2hΔ¹³C2 values at a given N1–N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical ^2hΔ¹³C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on ^2hΔ¹³C2 values. Furthermore, ^2hΔ¹³C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that ^2hΔ¹³C2 is context dependent and that this dependence is similar for RNA and DNA. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

General method of preparation of uniformly 13C, 15N-labeled DNA fragments for NMR analysis of DNA structures

Summary ¹³C, ¹⁵N labeling of biomolecules allows easier assignments of NMR resonances and provides a larger number of NMR parameters, which greatly improves the quality of DNA structures. However, there is no general DNA-labeling procedure, like those employed for proteins and RNAs. Here, we describe a general and widely applicable approach designed for preparation of isotopically labeled DNA fragments that can be used for NMR studies. The procedure is based on the PCR amplification of oligonucleotides in the presence of labeled deoxynucleotides triphosphates. It allows great flexibility thanks to insertion of a short DNA sequence (linker) between two repeats of DNA sequence to study. Size and sequence of the linker are designed as to create restriction sites at the junctions with DNA of interest. DNA duplex with desired sequence and size is released upon enzymatic digestion of the PCR product. The suitability of the procedure is validated through the preparation of two biological relevant DNA fragments.The first two authors contributed equally to this work.     

Thematic review series: patient-oriented research. What we have learned about VLDL and LDL metabolism from human kinetics studies

Lipoprotein metabolism is the result of a complex network of many individual components. Abnormal lipoprotein concentrations can result from changes in the production, conversion, or catabolism of lipoprotein particles. Studies in hypolipoproteinemia and hyperlipoproteinemia have elucidated the processes that control VLDL secretion as well as VLDL and LDL catabolism. Here, we review the current knowledge regarding apolipoprotein B (apoB) metabolism, focusing on selected clinically relevant conditions. In hypobetalipoproteinemia attributable to truncations in apoB, the rate of secretion is closely linked to the length of apoB. On the other hand, in patients with the metabolic syndrome, it appears that substrate, in the form of free fatty acids, coupled to the state of insulin resistance can induce hypersecretion of VLDL-apoB. Studies in patients with familial hypercholesterolemia, familial defective apoB, and mutant forms of proprotein convertase subtilisin/kexin type 9 show that mutations in the LDL receptor, the ligand for the receptor, or an intracellular chaperone for the receptor are the most important determinants in regulating LDL catabolism. This review also demonstrates the variance of results within similar, or even the same, phenotypic conditions. This underscores the sensitivity of metabolic studies to methodological aspects and thus the importance of the inclusion of adequate controls in studies.