GENSTAT programs for performing Muir's alternative partitioning of genotype-by-environment interaction.

Genotype-by-environment (GE) interaction exists when different cultivars or strains have different phenotypic responses to environmental variation (Merila and Fry 1998). The phenomenon is of major concern in plant breeding, as it can limit gains in selecting superior cultivars. In animal breeding, the problem is also an important issue because breeding stocks are developed by a few companies but are used worldwide (Lin and Togashi 2002).

Macaque thresholds for detecting increases in intensity: effects of formant structure.

Macaque monkeys, like humans, are more sensitive to differences in formant frequency than to differences in the frequency of pure tones (see Sinnott et al. (1987) J. Comp. Psychol. 94, 401-415; Pfingst (1993) J. Acoust. Soc. Am. 93, 2124-2129; Prosen et al. (1990) J. Acoust. Soc. Am. 88, 2152-2158; Sinnott et al. (1985) J. Acoust. Soc. Am. 78, 1977-1985; Sinnott and Kreiter (1991) J. Acoust. Soc. Am. 89, 2421-2429; for summary, see May et al. (1996) Aud. Neurosci. 3, 135-162). In the discrimination of formant frequency, it appears that the relevant cue for macaque monkeys is relative level differences of the component frequencies (Sommers et al. (1992) J. Acoust. Soc. Am. 91, 3499-3510). To further explore the result of Sommers et al., we trained macaque monkeys (Macaca fuscata) to report detection of a change in the spectral shape of multi-component harmonic complexes. Spectral shape changes were produced by the addition of intensity increments. When the amplitude spectrum of the comparison stimulus was modeled after the /ae/ vowel sound, thresholds for detecting a change from the comparison stimulus were lowest when intensity increments were added at spectral peaks. These results parallel previous data from human subjects, suggesting that both human and monkey subjects may process vowel spectra through simultaneous comparisons of component levels across the spectrum. When the subjects were asked to detect a change from a comparison stimulus with a flat amplitude spectrum, the subjects showed sensitivity that was relatively comparable to that of human subjects tested in other investigations (e.g. Zera et al. (1993) J. Acoust. Soc. Am. 93, 3431-3441). In additional experiments, neither increasing the dynamic range of the /ae/ spectrum nor dynamically varying the amplitude of the increment during the stimulus presentation reliably affected detection thresholds.

Polyisoprenyl glycolipids as targets of CD1-mediated T cell responses.

T cells are well known to recognize peptide antigens presented by major histocompatibility (MHC) class I or class II molecules. More recently, the CD1 family of antigen-presenting molecules has been shown to present both mammalian and microbial glycolipid antigens for specific recognition by T cells. Human CD1c proteins mediate T cell recognition of polyisoprenyl glycolipids, evolutionarily conserved phosphoglycolipids, which function in glycan synthesis pathways. This family of antigenic molecules is particularly attractive for the study of the molecular features that control T cell recognition of self and foreign glycolipids because natural polyisoprenols from mammals, fungi, protozoa, mycobacteria and eubacteria differ in structure. Moreover, these naturally occurring structural differences can influence their recognition by CDlc-restricted T cells. This review of the structural diversity and evolutionary relationships of polyisoprenoid glycolipids emphasizes those features of polyisoprenyl glycolipid biosynthesis that are relevant to their functions as targets of CD1-mediated T cell responses.

Glycolipid targets of CD1-mediated T-cell responses.

Members of the CD1 family of antigen-presenting molecules bind and present a variety of mammalian and microbial glycolipids for specific recognition by T cells. CD1 proteins accomplish their antigen-presenting function by binding the alkyl chains of the antigens within a deep, hydrophobic groove on the membrane distal surface of CD1, making the hydrophilic elements of the antigen available for contact with the variable regions of antigen-specific T-cell receptors. Most models of CD1-restricted T cells function in infectious, neoplastic, or autoimmune diseases and are based on the premise that CD1-restricted T-cell responses are initiated by alterations in cellular glycolipid content. Although a growing number of self, altered self and foreign glycolipid antigens have been identified, the cellular mechanisms that could lead to the generation of antigenic glycolipids within cells, or control the presentation of particular classes of altered self or microbial glycolipids in disease states have only recently come under investigation. Here we review the structures of known glycolipid antigens for T cells and discuss how the chemical nature of these antigens, which is quite different from that of peptides, influences their recognition by T cells.

CD1 trafficking: invariant chain gives a new twist to the tale.

The CD1 family of MHC class I-related proteins present foreign and self-lipid antigens for specific recognition by T cells. Based on previous experience with MHC class I and II molecules, it seems likely that a thorough knowledge of the intracellular trafficking and localization of CD1 proteins will be essential to fully understand their functions in antigen presentation and immune responses. Two studies in this issue of Immunity take a detailed look at factors affecting the localization of mouse CD1 proteins to the endocytic system of antigen-presenting cells. Their results provide intriguing evidence for the involvement of two critical components of the MHC class II endosomal processing pathway, cathepsin S and the invariant chain, in the normal functioning of CD1.

CD1b-mediated T cell recognition of a glycolipid antigen generated from mycobacterial lipid and host carbohydrate during infection.

T cells recognize microbial glycolipids presented by CD1 proteins, but there is no information regarding the generation of natural glycolipid antigens within infected tissues. Therefore, we determined the molecular basis of CD1b-restricted T cell recognition of mycobacterial glycosylated mycolates, including those produced during tissue infection in vivo. Transfection of the T cell receptor (TCR) alpha and beta chains from a glucose monomycolate (GMM)-specific T cell line reconstituted GMM recognition in TCR-deficient T lymphoblastoma cells. This TCR-mediated response was highly specific for natural mycobacterial glucose-6-O-(2R, 3R) monomycolate, including the precise structure of the glucose moiety, the stereochemistry of the mycolate lipid, and the linkage between the carbohydrate and the lipid. Mycobacterial production of antigenic GMM absolutely required a nonmycobacterial source of glucose that could be supplied by adding glucose to media at concentrations found in mammalian tissues or by infecting tissue in vivo. These results indicate that mycobacteria synthesized antigenic GMM by coupling mycobacterial mycolates to host-derived glucose. Specific T cell recognition of an epitope formed by interaction of host and pathogen biosynthetic pathways provides a mechanism for immune response to those pathogenic mycobacteria that have productively infected tissues, as distinguished from ubiquitous, but innocuous, environmental mycobacteria.

Factors influencing the salience of temporal cues in the discrimination of synthetic Japanese monkey (Macaca fuscata) coo calls.

If temporal position of a frequency inflection is the most salient communication cue in Japanese macaque smooth early and smooth late high coos, then macaques should perceive coos differing only along the early-late dimension as belonging to different classes. The perceived similarity of synthetic coos and temporally reversed variants were evaluated, using multidimensional scaling of macaque discrimination latencies. Original calls and calls temporally reversed in the frequency domain could be discriminated if the peak was near a call endpoint but not if the frequency peak in the original call was near the coo midpoint. Perceived similarity of such calls was inversely related to the amount of frequency modulation. Temporal reversals of amplitude contours were also conducted. Although macaques are quite sensitive to amplitude increments, reversal of the relatively flat amplitude contours of these calls did not affect discrimination responses.

Glycosyl-phosphatidylinositol reanchoring unmasks distinct antigen-presenting pathways for CD1b and CD1c.

Human CD1 proteins present lipid and glycolipid Ags to T cells. Cellular trafficking patterns of CD1 proteins may determine the ability of differing isoforms of CD1 to acquire, bind, and present these Ags to T cells. To test this hypothesis, glycosyl-phosphatidylinositol (GPI)-modified variants of CD1b and CD1c were engineered by chimerization with a GPI modification signal sequence derived from decay-accelerating factor (DAF). GPI reanchoring was confirmed by demonstrating the phosphatidylinositol-specific phospholipase C sensitivity of the CD1b. DAF and CD1c. DAF fusion proteins expressed on transfectant cell surfaces. Using cytotoxicity and cytokine release assays as functional readouts, we demonstrated that CD1c. DAF is as efficient as native CD1c in presenting mycobacterial Ags to the human CD1c-restricted T cell line CD8-1. In contrast, CD1b. DAF, although also capable of presenting Ag (in this case to the CD1b-restricted T cell line LDN5), was less efficient than its native CD1b counterpart. The data support the idea that CD1c. DAF maintains the capacity to access CD1c Ag-loading compartment(s), whereas CD1b. DAF is diverted by its GPI anchor away from the optimal CD1b Ag-loading compartment(s). This constitutes the first GPI reanchoring of CD1 proteins and provides evidence that CD1b and CD1c have nonoverlapping Ag-presenting pathways, suggesting that these two Ag-presenting molecules may have distinct roles in lipid Ag presentation.

CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection.

The discovery of the CD1 antigen presentation pathway has expanded the spectrum of T-cell antigens to include lipids, but the range of natural lipid antigens and functions of CD1-restricted T cells in vivo remain poorly understood. Here we show that the T-cell antigen receptor and the CD1c protein mediate recognition of an evolutionarily conserved family of isoprenoid glycolipids whose members include essential components of protein glycosylation and cell-wall synthesis pathways. A CD1c-restricted, mycobacteria-specific T-cell line recognized two previously unknown mycobacterial hexosyl-1-phosphoisoprenoids and structurally related mannosyl-beta1-phosphodolichols. Responses to mannosyl-beta1-phosphodolichols were common among CD1c-restricted T-cell lines and peripheral blood T lymphocytes of human subjects recently infected with M. tuberculosis, but were not seen in naive control subjects. These results define a new class of broadly distributed lipid antigens presented by the CD1 system during infection in vivo and suggest an immune mechanism for recognition of senescent or transformed cells that are known to have altered dolichol lipids.

Diversification of CD1 proteins: sampling the lipid content of different cellular compartments.

Four human CD1 isoforms (CD1a, -b,-c and -d) are now known to be antigen presenting molecules with the unique ability to present lipid antigens to T cells. CD1b and CD1d are found in acidic, late endocytic compartments, whereas CD1a and CD1c molecules accumulate at the plasma membrane and in early endosomes. Consistent with their differences in intracellular localization, most studies show antigen presentation by CD1b/CD1d to be dependent on endosomal acidification while CD1a/CD1c mediated antigen presentation is not. Taken together, recent advances in the analysis of CD1 molecules reinforce the hypothesis that the different CD1 isoforms are specialized to survey the lipid content of distinct intracellular compartments. This may help to explain the duplication and diversification of CD1 genes in humans and other mammalian species.

Uptake and processing of glycosylated mycolates for presentation to CD1b-restricted T cells.

Antigen presenting cells (APCs) expressing CD1b mediate the specific T cell recognition of mycobacterial lipid antigens. These lipid antigens require internalization by APCs prior to presentation, but the detailed mechanisms of uptake and intracellular processing are not known. Here we have examined several steps in the presentation of two related classes of CD1b-presented antigens, free and glycosylated mycolates. T cell recognition of glucose monomycolate (GMM) was blocked by agents that fix APC membranes or neutralize the pH of endosomes, indicating a requirement for GMM uptake into an acidic compartment prior to recognition. Different T cell lines responded to free mycolate or GMM without crossreactivity, yet both antigens were taken up by APCs at the same rate. This demonstrated that differential recognition of these antigens resulted from T cell specificity for their hydrophilic caps and that APCs were unable to interconvert these antigens by enzymatic or chemical deglycosylation or glycosylation. APCs were also unable to cleave mycobacterial trehalose dimycolate (TDM) at its most chemically labile linkages to yield antigenic free mycolates or GMM. Our results indicate that these mycolate-containing antigens are resistant to chemical or enzymatic cleavage by APCs, suggesting that molecular trimming is not a universal feature of lipid antigen processing.

Mechanisms of lipid antigen presentation by CD1.

CD1 is a family of cell surface glycoproteins that are related in structure and evolutionary origin to the major histocompatibility complex (MHC)-encoded antigen-presenting molecules. In contrast to MHC-encoded antigen-presenting molecules, CD1 binds and presents lipid and glycolipid antigens for specific recognition by T cell antigen receptors. Recent work shows that several CD1 family members colocalize with MHC class II proteins within the endocytic system of antigen-presenting cells. Detailed studies of the intracellular trafficking of CD1 proteins reveal new mechanisms controlling delivery of antigen-presenting molecules to particular compartments within cells. The combination of overlapping yet distinct trafficking routes for the various CD1 family members, combined with emerging information on the heterogeneity of CD1-presented lipid antigens, suggest a model whereby different members of the CD1 family could present antigens that occur in various cellular compartments. Furthermore, the CD1 family as a group may present antigens from pathogens that are not normally accessible to or efficiently surveyed by the MHC Class I or II systems. The discovery of this third pathway for antigen presentation, together with the appreciation of a previously unrecognized universe of nonpeptide lipid antigens for T cell responses, are likely to have broad implications for our understanding of the cell-mediated immune response and its role in health and disease.

The molecular basis of CD1-mediated presentation of lipid antigens.

The CD1 family of proteins mediates a newly described pathway for presentation of lipids and glycolipids for specific recognition by T cells. All four of the known human CD1 proteins (CD1a, CD1b, CD1c and CD1d) as well as murine CD1d have now been shown to mediate T-cell recognition of lipid or glycolipid antigens. These antigens include naturally occurring foreign glycolipids from intracellular pathogens or synthetic glycolipids that are related in structure to mammalian glycolipids. The CD1b and CD1d-presented antigens differ in their fine structures but reveal a general motif in which a rigid hydrophilic cap is bound to two aliphatic hydrocarbon chains. Different T-cell populations recognize individual antigens without cross-reactivity to closely related antigen structures or CD1 isoforms, documenting the complexity and fine specificity of CD1-mediated T-cell responses. Mapping of the molecular determinants of recognition for CD1b and CD1d-presented antigens reveals that T cells discriminate the fine structure of the hydrophilic cap of the antigen, but both the length and structure of the lipid chains may be altered without loss of recognition. This pattern of lipid antigen recognition may be accounted for by a simple molecular mechanism of presentation that parallels the known mechanism for presentation of peptides, but solves the special problems related to the hydrophobic chemical nature of the lipid antigens. We propose that CD1 binds antigen by accommodating the two lipid tails within the hydrophobic groove of its two membrane distal domains, positioning the rigid hydrophilic cap of the antigen on the solvent-exposed surface of the CD1 protein, where it can directly contact the T-cell antigen receptor. This model provides a molecular basis for recognition of a new and diverse set of T-cell antigens contained within the lipid bilayers of cellular membranes.

Monaural phase discrimination by macaque monkeys: use of multiple cues.

Research examining the discrimination of monaural phase change has suggested that temporal envelope shape, which varies with phase, may be an important cue. Much of that research employed stimuli consisting of three components, a center frequency (Fc), which is varied in phase, and an upper and lower sideband separated from the carrier by some frequency (delta F). As the phase of the center component is varied, both temporal envelope and temporal fine structure change. The present research explored the salience of both envelope and fine structure as cues in a phase discrimination task. Monkeys were trained to report detection of a change from a three-tone complex with 90 degrees starting phase for the center component to one in which the starting phase was smaller. In general, for the values of Fc tested, thresholds for phase change decreased as delta F increased. When tested with comparison stimuli that had a temporal envelope closely matched to that of the standard, but 0 degree starting phase, subjects had difficulty discriminating these stimuli from the standard for smaller delta F, but readily discriminated them at larger delta F values. These findings suggest that temporal envelope is a critical cue in discrimination of three-tone complexes on the basis of the starting phase of the center component at small values of delta F, but that other cues are used at larger delta F values.

CD1--a new paradigm for antigen presentation and T cell activation.

Despite identification of the CD1 family of molecules in the late 1970s, the function of CD1 was undetermined for more than a decade. Recent evidence has established that CD1 molecules comprise a novel lineage of antigen-presenting molecules, distinct from major histocompatibility complex (MHC) class I and class II molecules. Unlike the MHC molecules, which bind short peptides in their antigen-binding groove for presentation to either CD4+ or CD8+ T cells bearing alpha beta T cell receptors, the CD1 molecules appear to accommodate lipid and glycolipid antigens in their hydrophobic cavity for presentation to a wide variety of T cells, including double-negative alpha beta and gamma delta T cells and CD8+ alpha beta T cells. By using a unique cytoplasmic signal, some CD1 molecules traffic to endosomal compartments for sampling mycobacteria-derived lipid antigens, and subsequently lipid antigen-loaded CD1 molecules are expressed on the cell surface to activate specific T cells. These CD1-restricted T cells kill mycobacteria-infected cells and secrete interferon-gamma, indicating a potential role of CD1-mediated T cell responses in clearing mycobacterial infection. The identification of an MHC-independent antigen presentation pathway for nonpeptide antigens provides new insights into immunoregulation and host defense.

Molecular interaction of CD1b with lipoglycan antigens.

The ability of human CD1b molecules to present nonpeptide antigens is suggested by the T cell recognition of microbial lipids and lipoglycans in the presence of CD1b-expressing antigen-presenting cells. We demonstrate the high-affinity interaction of CD1b molecules with the acyl side chains of known T cell antigens, lipoarabinomannan, phosphatidylinositol mannoside, and glucose monomycolate. Furthermore, CD1b-antigen binding was optimal at acidic pH, consistent with the known requirement for endosomal acidification in CD1b-restricted antigen presentation. The mechanism for CD1b-ligand interaction involves the partial unfolding of the alpha helices of CD1b at acidic pH, revealing a hydrophobic binding site that could accommodate lipid. These data provide direct evidence that the CD1b molecule has evolved unique biochemical properties that enable the binding of lipid-containing antigens from intracellular pathogens.

The tyrosine-containing cytoplasmic tail of CD1b is essential for its efficient presentation of bacterial lipid antigens.

CD1b is an antigen-presenting molecule that mediates recognition of bacterial lipid and glycolipid antigens by specific T cells. We demonstrate that the nine-amino acid cytoplasmic tail of CD1b contains all of the signals required for its normal endosomal targeting, and that the single cytoplasmic tyrosine is a critical component of the targeting motif. Mutant forms of CD1b lacking the endosomal targeting motif are expressed at high levels on the cell surface but are unable to efficiently present lipid antigens acquired either exogenously or from live intracellular organisms. These results define the functional role of the CD1b targeting motif in a physiologic setting and demonstrate its importance in delivery of this antigen-presenting molecule to appropriate intracellular compartments.

Structural requirements for glycolipid antigen recognition by CD1b-restricted T cells.

The human CD1b protein presents lipid antigens to T cells, but the molecular mechanism is unknown. Identification of mycobacterial glucose monomycolate (GMM) as a CD1b-presented glycolipid allowed determination of the structural requirements for its recognition by T cells. Presentation of GMM to CD1b-restricted T cells was not affected by substantial variations in its lipid tails, but was extremely sensitive to chemical alterations in its carbohydrate or other polar substituents. These findings support the view that the recently demonstrated hydrophobic CD1 groove binds the acyl chains of lipid antigens relatively nonspecifically, thereby positioning the hydrophilic components for highly specific interactions with T cell antigen receptors.

Perceptual salience of acoustic features of Japanese monkey coo calls.

Smooth early high (SEH) and smooth late high (SLH) coo calls differ in the temporal location of a frequency inflection and are generally used in different situations. Coo quality is also influenced by additional features, such as relative harmonic level, which may have communicative significance. The authors used multidimensional scaling to analyze the perceptual similarity of SEH and SLH coos. Neither the temporal position of the frequency inflection nor caller identity could explain the coo groupings. Only the temporal relationships of the relative harmonic levels consistently differed between stimulus clusters. Relative level manipulations were conducted on synthetic coo replicas, resulting in substantial stimulus space reorganization. Although temporal position of the frequency inflection may provide the basis for coo classification, the authors suggest that relative harmonic amplitude can also influence response properties.