Inter-population differences in diving behaviour of adult male southern elephant seals (Mirounga leonina)

Access to different environments may lead to inter-population behavioural changes within a species that allow populations to exploit their immediate environments. Elephant seals from Marion Island (MI) and King George Island (KGI) (Isla 25 de Mayo) forage in different oceanic environments and evidently employ different foraging strategies. This study elucidates some of the factors influencing the diving behaviour of male southern elephant seals from these populations tracked between 1999 and 2002. Mixed-effects models were used to determine the influence of bathymetry, population of origin, body length (as a proxy for size) and individual variation on the diving behaviour of adult male elephant seals from the two populations. Males from KGI and MI showed differences in all dive parameters. MI males dived deeper and longer (median: 652.0?m and 34.00?min) than KGI males (median: 359.1?m and 25.50?min). KGI males appeared to forage both benthically and pelagically while MI males in this study rarely reached depths close to the seafloor and appeared to forage pelagically. Model outputs indicate that males from the two populations showed substantial differences in their dive depths, even when foraging in areas of similar water depth. Whereas dive depths were not significantly influenced by the size of the animals, size played a significant role in dive durations, though this was also influenced by the population that elephant seals originated from. This study provides some support for inter-population differences in dive behaviour of male southern elephant seals.     

Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution

Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. Regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. What evolutionary forces explain widespread divergence in cis regulation? AI was assessed in Drosophila melanogaster-Drosophila simulans hybrid female heads using RNA-seq technology. Mapping bias was virtually eliminated by using genotype-specific references. Allele representation in DNA sequencing was used as a prior in a novel Bayesian model for the estimation of AI in RNA. Cis regulatory divergence was common in the organs and tissues of the head with 41% of genes analyzed showing significant AI. Using existing population genomic data, the relationship between AI and patterns of sequence evolution was examined. Evidence of positive selection was found in 30% of cis regulatory divergent genes. Genes involved in defense, RNAi/RISC complex genes, and those that are sex regulated are enriched among adaptively evolving cis regulatory divergent genes. For genes in these groups, adaptive evolution may play a role in regulatory divergence between species. However, there is no evidence that adaptive evolution drives most of the cis regulatory divergence that is observed. The majority of genes showed patterns consistent with stabilizing selection and neutral evolutionary processes.     

A chondroitin sulfate chain attached to the bone dentin matrix protein 1 NH2-terminal fragment

Dentin matrix protein 1 (DMP1) is an acidic noncollagenous protein shown by gene ablations to be critical for the proper mineralization of bone and dentin. In the extracellular matrix of these tissues DMP1 is present as fragments representing the NH2-terminal (37 kDa) and COOH-terminal (57 kDa) portions of the cDNA-deduced amino acid sequence. During our separation of bone noncollagenous proteins, we observed a high molecular weight, DMP1-related component (designated DMP1-PG). We purified DMP1-PG with a monoclonal anti-DMP1 antibody affinity column. Amino acid analysis and Edman degradation of tryptic peptides proved that the core protein for DMP1-PG is the 37-kDa fragment of DMP1. Chondroitinase treatments demonstrated that the slower migration rate of DMP1-PG is due to the presence of glycosaminoglycan. Quantitative disaccharide analysis indicated that the glycosaminoglycan is made predominantly of chondroitin 4-sulfate. Further analysis on tryptic peptides led us to conclude that a single glycosaminoglycan chain is linked to the core protein via Ser74, located in the Ser74-Gly75 dipeptide, an amino acid sequence specific for the attachment of glycosaminoglycans. Our findings show that in addition to its existence as a phosphoprotein, the NH2-terminal fragment from DMP1 occurs as a proteoglycan. Amino acid sequence alignment analysis showed that the Ser74-Gly75 dipeptide and its flanking regions are highly conserved among a wide range of species from caiman to the Homo sapiens, indicating that this glycosaminoglycan attachment domain has survived an extremely long period of evolution pressure, suggesting that the glycosaminoglycan may be critical for the basic biological functions of DMP1.     

The cold and menthol receptor TRPM8 contains a functionally important double cysteine motif

We have investigated the glycosylation, disulfide bonding, and subunit structure of mouse TRPM8. To do this, amino-terminal c-myc or hemagglutinin epitope-tagged proteins were incorporated and expressed in Chinese hamster ovary cells. These modifications had no obvious effects on channel function in intracellular calcium imaging assays upon application of agonists, icilin or menthol, and cold temperatures. Unmodified TRPM8 migrates with an apparent mass of 129 kDa and can be glycosylated in Chinese hamster ovary cells to give glycoproteins with apparent masses of 136 and 147 kDa. We identified two potential N-linked glycosylation sites in TRPM8 (Asn-821 and Asn-934) and mutated them to show that only the site in the putative pore region at position 934 is modified and that glycosylation of this site is not absolutely necessary for cell surface expression or responsiveness to icilin, menthol, and cool temperatures. Enzymatic cleavage of the carbohydrate chains indicated that they are complex carbohydrate. The glycosylation site is flanked in the pore by two cysteine residues that we mutated, to prove that they are involved in a conserved double cysteine motif, which is essential for channel function. Mutation of either of these cysteines abolishes function and forces the formation of a non-functional complex of the size of a homodimer. The double cysteine mutant is also non-functional. Finally, we showed in Perfluoro-octanoic acid-polyacrylamide gels that TRPM8 can form a tetramer (in addition to dimer and trimer forms), consistent with current thinking that functional TRP ion channels are tetrameric.     

Notes on the natural diet and habitat of eight danionin fishes, including the zebrafish Danio rerio

The diet and habitat of eight danionin species ( Danio and Devario ) from 18 sites in India and Thailand are reported. At every site, habitat characteristics, including pH, light penetration, water temperature, current speed, stream dimensions, canopy cover and substratum type, were recorded. Danionins were found primarily in warm (24–35° C), moving water of moderate clarity and pH (6·6–8·2) and there were significant differences among species in water temperature, pH and current speed. Deep-bodied Devario species were generally associated with faster water currents than more slender-bodied Danio species. Gut content analyses of 327 individuals representing 17 populations showed that insects were the primary food resource for the eight Danio and Devario species. Crustaceans, fish scales, algae and detritus were also important supplements for particular species. Stable isotope data from syntopic species indicated long-term differences in consumption of terrestrial v. aquatic insects in one of two population pairs.     

Contrasting roles for domain 4 of VCAM-1 in the regulation of cell adhesion and soluble VCAM-1 binding to integrin alpha4beta1

Cell adhesion mediated by the interaction between integrin alpha4beta1 and VCAM-1 is important in normal physiologic processes and in inflammatory and autoimmune disease. Numerous studies have mapped the alpha4beta1 binding sites in VCAM-1 that mediate cell adhesion; however, little is known about the regions in VCAM-1 important for regulating soluble binding. In the present study, we demonstrate that 6D VCAM-1 (an alternatively spliced isoform of VCAM-1 lacking Ig-like domain 4) binds alpha4beta1 with a higher relative affinity than does the full-length form of VCAM-1 containing 7 Ig-like extracellular domains (7D VCAM-1). In indirect binding assays, the EC50 of soluble 6D VCAM-1 binding to alpha4beta1 on Jurkat cells (in 1 mM MnCl2) was 2 x 10(-9) M, compared with 7D VCAM-1 at 11 x 10(-9) M. When used in solution to inhibit alpha4beta1 mediated cell adhesion, the IC50 of 6D VCAM-1 was 13 x 10(-9) M, compared with 7D VCAM-1 measured at 150 x 10(-9) M. Removal of Ig-like domains 4, 5, or 6, or simply substituting Asp328 in domain 4 of 7D VCAM-1 with alanine, caused increased binding of soluble 7D VCAM-1 to alpha4beta1. In contrast, cells adhered more avidly to 7D VCAM-1 under shear force, as it induced cell spreading at lower concentrations than did 6D VCAM-1. Finally, soluble 6D VCAM-1 acts as an agonist through alpha4beta1 by augmenting cell migration and inducing cell aggregation. These results indicate that the domain 4 of VCAM-1 plays a contrasting role when VCAM-1 is presented in solution or as a cell surface-expressed adhesive substrate.     

LFA-1 Affinity Regulation Is Necessary for the Activation and Proliferation of Naive T Cells

The activation of LFA-1 (lymphocyte function-associated antigen) is a critical event for T cell co-stimulation. The mechanism of LFA-1 activation involves both affinity and avidity regulation, but the role of each in T cell activation remains unclear. We have identified antibodies that recognize and block different affinity states of the mouse LFA-1 I-domain. Monoclonal antibody 2D7 preferentially binds to the low affinity conformation, and this specific binding is abolished when LFA-1 is locked in the high affinity conformation. In contrast, M17/4 can bind both the locked high and low affinity forms of LFA-1. Although both 2D7 and M17/4 are blocking antibodies, 2D7 is significantly less potent than M17/4 in blocking LFA-1-mediated adhesion; thus, blocking high affinity LFA-1 is critical for preventing LFA-1-mediated adhesion. Using these reagents, we investigated whether LFA-1 affinity regulation affects T cell activation. We found that blocking high affinity LFA-1 prevents interleukin-2 production and T cell proliferation, demonstrated by TCR cross-linking and antigen-specific stimulation. Furthermore, there is a differential requirement of high affinity LFA-1 in the activation of CD4⁺ and CD8⁺ T cells. Although CD4⁺ T cell activation depends on both high and low affinity LFA-1, only high affinity LFA-1 provides co-stimulation for CD8⁺ T cell activation. Together, our data demonstrated that the I-domain of LFA-1 changes to the high affinity state in primary T cells, and high affinity LFA-1 is critical for facilitating T cell activation. This implicates LFA-1 activation as a novel regulatory mechanism for the modulation of T cell activation and proliferation.LFA-1 (lymphocyte function-associated antigen), an integrin family member, is important in regulating leukocyte adhesion and T cell activation (1, 2). LFA-1 consists of the α_L (CD11a) and β₂ (CD18) heterodimer. The ligands for LFA-1, including intercellular adhesion molecule ICAM³-1, ICAM-2, and ICAM-3, are expressed on antigen-presenting cells (APCs), endothelial cells, and lymphocytes (1). Mice that are deficient in LFA-1 have defects in leukocyte adhesion, lymphocyte proliferation, and tumor rejection (3–5). Blocking LFA-1 with antibodies can prevent inflammation, autoimmunity, organ graft rejection, and graft versus host disease in human and murine models (6–10).LFA-1 is constitutively expressed on the surface of leukocytes in an inactive state. Activation of LFA-1 is mediated by inside-out signals from the cytoplasm (1, 11). Subsequently, activated LFA-1 binds to the ligands and transduces outside-in signals back into the cytoplasm that result in cell adhesion and activation (12, 13). The activation of LFA-1 is a critical event in the formation of the immunological synapse, which is important for T cell activation (2, 14, 15). The active state of LFA-1 is regulated by chemokines and the T cell receptor (TCR) through Rap1 signaling (16). LFA-1 ligation lowers the activation threshold and affects polarization in CD4⁺ T cells (17). Moreover, productive LFA-1 engagement facilitates efficient activation of cytotoxic T lymphocytes and initiates a distinct signal essential for the effector function (18–20). Thus, LFA-1 activation is essential for the optimal activation of T cells.The mechanism of LFA-1 activation involves both affinity (conformational changes within the molecule) and avidity (receptor clustering) regulation (21–23). The I-domain of the LFA-1 α_L subunit is the primary ligand-binding site and has been proposed to change conformation, leading to an increased affinity for ligands (24–26). The structural basis of the conformational changes in the I-domain of LFA-1 has been extensively characterized (27). Previously, we have demonstrated that the conformation of the LFA-1 I-domain changes from the low affinity to the high affinity state upon activation. By introducing disulfide bonds into the I-domain, LFA-1 can be locked in either the closed or open conformation, which represents the “low affinity” or “high affinity” state, respectively (28, 29). In addition, we identified antibodies that are sensitive to the affinity changes in the I-domain of human LFA-1 and showed that the activation-dependent epitopes are exposed upon activation (30). This study supports the presence of the high affinity conformation upon LFA-1 activation in cell lines. It has been demonstrated recently that therapeutic antagonists, such as statins, inhibit LFA-1 activation and immune responses by locking LFA-1 in the low affinity state (31–34). Furthermore, high affinity LFA-1 has been shown to be important for mediating the adhesion of human T cells (35, 36). Thus, the affinity regulation is a critical step in LFA-1 activation.LFA-1 is a molecule of great importance in the immune system, and its activation state influences the outcome of T cell activation. Our previous data using the activating LFA-1 I-domain-specific antibody MEM83 indicate that avidity and affinity of the integrin can be coupled during activation (37). However, whether affinity or avidity regulation of LFA-1 contributes to T cell activation remains controversial (23, 38, 39). Despite the recent progress suggesting that conformational changes represent a key step in the activation of LFA-1, there are considerable gaps to be filled. When LFA-1 is activated, the subsequent outside-in signaling contributes to T cell activation via immunological synapse and LFA-1-dependent signaling. It is critical to determine whether high affinity LFA-1 participates in the outside-in signaling and affects the cellular activation of T cells. Nevertheless, the rapid and dynamic process of LFA-1 activation has hampered further understanding of the role of high affinity LFA-1 in primary T cell activation. The affinity of LFA-1 for ICAM-1 increases up to 10,000-fold within seconds and involves multiple reversible steps (23). In addition, the activation of LFA-1 regulates both adhesion and activation of T cells, two separate yet closely associated cellular functions. When LFA-1 is constitutively expressed in the active state in mice, immune responses are broadly impaired rather than hyperactivated, suggesting the complexity of affinity regulation (40). Therefore, it is difficult to dissect the mechanisms by which high affinity LFA-1 regulates stepwise activation of T cells in the whole animal system.In the present study, we identified antibodies recognizing and blocking different affinity states of mouse LFA-1. These reagents allowed us to determine the role of affinity regulation in T cell activation. We found that blocking high affinity LFA-1 inhibited IL-2 production and proliferation in T cells. Furthermore, there is a differential requirement of high affinity LFA-1 in antigen-specific activation of CD4⁺ and CD8⁺ T cells. The activation of CD4⁺ T cells depends on both high and low affinity LFA-1. For CD8⁺ T cell activation, only high affinity LFA-1 provides co-stimulation. Thus, affinity regulation of LFA-1 is critical for the activation and proliferation of naive T cells.     

The Complex Genetic Structure of Sugarcane Limits Identification of Additional SNP-Defined Simplex Alleles in Microsatellite Loci

Cultivated sugarcane possesses a large number of chromosomes (typically >80) which can be organised into eight homology groups, each containing approximately 12 homo(eo)logous chromosomes. Currently, microsatellite (SSR) markers are the most easily used markers for marker-assisted selection and other genetic applications. However, only SSR alleles that segregate as simplex and duplex markers can be incorporated into sugarcane maps using populations of ～300 progeny. Consequently only a subset of possible alleles have been mapped for a given SSR locus and are available for subsequent QTL analyses. Three sugarcane SSR loci, mSSCIR8, mSSCIR17 and mSSCIR18, were amplified, cloned and sequenced from the parents of an Australian sugarcane mapping population, IJ76-514 and . The sequences were examined to identify nucleotide sequence polymorphisms in the flanking regions that could provide additional simplex SSR allele markers. Alignment of the sequences revealed SNP, indel and repeat length variation and the pattern of sequence variation suggested multiple alleles for each SSR, including all of the alleles previously scored by fragment length. While the flanking regions of the SSR loci contained numerous SNPs and indels, none defined new simplex alleles within multiplex fragments and no new SSR simplex alleles were mapped. Furthermore, many of the sequence-defined alleles appear to be spurious and may have arisen from PCR-mediated recombination. These results confirm the difficulties associated with characterising allelic diversity in a polyploid species and the complexity of mapping in sugarcane.