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Robert D Miller

Publications and source records attributed to Robert D Miller.

At least 19 recordsLinked to original sources
PubMed2006

Modo-UG, a marsupial nonclassical MHC class I locus.

Modo-UG is a class I gene located in the MHC of the marsupial Monodelphis domestica, the gray, short-tailed opossum. Modo-UG is expressed as three alternatively spliced mRNA forms, all of which encode a transmembrane form with a short cytoplasmic tail that lacks phosphorylation sites typically found in classical class I molecules. The three alternative mRNAs would encode a full-length form, an isoform lacking the alpha2 domain, and one lacking both alpha2 and alpha3 domains. Genotyping both captive-bred and wild M. domestica from different geographic regions revealed no variation in the residues that make up Modo-UG's peptide-binding groove. Modo-UG's low polymorphism is contrasting to that of a nearby class I locus, Modo-UA1, which has a highly polymorphic peptide-binding region. Absence of functional polymorphism in Modo-UG is therefore not a general feature of opossum class I genes but the result of negative selection. Modo-UG is the first MHC linked marsupial class I to be described that appears to clearly have nonclassical features.

Alternative Splicing↗
PubMed2006

Isolation of major histocompatibility complex Class I genes from the tammar wallaby (Macropus eugenii).

The major histocompatibility complex (MHC) plays an essential role in the adaptive immune system of vertebrates through antigen recognition. Although MHC genes are found in all vertebrates, the MHC region is dynamic and has changed throughout vertebrate evolution, making it an important tool for comparative genomics. Marsupials occupy an important position in mammalian phylogeny, yet the MHC of few marsupials has been studied in detail. We report the isolation and analysis of expressed MHC Class I genes from the tammar wallaby, a model marsupial used extensively for the study of mammalian reproduction, genetics, and immunology. We determined that there are at least 11 Class I loci in the tammar genome and isolated six expressed Class I sequences from spleen and testes cDNA libraries, representing at least four loci. Two of the Class I sequences contain substitutions at sites known to be important for antigen binding, perhaps impacting their ability to bind peptides, or the types of peptide to which they bind. Phylogenetic analysis of tammar wallaby Class I sequences and other mammalian Class I sequences suggests that some tammar wallaby and red-necked wallaby loci evolved from common ancestral genes.

Amino Acid Sequence↗
PubMed2006

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.

The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.

Animals↗
PubMed2006

Monolayer transistor using a highly ordered conjugated polymer as the channel.

Field-effect transistor structures based on polydiacetylene (PDA) derivatives have been fabricated. Monolayer channels of UV polymerized pentacosa-10,12-diynoic ethanolamide exhibit modulation of source-drain current on application of a gating voltage. Comparison of the two-dimensional crystal morphology of this material with several closely related derivatives that show no gating suggests that a high degree of alignment and order in the polymer chains is necessary for the observed transistor action.

Journal Article↗
PubMed2006

Major histocompatibility complex alleles, sexual responsivity, and unfaithfulness in romantic couples.

Preferences for mates that possess genes dissimilar to one's own at the major histocompatibility complex (MHC), a polymorphic group of loci associated with the immune system, have been found in mice, birds, fish, and humans. These preferences may help individuals choose genetically compatible mates and may adaptively function to prevent inbreeding or to increase heterozygosity and thereby immunocompetence of offspring. MHC-dissimilar mate preferences may influence the psychology of sexual attraction. We investigated whether MHC similarity among romantically involved couples (N= 48) predicted aspects of their sexual relationship. All women in our sample normally ovulated, and alleles at three MHC loci were typed for each person. As the proportion of MHC alleles couples shared increased, women's sexual responsivity to their partners decreased, their number of extrapair sexual partners increased, and their attraction to men other than their primary partners increased, particularly during the fertile phase of their cycles.

Adolescent↗
PubMed2005

TCR gamma chain diversity in the spleen of the duckbill platypus (Ornithorhynchus anatinus).

TCR gamma (TRG) chain diversity in splenic gammadelta T cells was determined for an egg-laying mammal (or monotreme), the duckbill platypus. Three distinct V subgroups were found in the expressed TRG chains and these three subgroups are members of a clade not found so far in eutherian mammals or birds. Each subgroup contains approximately five V gene segments, and their overall divergence is much less than is found in eutherians and birds, consistent with their recent evolution from an ancestral V gene segment. The platypus TRG locus also contains three C region genes and many of the residues involved in TCR function, such as interactions with CD3, were conserved in the monotreme C regions. All non-eutherian mammals (monotremes and marsupials) lacked the second cysteine residue necessary to form the intradomain disulfide bond in the C region, a loss apparently due to independent mutations in marsupials and monotremes. Monotreme TRGC regions also had among the most variation in the length of the connecting peptide region described for any species due to repeated motifs.

Amino Acid Sequence↗
PubMed2005

Unusually similar patterns of antibody V segment diversity in distantly related marsupials.

A pattern of coevolution between the V gene segments of Ig H and L chains has been noted previously by several investigators. Species with restricted germline V(H) diversity tend to have limited germline V(L) diversity, whereas species with high levels of germline V(H) diversity have more diverse V(L) gene segments. Evidence for a limited pool of V(H) but diverse V(L) gene segments in a South American opossum, Monodelphis domestica, is consistent with this marsupial being an exception to the pattern. To determine whether M. domestica is unique or the norm for marsupials, the V(H) and V(L) of an Australian possum, Trichosurus vulpecula, were characterized. The Ig repertoire in T. vulpecula is also derived from a restricted V(H) pool but a diverse V(L) pool. The V(L) gene segments of T. vulpecula are highly complex and contain lineages that predate the separation of marsupials and placental mammals. Thus, neither marsupial follows a pattern of coevolution of V(H) and V(L) gene segments observed in other mammals. Rather, marsupial V(H) and V(L) complexity appears to be evolving divergently, retaining diversity in V(L) perhaps to compensate for limited V(H) diversity. There is a high degree of similarity between the V(H) and V(L) in M. domestica and T. vulpecula, with the majority of V(L) families being shared between both species. All marsupial V(H) sequences isolated so far form a common clade of closely related sequences, and in contrast to the V(L) genes, the V(H) likely underwent a major loss of diversity early in marsupial evolution.

Animals↗
PubMed2005

High variability in complementarity-determining regions compensates for a low number of V gene families in the lambda light chain locus of the platypus.

Based on the analysis of a panel of variable (V) region sequences from the Australian duck-billed platypus and the Australian short beaked echidna, the monotremes were found to express a highly diversified Vlambda repertoire. High variability was observed both in sequence and in length of all three CDR regions. However, all monotreme sequences were found to form a separate branch on a distance tree, and the monotremes appear to express only two Vlambda gene families. The appearance of all Vlambda gene segments in one branch on the distance tree gives further support for the notion that deletions of entire V region clans or families, followed by successive rounds of gene duplications may be a relatively common phenomenon during vertebrate evolution. Four different constant region sequences were also identified and a preferential use of certain J segments to each constant region was observed. A more detailed picture of the locus was obtained by analysis of genomic DNA by Southern blot and PCR. The organization of the lambda locus involves multiple V and several constant region genes with one or several joining segments positioned upstream of each constant region, similar to the organization in mouse and man. An mRNA frequency analysis shows that the lambda light chain accounts for more than 90% of the light chain transcripts in the spleen. The abundance and the high variability indicate that light chain diversity at the lambda locus contributes significantly to the antigen-binding repertoire in monotremes. A high lambda to kappa light chain ratio also indicates that variability in the CDR regions is more important for the repertoire size than the total number of V gene families.

Amino Acid Sequence↗
PubMed2005

Oriented mesoporous organosilicate thin films.

Coassemblies of block copolymers and inorganic precursors offer a path to ordered inorganic nanostructures. In thin films, these materials combined with domain alignment provide highly robust nanoscopic templates. We report a simple path to control the morphology, scaling, and orientation of ordered mesopores in organosilicate thin films through the coassembly of a diblock copolymer, poly(styrene-b-ethylene oxide) (PS-b-PEO), and an oligomeric organosilicate precursor that is selectively miscible with PEO. Continuous films containing cylindrical or spherical pores are generated by varying the mixing composition of symmetric PS-b-PEO and an organosilicate precursor. Tuning interfacial energy at both air/film and film/substrate interfaces allows the control of cylindrical pore orientation normal to the supported film surfaces. Our method provides well-ordered mesoporous structures within organosilicate thin films that find broad applications as highly stable nanotemplates.

Journal Article↗
PubMed2004

The complexity of expressed kappa light chains in egg-laying mammals.

Complementary DNAs encoding immunoglobulin light chains were isolated from two monotreme species, Ornithorhynchus anatinus (duckbill platypus) and Tachyglossus aculeatus (echidna). The sequences of both the variable and constant regions of these clones had greater similarity to IGK than to other light chain classes and phylogenetic analyses place them squarely within the mammalian IGK group, establishing them as monotreme IGK homologues. The constant region sequences of all clones were essentially identical within each species and, along with Southern blot results, the data are consistent with a single IGKC in each species. The expressed IGKV repertoires from both platypus and echidna were randomly sampled and there appear to be at least four platypus and at least nine echidna IGKV subgroups. The IGKV subgroups are highly divergent within species, in some cases sharing as little as 57% nucleotide identity. Two of the IGKV subgroups are present in both species, so there is some degree of overlap in the germline repertoires of these two monotremes. Overall the complexity seen in platypus and echidna IGK light chains is comparable with that of other mammals considered to have high levels of germline diversity and is in contrast to what has been found so far for monotreme IGL.

Amino Acid Sequence↗
PubMed2004

A buckling-based metrology for measuring the elastic moduli of polymeric thin films.

As technology continues towards smaller, thinner and lighter devices, more stringent demands are placed on thin polymer films as diffusion barriers, dielectric coatings, electronic packaging and so on. Therefore, there is a growing need for testing platforms to rapidly determine the mechanical properties of thin polymer films and coatings. We introduce here an elegant, efficient measurement method that yields the elastic moduli of nanoscale polymer films in a rapid and quantitative manner without the need for expensive equipment or material-specific modelling. The technique exploits a buckling instability that occurs in bilayers consisting of a stiff, thin film coated onto a relatively soft, thick substrate. Using the spacing of these highly periodic wrinkles, we calculate the film's elastic modulus by applying well-established buckling mechanics. We successfully apply this new measurement platform to several systems displaying a wide range of thicknessess (nanometre to micrometre) and moduli (MPa to GPa).

Crystallography↗
PubMed2004

Toughening of nanoporous glasses using porogen residuals.

Nanoporous glasses are inherently brittle materials that become increasingly fragile with increasing porosity. We show that remarkable increases in fracture energy can be obtained from remnants of the porogen molecules used to create the nanoscale pores. The interfacial fracture energy of approximately 2.6 J m(-2) for dense methylsilsesquioxane glass films is shown to increase by over one order of magnitude to >30 J m(-2) for glasses containing 50 vol.% porosity. The increased fracture resistance is related to a powerful molecular-bridging mechanism that was modelled using bridging mechanics. The study demonstrates that significant increases in interfacial fracture energy may be obtained using strategies involving controlled decomposition of the porogen molecule during processing of nanoporous glasses. The implications are important for a range of emerging optical, electronic and biological technologies that use nanoporous thin films, but are limited by the degradation of mechanical properties with increasing porosity.

Biotechnology↗
PubMed2004

Isolation of monotreme T-cell receptor alpha and beta chains.

Monotremes are an ancient mammalian lineage that last shared a common ancestor with the marsupial and eutherian (placental) mammals about 170 million years ago. Characterization of their immune genes is allowing us to gain insights into the evolutionary processes that lead to the 'mammalian' immune response. Here we describe the characterization of the first cDNA clones encoding T-cell receptors from a monotreme. Two TCR alpha-chain cDNAs ( TCRA) from the short-beaked echidna, Tachyglossus aculeatus, containing complete variable, joining and constant regions were isolated. The echidna TCRA constant region shares approximately 37% amino acid identity with other mammalian TCRA constant region sequences. The two variable regions belong to the TCRAV group C, which also contains V genes from humans, mice, cattle and chickens. One echidna TCR beta-chain cDNA ( TCRB) containing the entire constant region was isolated and sequenced. It shares about 63% identity with other mammalian TCRB constant region sequences. The echidna TCRBV belongs to TCRBV group A, which also contains V genes from various eutherian species. Southern blot analysis indicates that, like in other mammalian species, there is only one TCRA constant region copy in the echidna genome, but at least two TCRB constant regions.

Amino Acid Sequence↗
PubMed2004

Interfacial glass transition profiles in ultrathin, spin cast polymer films.

Interfacial glass transition temperature (T(g)) profiles in spin cast, ultrathin films of polystyrene and derivatives were investigated using shear-modulated scanning force microscopy. The transitions were measured as a function of film thickness (delta), molecular weight, and crosslinking density. The T(g)(delta) profiles were nonmonotonic and exhibited two regimes: (a) a sublayer extending about 10 nm from the substrate, with T(g) values lowered up to approximately 10 degrees C below the bulk value, and (b) an intermediate regime extending over 200 nm beyond the sublayer, with T(g) values exceeding the bulk value by up to 10 degrees C. Increasing the molecular weight was found to shift the T(g)(delta) profiles further from the substrate interface, on the order of 10 nm/kDa. Crosslinking the precast films elevated the absolute T(g) values, but had no effect on the spatial length scale of the T(g)(delta) profiles. These results are explained in the context of film preparation history and its influence on molecular mobility. Specifically, the observed rheological anisotropy is interpreted based on the combined effects of shear-induced structuring and thermally activated interdiffusion.

Journal Article↗
PubMed2004

Pore morphologies in disordered nanoporous thin films.

Materials with nanometer size heterogeneities are commonplace in the chemical and biological sciences (e.g, polymer blends, microemulsions, gels) and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties, it is often difficult to accurately characterize. We describe a method, using small-angle X-ray scattering data, of generating representative three-dimensional morphologies of isotropic two-phase materials where the morphology is disordered, and we apply this to thin films containing nanometer sized pores with a range of porosities (4-44%). These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology.

Letter↗
PubMed2004

Molecular cloning and characterization of the polymorphic MHC class II DBB from the tammar wallaby (Macropus eugenii).

Genes of the major histocompatibility complex (MHC) have been characterized in all extant lineages of mammals. The tammar wallaby (Macropus eugenii) is well established as a model marsupial species; however, no classical MHC sequences have been described from this species. We have isolated two MHC class II beta-chain sequences from a tammar wallaby spleen cDNA library using a tammar MHC class II beta probe. These sequences belong to the marsupial MHC class II DBB gene family. Two additional DBB sequences were amplified from tammar wallaby genomic DNA. All four sequences were obtained from the same individual, indicating that there are at least two DBB loci in the tammar wallaby.

Amino Acid Sequence↗
PubMed2004

Analysis of a marsupial MHC region containing two recently duplicated class I loci.

A 37-kb cosmid containing two complete major histocompatibility complex (MHC) class I alpha chain loci from the opossum Monodelphis domestica was isolated, fully sequenced, and characterized. This sequence represents the largest contiguous genomic sequence reported for the MHC region of a nonplacental mammal. Based on particular conserved amino acid residues, and limited expression analyses, the two MHC-I loci, designated ModoUB and ModoUC, appear to encode functional MHC-I molecules. The two coding regions are 98% identical at the nucleotide level; however, their promoter regions differ significantly. Two CpG islands present in the cosmid sequence correspond to the two coding regions. Twelve microsatellites and six retroelements were also present in the cosmid. The retroelements share highest sequence homology to the CORE-SINE family of retroelements. Due to high sequence identity, it is very likely that ModoUB and ModoUC loci are products of recent gene duplication that occurred less than 4 million years ago.

Amino Acid Sequence↗