Comparison of Reptilian Genomes Reveals Deletions Associated with the Natural Loss of γδ T Cells in Squamates.

T lymphocytes or T cells are key components of the vertebrate response to pathogens and cancer. There are two T cell classes based on their TCRs, αß T cells and γδ T cells, and each plays a critical role in immune responses. The squamate reptiles may be unique among the vertebrate lineages by lacking an entire class of T cells, the γδ T cells. In this study, we investigated the basis of the loss of the γδ T cells in squamates. The genome and transcriptome of a sleepy lizard, the skink Tiliqua rugosa, were compared with those of tuatara, Sphenodon punctatus, the last living member of the Rhynchocephalian reptiles. We demonstrate that the lack of TCRγ and TCRδ transcripts in the skink are due to large deletions in the T. rugosa genome. We also show that tuataras are on a growing list of species, including sharks, frogs, birds, alligators, and platypus, that can use an atypical TCRδ that appears to be a chimera of a TCR chain with an Ab-like Ag-binding domain. Tuatara represents the nearest living relative to squamates that retain γδ T cells. The loss of γδTCR in the skink is due to genomic deletions that appear to be conserved in other squamates. The genes encoding the αßTCR chains in the skink do not appear to have increased in complexity to compensate for the loss of γδ T cells.

Linking Interfacial Bonding and Thermal Conductivity in Molecularly-Confined Polymer-Glass Nanocomposites with Ultra-High Interfacial Density.

Thermal transport in polymer nanocomposites becomes dependent on the interfacial thermal conductance due to the ultra-high density of the internal interfaces when the polymer and filler domains are intimately mixed at the nanoscale. However, there is a lack of experimental measurements that can link the thermal conductance across the interfaces to the chemistry and bonding between the polymer molecules and the glass surface. Characterizing the thermal properties of amorphous composites are a particular challenge as their low intrinsic thermal conductivity leads to poor measurement sensitivity of the interfacial thermal conductance. To address this issue here, polymers are confined in porous organosilicates with high interfacial densities, stable composite structure, and varying surface chemistries. The thermal conductivities and fracture energies of the composites are measured with frequency dependent time-domain thermoreflectance (TDTR) and thin-film fracture testing, respectively. Effective medium theory (EMT) along with finite element analysis (FEA) is then used to uniquely extract the thermal boundary conductance (TBC) from the measured thermal conductivity of the composites. Changes in TBC are then linked to the hydrogen bonding between the polymer and organosilicate as quantified by Fourier-transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopy. This platform for analysis is a new paradigm in the experimental investigation of heat flow across constituent domains.

Analysis of the Chinese Alligator TCRα/δ Loci Reveals the Evolutionary Pattern of Atypical TCRδ/TCRµ in Tetrapods.

Atypical TCRδ found in sharks, amphibians, birds, and monotremes and TCRµ found in monotremes and marsupials are TCR chains that use Ig or BCR-like variable domains (VHδ/Vµ) rather than conventional TCR V domains. These unconventional TCR are consistent with a scenario in which TCR and BCR, although having diverged from each other more than 400 million years ago, continue to exchange variable gene segments in generating diversity for Ag recognition. However, the process underlying this exchange and leading to the evolution of these atypical TCR receptor genes remains elusive. In this study, we identified two TCRα/δ gene loci in the Chinese alligator (Alligator sinensis). In total, there were 144 V, 154 Jα, nine Jδ, eight Dδ, two Cα, and five Cδ gene segments in the TCRα/δ loci of the Chinese alligator, representing the most complicated TCRα/δ gene system in both genomic structure and gene content in any tetrapod examined so far. A pool of 32 VHδ genes divided into 18 subfamilies was found to be scattered over the two loci. Phylogenetic analyses revealed that these VHδ genes could be related to bird VHδ genes, VHδ/Vµ genes in platypus or opossum, or alligator VH genes. Based on these findings, a model explaining the evolutionary pattern of atypical TCRδ/TCRµ genes in tetrapods is proposed. This study sheds new light on the evolution of TCR and BCR genes, two of the most essential components of adaptive immunity.

Opossum milk IgG is from maternal circulation and timing of transfer correlates with neonatal immune development.

Marsupials, with short gestation times, have more complex and changing patterns of milk composition than eutherians. Maternal immunoglobulins (Ig) that confer immunity on offspring are among the components that change during marsupial lactation. In the present study we quantified the abundance of mammary transcripts encoding Ig heavy chains and their corresponding transporters in the laboratory opossum Monodelphis domestica. IgA transcripts were the most abundant in opossum mammary and, with IgM, increased in abundance linearly from birth to weaning. Similarly, the Fc receptor for IgA, the poly-Ig receptor, also increased in abundance throughout lactation. There were few transcripts for IgG or IgE within the opossum mammaries. This is in contrast with reports for Australian marsupial species. Transcripts for the Neonatal Fc Receptor (FcRN), which transports IgG, were detected throughout lactation, and opossum milk is known to contain IgG. Therefore, milk IgG is likely to be taken from the maternal circulation, rather than resulting from local production. There is a parallel increase in FcRN in the newborn gut that declines around the time when neonates have matured to the point where they can make their own IgG. These results are consistent with a transfer of maternal Ig that is coordinated with the development of the neonatal immune system.

Electrically Conductive Copper Core-Shell Nanowires through Benzenethiol-Directed Assembly.

Ultrathin nanowires with <3 nm diameter have long been sought for novel properties that emerge from dimensional constraint as well as for continued size reduction and performance improvement of nanoelectronic devices. Here, we report on a facile and large-scale synthesis of a new class of electrically conductive ultrathin core-shell nanowires using benzenethiols. Core-shell nanowires are atomically precise and have inorganic five-atom copper-sulfur cross-sectional cores encapsulated by organic shells encompassing aromatic substituents with ring planes oriented parallel. The exact nanowire atomic structures were revealed via a two-pronged approach combining computational methods coupled with experimental synthesis and advanced characterizations. Core-shell nanowires were determined to be indirect bandgap materials with a predicted room-temperature resistivity of ∼120 Ω·m. Nanowire morphology was found to be tunable by changing the interwire interactions imparted by the functional group on the benzenethiol molecular precursors, and the nanowire core diameter was determined by the steric bulkiness of the ligand. These discoveries help define our understanding of the fundamental constituents of atomically well-defined and electrically conductive core-shell nanowires, representing significant advances toward nanowire building blocks for smaller, faster, and more powerful nanoelectronics.

A pronounced uterine pro-inflammatory response at parturition is an ancient feature in mammals.

Regulating maternal immunity is necessary for successful human pregnancy. Whether this is needed in mammals with less invasive placentation is subject to debate. Indeed, the short gestation times in marsupials have been hypothesized to be due to a lack of immune regulation during pregnancy. Alternatively, the maternal marsupial immune system may be unstimulated in the absence of a highly invasive placenta. Transcripts encoding pro-inflammatory cytokines were found to be overrepresented in the whole uterine transcriptome at terminal pregnancy in the opossum, Monodelphis domestica To investigate this further, immune gene transcripts were quantified throughout opossum gestation. Transcripts encoding pro-inflammatory cytokines remained relatively low during pre- and peri-attachment pregnancy stages. Levels dramatically increased late in gestation, peaking within 12 h prior to parturition. These results mirror the spike of inflammation seen at eutherian parturition but not at attachment or implantation. Our results are consistent with the role of pro-inflammatory cytokines at parturition being an ancient and conserved birth mechanism in therian mammals.

On the prenatal initiation of T cell development in the opossum Monodelphis domestica.

Thymus-dependent lymphocytes (T cells) are a critical cell lineage in the adaptive immune system of all jawed vertebrates. In eutherian mammals the initiation of T cell development takes place prenatally and the offspring of many species are born relatively immuno-competent. Marsupials, in contrast, are born in a comparatively altricial state and with a less well developed immune system. As such, marsupials are valuable models for studying the peri- and postnatal initiation of immune system development in mammals. Previous results supported a lack of prenatal T cell development in a variety of marsupial species. In the gray short-tailed opossum, Monodelphis domestica, however, there was evidence that αßT cells were present on postnatal day 1 and likely initiated development prenatally. Demonstrated here is the presence of CD3ε+ lymphocytes in late-stage embryos at a site in the upper thoracic cavity, the site of an early developing thymus. CD3ε+ cells were evident as early as 48 h prior to parturition. In day 14 embryos, where there is clear organogenesis, CD3ε+ cells were only found at the site of the early thymus, consistent with no extra-thymic sites of T cell development in the opossum. These observations are the first evidence of prenatal T cell lineage commitment in any marsupial.

The UT family of MHC class I loci unique to non-eutherian mammals has limited polymorphism and tissue specific patterns of expression in the opossum.

BACKGROUND: The Major Histocompatibility Complex (MHC) class I family of genes encode for molecules that have well-conserved structures, but have evolved to perform diverse functions. The availability of the gray, short-tailed opossum, Monodelphis domestica whole genome sequence has allowed for analysis of MHC class I gene content in this marsupial. Utilization of a novel method to search for MHC related domain structures revealed a previously unknown family of MHC class I-related genes. These genes, named UT1-17, are clustered on chromosome 1 in the opossum, unlinked to the MHC region. UT genes are only found in marsupial and monotreme genomes, consistent with being ancient in mammals yet lost in eutherian mammals. This study investigates the expression and polymorphism of the UT loci in the opossum to gain insight into their possible function. RESULTS: Of the 17 opossum UT genes, most have restricted tissue transcription patterns, with the thymus and skin being the most common sites. Full-length structure of 11 UT transcripts revealed genes varying between five and eight exons, typical for class I family members. There were only two alternative splice variants found. The UT genes also have limited polymorphism and little evidence of positive selection. One locus, UT8, was chosen for further analysis due to its conservation amongst marsupials and generic characteristics. UT8 transcription is limited to developing αß thymocytes, and is absent from mature αß T cells in peripheral lymphoid tissues. CONCLUSION: The overall characteristics and features of UT genes including low polymorphism and restricted tissue expression make it likely that the molecules encoded by UT genes perform roles other than antigenic peptide presentation.

Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage.

BACKGROUND: Major histocompatibility complex (MHC) class I genes are found in the genomes of all jawed vertebrates. The evolution of this gene family is closely tied to the evolution of the vertebrate genome. Family members are frequently found in four paralogous regions, which were formed in two rounds of genome duplication in the early vertebrates, but in some species class Is have been subject to additional duplication or translocation, creating additional clusters. The gene family is traditionally grouped into two subtypes: classical MHC class I genes that are usually MHC-linked, highly polymorphic, expressed in a broad range of tissues and present endogenously-derived peptides to cytotoxic T-cells; and non-classical MHC class I genes generally have lower polymorphism, may have tissue-specific expression and have evolved to perform immune-related or non-immune functions. As immune genes can evolve rapidly and are subject to different selection pressure, we hypothesised that there may be divergent, as yet unannotated or uncharacterised class I genes. RESULTS: Application of a novel method of sensitive genome searching of available vertebrate genome sequences revealed a new, extensive sub-family of divergent MHC class I genes, denoted as UT, which has not previously been characterized. These class I genes are found in both American and Australian marsupials, and in monotremes, at an evolutionary chromosomal breakpoint, but are not present in non-mammalian genomes and have been lost from the eutherian lineage. We show that UT family members are expressed in the thymus of the gray short-tailed opossum and in other immune tissues of several Australian marsupials. Structural homology modelling shows that the proteins encoded by this family are predicted to have an open, though short, antigen-binding groove. CONCLUSIONS: We have identified a novel sub-family of putatively non-classical MHC class I genes that are specific to marsupials and monotremes. This family was present in the ancestral mammal and is found in extant marsupials and monotremes, but has been lost from the eutherian lineage. The function of this family is as yet unknown, however, their predicted structure may be consistent with presentation of antigens to T-cells.

The opossum MHC genomic region revisited.

The gray short-tailed opossum Monodelphis domestica is one of the few marsupial species for which a high quality whole genome sequence is available and the major histocompatibility complex (MHC) region has been annotated. Previous analyses revealed only a single locus within the opossum MHC region, designated Modo-UA1, with the features expected for encoding a functionally classical class I α-chain. Nine other class I genes found within the MHC are highly divergent and have features usually associated with non-classical roles. The original annotation, however, was based on an early version of the opossum genome assembly. More recent analyses of allelic variation in individual opossums revealed too many Modo-UA1 sequences per individual to be accounted for by a single MHC class I locus found in the genome assembly. A reanalysis of a later generation assembly, MonDom5, revealed the presence of two additional loci, now designated Modo-UA3 and UA4, in a region that was expanded and more complete than in the earlier assembly. Modo-UA1, UA3, and UA4 are all transcribed, although Modo-UA4 transcripts are rarer. Modo-UA4 is also relatively non-polymorphic. Evidence presented support the accuracy of the later assembly and the existence of three related class I genes in the opossum, making opossums more typical of mammals and most tetrapods by having multiple apparent classical MHC class I loci.

A second TCRδ locus in Galliformes uses antibody-like V domains: insight into the evolution of TCRδ and TCRµ genes in tetrapods.

Analyses of the available avian genomes revealed the presence of a second TCRδ locus in the Galliformes. This second TCRδ locus is nonsyntenic to the conventional TCRα/δ and is unusual in that the V genes are more related to IgH V genes (VH) than to TCR V genes. The second TCRδ is not found in another avian lineage, the passerine zebra finch. Rather the finch's conventional TCRα/δ locus contains VH genes that are expressed with the conventional Cδ gene, similar to what has been found in amphibians. A comparison between Galliformes and Passeriformes genomic organization suggests an origin of the second TCRδ in the former lineage involving gene duplication. Expression of these atypical TCRδ transcripts with a VH domain paired with Cδ was found in lymphoid tissues of both avian lineages. The configuration of the second TCRδ in chicken and turkey is reminiscent of the TCRδ duplication that is present in nonplacental mammals and provides insight into the origin of the uniquely mammalian TCRµ locus.

Those other mammals: the immunoglobulins and T cell receptors of marsupials and monotremes.

This review summarizes analyses of marsupial and monotreme immunoglobulin and T cell receptor genetics and expression published over the past decade. Analyses of recently completed whole genome sequences from the opossum and the platypus have yielded insight into the evolution of the common antigen receptor systems, as well as discovery of novel receptors that appear to have been lost in eutherian mammals. These species are also useful for investigation of the development of the immune system in organisms notable for giving birth to highly altricial young, as well as the evolution of maternal immunity through comparison of oviparous and viviparous mammals.

A family of olfactory receptors uniquely expanded in marsupial and monotreme genomes are expressed by a T cell subset also unique to marsupials and monotremes.

Olfactory receptors (OR), expressed on olfactory neurons, mediate the sense of smell. Recently, OR have also been shown to be expressed in non-olfactory tissues, including cells of the immune system. An analysis of single-cell transcriptomes of splenocytes of the grey short-tailed opossum (Monodelphis domestica) found OR are expressed on a subset of T cells, the γµ T cells, that are unique to marsupials and monotremes. A majority of opossum γµ T cells transcriptomes contain OR family 14 transcripts, specifically, from the OR14C subfamily. Amongst the mammals, the OR14 gene family is expanded in the genomes of marsupials and monotremes, and rarer or absent in placental mammals. In summary, here we demonstrate the intriguing correlation that a family of OR genes, abundant in the genomes of marsupials and monotremes, are ectopically expressed in a particular subset of T cells unique to the marsupials and monotremes.

A model for the evolution of the mammalian t-cell receptor α/δ and µ loci based on evidence from the duckbill Platypus.

The specific recognition of antigen by T cells is critical to the generation of adaptive immune responses in vertebrates. T cells recognize antigen using a somatically diversified T-cell receptor (TCR). All jawed vertebrates use four TCR chains called α, ß, γ, and δ, which are expressed as either a αß or γδ heterodimer. Nonplacental mammals (monotremes and marsupials) are unusual in that their genomes encode a fifth TCR chain, called TCRµ, whose function is not known but is also somatically diversified like the conventional chains. The origins of TCRµ are also unclear, although it appears distantly related to TCRδ. Recent analysis of avian and amphibian genomes has provided insight into a model for understanding the evolution of the TCRδ genes in tetrapods that was not evident from humans, mice, or other commonly studied placental (eutherian) mammals. An analysis of the genes encoding the TCRδ chains in the duckbill platypus revealed the presence of a highly divergent variable (V) gene, indistinguishable from immunoglobulin heavy (IgH) chain V genes (VH) and related to V genes used in TCRµ. They are expressed as part of TCRδ repertoire (VHδ) and similar to what has been found in frogs and birds. This, however, is the first time a VHδ has been found in a mammal and provides a critical link in reconstructing the evolutionary history of TCRµ. The current structure of TCRδ and TCRµ genes in tetrapods suggests ancient and possibly recurring translocations of gene segments between the IgH and TCRδ genes, as well as translocations of TCRδ genes out of the TCRα/δ locus early in mammals, creating the TCRµ locus.

Platypus TCRµ provides insight into the origins and evolution of a uniquely mammalian TCR locus.

TCRµ is an unconventional TCR that was first discovered in marsupials and appears to be absent from placental mammals and nonmammals. In this study, we show that TCRµ is also present in the duckbill platypus, an egg-laying monotreme, consistent with TCRµ being ancient and present in the last common ancestor of all extant mammals. As in marsupials, platypus TCRµ is expressed in a form containing double V domains. These V domains more closely resemble Ab V than that of conventional TCR. Platypus TCRµ differs from its marsupial homolog by requiring two rounds of somatic DNA recombination to assemble both V exons and has a genomic organization resembling the likely ancestral form of the receptor genes. These results demonstrate that the ancestors of placental mammals would have had TCRµ but it has been lost from this lineage.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

Softening of PEO-LiTFSI/LLZTO Composite Polymer Electrolytes for Solid-State Batteries under Cyclic Compression.

Composite polymer electrolytes (CPEs) strike an effective balance between ionic conductivity and mechanical flexibility for lithium-ion solid-state batteries. Long-term performance, however, is limited by capacity fading after hundreds of charge and discharge cycles. The causes of performance degradation include multiple contributing factors such as dendrite formation, physicochemical changes in electrolytes, and structural remodeling of porous electrodes. Among the many factors that contribute to performance degradation, the effect of stress specifically on the composite electrolyte is not well understood. This study examines the mechanical changes in a poly(ethylene oxide) electrolyte with bis(trifluoromethane) sulfonimide. Two different sizes of Li6.4La3Zr1.4Ta0.6O12 particles (500 nm and 5 µm) are compared to evaluate the effect of the surface-to-volume ratio of the ion-conducting fillers within the composite. Cyclic compression was applied to mimic stress cycling in the electrolyte, which would be caused by asymmetric volume changes that occur during charging and discharging cycles. The electrolytes exhibited fatigue softening, whereby the compressive modulus gradually decreased with an increase in the number of cycles. When the electrolyte was tested for 500 cycles at 30% compressive strain, the compressive modulus of the electrolyte was reduced to approximately 80% of the modulus before cycling. While the extent of softening was similar regardless of particle size, CPEs with 500 nm particles exhibited a significant reduction in ionic conductivity after cyclic compression (1.4 × 10-7 ± 2.3 × 10-8 vs 1.1 × 10-7 ± 2.0 × 10-8 S/cm, mean ± standard deviation, n = 4), whereas there was no significant change in ionic conductivity for CPEs with 5 µm particles. These observations -performed deliberately in the absence of charge-discharge cycles -show that repetitive mechanical stresses can play a significant role in altering the performance of CPEs, thereby revealing another possible mechanism for performance degradation in all-solid-state batteries.

Recombination, transcription, and diversity of a partially germline-joined VH in a mammal.

Full or partially germline-joined V genes have been described in a number of different vertebrate lineages where they can contribute to the expressed antibody repertoire through different mechanisms. Here we demonstrate that VH3.1, a partially germline-joined VH gene in the opossum Monodelphis domestica, can undergo V(D)J recombination to generate productive IgH transcripts. VH3.1 is fused to a DH gene segment in the germline DNA and is the only known example of a germline-joined VH in a mammal. B cells that have recombined VH3.1 were not detected until nearly 2 months of age, around the time of weaning, and much later than B cells using the conventional VH. Compared to opossum IgH transcripts using the conventional VH genes, those with VH3.1 have unusually long CDR3 due to the length of the germline-joined DH.

A VpreB3 homologue in a marsupial, the gray short-tailed opossum, Monodelphis domestica.

A VpreB surrogate light (SL) chain was identified for the first time in a marsupial, the opossum Monodelphis domestica. Comparing the opossum VpreB to homologues from eutherian (placental mammals) and avian species supported the marsupial gene being VpreB3. VpreB3 is a protein that is not known to traffic to the cell surface as part of the pre-B cell receptor. Rather, VpreB3 associates with nascent immunoglobulin chains in the endoplasmic reticulum. Homologues of other known SL chains VpreB1, VpreB2, and λ5, which are found in eutherian mammals, were not found in the opossum genome, nor have they been identified in the genomes of nonmammals. VpreB3 likely evolved from earlier gene duplication, independent of that which generated VpreB1 and VpreB2 in eutherians. The apparent absence of VpreB1, VpreB2, and λ5 in marsupials suggests that an extracellular pre-B cell receptor containing SL chains, as it has been defined in humans and mice, may be unique to eutherian mammals. In contrast, the conservation of VpreB3 in marsupials and its presence in nonmammals is consistent with previous hypotheses that it is playing a more primordial role in B cell development.

Comparative analysis of the chicken TCRα/δ locus.

The access to whole genome sequences has provided the opportunity to study the evolution and organization of immunologically related genes on a large scale. The genes encoding the T cell receptor (TCR) α and δ chains are part of a complex locus that has shown remarkable conserved organization across different amniote lineages. In this study we have examined and annotated the TCRα/δ locus in chicken (Gallus gallus) and compared it to that of zebra finch (Taeniopygia guttata) and other avian species using the current available genome data. We also analyzed the expressed chicken TCRα/δ transcript repertoire and compared it with that previously described for zebra finch. The analyses conducted in this study show that the TCRα/δ locus in birds has undergone major rearrangements and expansion of the germ line repertoire in chicken, compared to zebra finch. A major expansion of the chicken variable gene repertoire appears to be driven by selection for genes from a limited number of subgroups.