Digital gene expression analysis of the zebra finch genome

Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates

Reproductive isolation in the acoustically divergent groups of tettigoniid, Mecopoda elongata.

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Sympatric divergent populations of the same species provide an opportunity to study the evolution and maintenance of reproductive isolation. Male mating calls are important in sexual selection in acoustically communicating species, and they also have the potential to maintain isolation among species or incipient species. We studied divergent south Indian populations of the bush cricket Mecopoda elongata which are extremely difficult to distinguish morphologically, but which exhibit striking divergence in male acoustic signals. We performed phonotactic experiments investigating the relative preference of females of the "Chirper" song type for calls of all 5 of the song types found in the region (in varying degrees of sympatry). We found that Chirper females preferred their own song type and were completely unresponsive to three trilling song types. Chirper females were occasionally attracted to the call type "Double Chirper" (the call most similar to their own type), suggesting call preference alone cannot provide a complete isolating mechanism. To investigate the basis of call preference we investigated the response of chirper females to variation in chirp rate. Chirper females responded most frequently to a mean chirp rate characteristic of their own song type rather than a higher chirp rate which would be more characteristic of the Double-Chirper song type. This suggests females drive stabilising selection on male chirp rate, which may contribute to the maintenance of isolation. Finally, a no-choice mating experiment using Chirper females and Chirper and Double Chirper males revealed a significant preference of Chirper females to mate with their own song type, even without a requirement for phonotaxis. Overall, the strong specificity of Chirper females for their 'own' song type provides evidence for behavioural isolation among divergent sympatric Mecopoda song types being maintained by female preference for both male song type and subsequent mating probability driven by other cues.The research was funded by University of Exeter, and necessary logistical support was provided by IISc, Bangalore

Divergence in potential contact pheromones and genital morphology among sympatric song types of the bush cricket Mecopoda elongata

This is the final version. Available from Frontiers Media via the DOI in this record. A well-established route to speciation in animals is via the evolution of divergent male mating signals and female preferences within a species. However, an open question is how common it is for near complete isolation to be achieved through a single signal-receiver system as opposed to multiple aspects of the mate-recognition system diverging simultaneously. The five highly divergent mate-attraction song types of the bush cricket Mecopoda elongata exemplify reproductive isolation in sympatry through long-distance mating signals. Female preference for their own song type has been established as a strong pre-mating reproductive barrier, but the potential existence of additional isolating mechanisms has not been investigated. We quantify divergence in cuticular lipid profiles and external genital structures between song types. These traits show significant variation among species of Orthoptera and are known to be used in mate recognition following contact. We show that divergence among sympatric Mecopoda song types in both cuticular lipid profiles and two external genital structures is sufficiently extensive that either of them can be used to identify individual song type with 90% accuracy. Our findings suggest that multiple isolating mechanisms are likely to evolve simultaneously facilitating a more robust reproductive isolation. Our study indicates a role for sexual selection in the divergence and potential future speciation of these populations and suggests that reproductive isolation may frequently evolve through simultaneous divergence across different aspects of mate recognition systems.University of Exete

Intellectual evolution of social innovation: a bibliometric analysis and avenues for future research trends

Despite the fact that the concept of social innovation is extensively employed by scholars and practitioners, yet the conceptualisation and the research structure remained fragmented and scattered, because no rigorous attempt has been made to understand the core concept of social innovation. The notion of social innovation is multi-faceted and multi-disciplinary fluctuating from public-policy to environmental sustainability; which makes an investigation of the concept essential for business-to-business practitioners and scholars. By processing 370 publications from a sample of 125 journals and books with a total of 2941 citations, the authors unpack/unfold the intellectual foundation of social innovation in business and management domains by performing four bibliometric analyses and they evaluate the research domain qualitatively (1970-2019). By using co-citation, network visualisation through co-occurrence data, multi-dimensional scaling, and hierarchical cluster analysis, this research sheds light to the intellectual structure of social innovation including social value, economic value, societal impact, and bifocal innovations. This research reveals the key research clusters embodied by social innovation foundation. The present study identifies four important components for the future avenues of social innovation (i.e. opportunity, innovation practice, opportunity exploiter, value), and proposes a potential research framework to the researchers and practitioners, hoping to provide insights on social innovation

Studies of the superconducting properties of Sn1-xInxTe (x=0.38 to 0.45) using muon-spin spectroscopy

The superconducting properties of Sn1-xInxTe (x = 0.38 to 0.45) have been studied using magnetization and muon-spin rotation or relaxation (muSR) measurements. These measurements show that the superconducting critical temperature Tc of Sn1-xInxTe increases with increasing x, reaching a maximum at around 4.8 K for x = 0.45. Zero-field muSR results indicate that time-reversal symmetry is preserved in this material. Transverse-field muon-spin rotation has been used to study the temperature dependence of the magnetic penetration depth lambda(T) in the mixed state. For all the compositions studied, lambda(T) can be well described using a single-gap s-wave BCS model. The magnetic penetration depth at zero temperature lambda(0) ranges from 500 to 580 nm. Both the superconducting gap Delta(0) at 0 K and the gap ratio Delta(0)/kBTc indicate that Sn1-xInxTe (x = 0.38 to 0.45) should be considered as a superconductor with intermediate to strong coupling.Comment: 7 pages, 6 figures, 3 table

Rate coefficients for rovibrational transitions in H_2 due to collisions with He

We present quantum mechanical and quasiclassical trajectory calculations of cross sections for rovibrational transitions in ortho- and para-H_2 induced by collisions with He atoms. Cross sections were obtained for kinetic energies between 10^-4 and 3 eV, and the corresponding rate coefficients were calculated for the temperature range 100<T<4000 K. Comparisons are made with previous calculations.Comment: 21 pages, 2 figures, AAS, eps

Superconducting and normal-state properties of the noncentrosymmetric superconductor Re6Zr

We systematically investigate the normal and superconducting properties of non-centrosymmetric Re$_{6}$Zr using magnetization, heat capacity, and electrical resistivity measurements. Resistivity measurements indicate Re$_{6}$Zr has poor metallic behavior and is dominated by disorder. Re$_6$Zr undergoes a superconducting transition at $T_{\mathrm{c}} = \left(6.75\pm0.05\right)$ K. Magnetization measurements give a lower critical field, $\mu_{0}H_{\mathrm{c1}} = \left(10.3 \pm 0.1\right)$ mT. The Werthamer-Helfand-Hohenberg model is used to approximate the upper critical field $\mu_{0}H_{\mathrm{c2}} = \left(11.2 \pm 0.2\right)$ T which is close to the Pauli limiting field of 12.35 T and which could indicate singlet-triplet mixing. However, low-temperature specific-heat data suggest that Re$_{6}$Zr is an isotropic, fully gapped s-wave superconductor with enhanced electron-phonon coupling. Unusual flux pinning resulting in a peak effect is observed in the magnetization data, indicating an unconventional vortex state.Comment: 11 pages, 7 figures, 2 table

Density of states in graphene with vacancies: midgap power law and frozen multifractality

The density of states (DoS), $\varrho(E)$, of graphene is investigated numerically and within the self-consistent T-matrix approximation (SCTMA) in the presence of vacancies within the tight binding model. The focus is on compensated disorder, where the concentration of vacancies, $n_\text{A}$ and $n_\text{B}$, in both sub-lattices is the same. Formally, this model belongs to the chiral symmetry class BDI. The prediction of the non-linear sigma-model for this class is a Gade-type singularity $\varrho(E) \sim |E|^{-1}\exp(-|\log(E)|^{-1/x})$. Our numerical data is compatible with this result in a preasymptotic regime that gives way, however, at even lower energies to $\varrho(E)\sim E^{-1}|\log(E)|^{-\mathfrak{x}}$, $1\leq \mathfrak{x} < 2$. We take this finding as an evidence that similar to the case of dirty d-wave superconductors, also generic bipartite random hopping models may exhibit unconventional (strong-coupling) fixed points for certain kinds of randomly placed scatterers if these are strong enough. Our research suggests that graphene with (effective) vacancy disorder is a physical representative of such systems.Comment: References updated onl

Probing the superconducting ground state of the noncentrosymmetric superconductors CaTSi3 (T = Ir, Pt) using muon-spin relaxation and rotation

The superconducting properties of CaTSi3 (where T = Pt and Ir) have been investigated using muon spectroscopy. Our muon-spin relaxation results suggest that in both these superconductors time-reversal symmetry is preserved, while muon-spin rotation data show that the temperature dependence of the superfluid density is consistent with an isotropic s-wave gap. The magnetic penetration depths and upper critical fields determined from our transverse-field muon-spin rotation spectra are found to be 448(6) and 170(6) nm, and 3800(500) and 1700(300) G, for CaPtSi3 and CaIrSi3 respectively. The superconducting coherence lengths of the two materials have also been determined and are 29(2) nm for CaPtSi3 and 44(4) nm for CaIrSi3.Comment: 6 pages, 7 figure