Anomalous dressing of Dirac fermions in the topological surface state of Bi2Se3, Bi2Te3, and Cu-doped Bi2Se3

Quasiparticle dynamics on the topological surface state of Bi(2(3), Bi(2)Te(3), and superconducting Cu(x)Bi(2)Se(3) are studied by 7 eV laser-based angle resolved photoemission spectroscopy. We find strong mode couplings in the Dirac-cone surface states at energies of ~3 and ~15-20 meV associated with an exceptionally large coupling constant λ of ~3, which is one of the strongest ever reported for any material. This result is compatible with the recent observation of a strong Kohn anomaly in the surface phonon dispersion of Bi(2)Se(3), but it appears that the theoretically proposed "spin-plasmon" excitations realized in helical metals are also playing an important role. Intriguingly, the ~3 meV mode coupling is found to be enhanced in the superconducting state of Cu(x)Bi(2)Se(3).

Anomalous doping variation of the nodal low-energy feature of superconducting (Bi,Pb)2(Sr,La)2CuO(6+δ) crystals revealed by laser-based angle-resolved photoemission spectroscopy

The nodal band dispersion in (Bi,Pb)(2)(Sr,La)(2)CuO(6+δ) (Bi2201) is investigated over a wide range of doping by using 7-eV laser-based angle-resolved photoemission spectroscopy. We find that the low-energy band renormalization ("kink"), recently discovered in Bi(2)Sr(2)CaCu(2)O(8+δ) (Bi2212), also occurs in Bi2201, but at a binding energy around half that in Bi2212. Surprisingly, the coupling energy dramatically increases with a decrease of carrier concentration, showing a sharp enhancement across the optimal doping. These properties (material and doping dependence of the coupling energy) demonstrate the significant correlation among the mode coupling, the energy gap close to the node, and the strong electron correlation. Our results suggest forward scattering arising from the interplay between the electrons and in-plane polarized acoustic phonon branch as the origin of the low-energy renormalization.

Living-related liver transplantation in Diego blood group disparity: a case report

To date, only limited cases of Diego blood group disparity in liver transplantation have been reported, and no cases with a long-term clinical course have been documented. Herein, we report a case of Diego blood group disparity in liver transplantation with details of long-term follow-up. The recipient was a 47-year-old woman with primary biliary cirrhosis; her 18-year-old daughter was the donor. Both recipient and donor were of blood type O according to the ABO blood group system. Preoperative serological tests showed the presence of antibodies against the Di(a) antigen only in the recipient, and not in the donor. Thus, the Diego phenotype was Di(a+) in the donor and Di(a-) in the recipient. Living-related liver transplantation was performed in July 2009. Immediate graft function was obtained, and no signs of humoral or cellular rejection were observed during the postoperative period. Further, anti-Di(a) antibodies were not detected throughout the postoperative course. The patient is alive and shows no signs of humoral rejection 34 months after liver transplantation. Liver transplantation has been performed successfully in cases of Diego blood group disparity.

Triangulating the provenance of African elephants using mitochondrial DNA

African elephant mitochondrial (mt) DNA follows a distinctive evolutionary trajectory. As females do not migrate between elephant herds, mtDNA exhibits low geographic dispersal. We therefore examined the effectiveness of mtDNA for assigning the provenance of African elephants (or their ivory). For 653 savanna and forest elephants from 22 localities in 13 countries, 4258 bp of mtDNA was sequenced. We detected eight mtDNA subclades, of which seven had regionally restricted distributions. Among 108 unique haplotypes identified, 72% were found at only one locality and 84% were country specific, while 44% of individuals carried a haplotype detected only at their sampling locality. We combined 316 bp of our control region sequences with those generated by previous trans-national surveys of African elephants. Among 101 unique control region haplotypes detected in African elephants across 81 locations in 22 countries, 62% were present in only a single country. Applying our mtDNA results to a previous microsatellite-based assignment study would improve estimates of the provenance of elephants in 115 of 122 mis-assigned cases. Nuclear partitioning followed species boundaries and not mtDNA subclade boundaries. For taxa such as elephants in which nuclear and mtDNA markers differ in phylogeography, combining the two markers can triangulate the origins of confiscated wildlife products.

Evidence for selection at HIV host susceptibility genes in a West Central African human population

Background

HIV-1 derives from multiple independent transfers of simian immunodeficiency virus (SIV) strains from chimpanzees to human populations. We hypothesized that human populations in west central Africa may have been exposed to SIV prior to the pandemic, and that previous outbreaks may have selected for genetic resistance to immunodeficiency viruses. To test this hypothesis, we examined the genomes of Biaka Western Pygmies, who historically resided in communities within the geographic range of the central African chimpanzee subspecies (Pan troglodytes troglodytes) that carries strains of SIV ancestral to HIV-1.

Results

SNP genotypes of the Biaka were compared to those of African human populations who historically resided outside the range of P. t. troglodytes, including the Mbuti Eastern Pygmies. Genomic regions showing signatures of selection were compared to the genomic locations of genes reported to be associated with HIV infection or pathogenesis. In the Biaka, a strong signal of selection was detected at CUL5, which codes for a component of the vif-mediated APOBEC3 degradation pathway. A CUL5 allele protective against AIDS progression was fixed in the Biaka. A signal of selection was detected at TRIM5, which codes for an HIV post-entry restriction factor. A protective mis-sense mutation in TRIM5 had the highest frequency in Biaka compared to other African populations, as did a protective allele for APOBEC3G, which codes for an anti-HIV-1 restriction factor. Alleles protective against HIV-1 for APOBEC3H, CXCR6 and HLA-C were at higher frequencies in the Biaka than in the Mbuti. Biaka genomes showed a strong signal of selection at TSG101, an inhibitor of HIV-1 viral budding.

Conclusions

We found protective alleles or evidence for selection in the Biaka at a number of genes associated with HIV-1 infection or progression. Pygmies have also been reported to carry genotypes protective against HIV-1 for the genes CCR5 and CCL3L1. Our hypothesis that HIV-1 may have shaped the genomes of some human populations in West Central Africa appears to merit further investigation.

Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus)

Background

The koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19^th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 1800s and early 1900s. To examine the effects of these reductions in population size on koala genetic diversity, we sequenced part of the hypervariable region of mitochondrial DNA (mtDNA) in koala museum specimens collected in the 19^th and 20^th centuries, hypothesizing that the historical samples would exhibit greater genetic diversity.

Results

The mtDNA haplotypes present in historical museum samples were identical to haplotypes found in modern koala populations, and no novel haplotypes were detected. Rarefaction analyses suggested that the mtDNA genetic diversity present in the museum samples was similar to that of modern koalas.

Conclusions

Low mtDNA diversity may have been present in koala populations prior to recent population declines. When considering management strategies, low genetic diversity of the mtDNA hypervariable region may not indicate recent inbreeding or founder events but may reflect an older historical pattern for koalas.

Characterization of natural resin shellac by reactive pyrolysis-gas chromatography in the presence of organic alkali

A method to determine chemical composition of natural resin shellac was developed on the basis of reactive pyrolysis-gas chromatography (Py-GC) in the presence of an organic alkali, tetramethylammonium hydroxide ((CH(3))(4)NOH, TMAH). Py-GC using 25% TMAH aqueous solution enabled the highly sensitive determination of terpenic acids, aleuritic acid, several minor fatty acids, and the wax components of shellac as their methyl derivatives on the resulting pyrograms with less than 2.0% relative standard deviations without using any cumbersome pretreatment. The observed average distributions of each resin acid component determined by reactive Py-GC for shellac samples from India and Thailand showed that the average ratios among terpenic acids, aleuritic acid, and the other fatty acids were about 53:34:14 for Indian shellac and 51:35:14 for Thailand shellac, respectively, suggesting a slightly significant difference. However, clearer discrimination of the shellac samples from the two different growing places was attainable by applying principal component analysis for the mole percent distributions of all the acidic components determined by reactive Py-GC.

One hundred twenty years of koala retrovirus evolution determined from museum skins

Although endogenous retroviruses are common across vertebrate genomes, the koala retrovirus (KoRV) is the only retrovirus known to be currently invading the germ line of its host. KoRV is believed to have first infected koalas in northern Australia less than two centuries ago. We examined KoRV in 28 koala museum skins collected in the late 19th and 20th centuries and deep sequenced the complete proviral envelope region from five northern Australian specimens. Strikingly, KoRV env sequences were conserved among koalas collected over the span of a century, and two functional motifs that affect viral infectivity were fixed across the museum koala specimens. We detected only 20 env polymorphisms among the koalas, likely representing derived mutations subject to purifying selection. Among northern Australian koalas, KoRV was already ubiquitous by the late 19th century, suggesting that KoRV evolved and spread among koala populations more slowly than previously believed. Given that museum and modern koalas share nearly identical KoRV sequences, it is likely that koala populations, for more than a century, have experienced increased susceptibility to diseases caused by viral pathogenesis.

Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions

Among elephants, the phylogeographic patterns of mitochondrial (mt) and nuclear markers are often incongruent. One hypothesis attributes this to sex differences in dispersal and in the variance of reproductive success. We tested this hypothesis by examining the coalescent dates of genetic markers within elephantid lineages, predicting that lower dispersal and lower variance in reproductive success among females would have increased mtDNA relative to nuclear coalescent dates. We sequenced the mitochondrial genomes of two forest elephants, aligning them to mitogenomes of African savanna and Asian elephants, and of woolly mammoths, including the most divergent mitogenomes within each lineage. Using fossil calibrations, the divergence between African elephant F and S clade mitochondrial genomes (originating in forest and savanna elephant lineages, respectively) was estimated as 5.5 Ma. We estimated that the (African) ancestor of the mammoth and Asian elephant lineages diverged 6.0 Ma, indicating that four elephantid lineages had differentiated in Africa by the Miocene-Pliocene transition, concurrent with drier climates. The coalescent date for forest elephant mtDNAs was c. 2.4 Ma, suggesting that the decrease in tropical forest cover during the Pleistocene isolated distinct African forest elephant lineages. For all elephantid lineages, the ratio of mtDNA to nuclear coalescent dates was much greater than 0.25. This is consistent with the expectation that sex differences in dispersal and in variance of reproductive success would have increased the effective population size of mtDNA relative to nuclear markers in elephantids, contributing to the persistence of incongruent mtDNA phylogeographic patterns.