Fragile charge order in the nonsuperconducting ground state of the underdoped high-temperature superconductors.

The normal state in the hole underdoped copper oxide superconductors has proven to be a source of mystery for decades. The measurement of a small Fermi surface by quantum oscillations on suppression of superconductivity by high applied magnetic fields, together with complementary spectroscopic measurements in the hole underdoped copper oxide superconductors, point to a nodal electron pocket from charge order in YBa2Cu3(6+δ). Here, we report quantum oscillation measurements in the closely related stoichiometric material YBa2Cu4O8, which reveals similar Fermi surface properties to YBa2Cu3(6+δ), despite the nonobservation of charge order signatures in the same spectroscopic techniques, such as X-ray diffraction, that revealed signatures of charge order in YBa2Cu3(6+δ). Fermi surface reconstruction in YBa2Cu4O8 is suggested to occur from magnetic field enhancement of charge order that is rendered fragile in zero magnetic fields because of its potential unconventional nature and/or its occurrence as a subsidiary to more robust underlying electronic correlations.B.T., A.S, and S.E.S. acknowledge support from the Royal Society, the Winton Programme for the Physics of Sustainability, and the European Research Council under the European Unions Seventh Framework Programme (grant number FP/2007-2013)/ ERC Grant Agreement number 337425. N.H., Z.Z., F.F.B., and B.J.R. acknowl- edge support for high-magnetic-field experiments from the US Department of Energy, Office of Science, BES- MSE `Science of 100 Tesla' programme. G.G.L. acknowl- edges support from EPSRC grant EP/K012894/1. Work at NIU was supported by The Institute for Nanoscience, Engineering, and Technology - InSET. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by NSF co-operative agreement number DMR-0654118, the state of Florida, and the DOE. We are grateful for the experimental assis- tance provided by National High Magnetic Field Labora- tory personnel, including J. B. Betts, Y. Coulter, M. Gor- don, C. H. Mielke, A. Parish, R. McDonald, D. Rickel, and D. Roybal.This is the author accepted manuscript. The final version is available from the National Academy of Sciences via http://dx.doi.org/10.1073/pnas.150416411

An explanation for a universality of transition temperatures in families of copper oxide superconductors

A remarkable mystery of the copper oxide high-transition-temperature (Tc) superconductors is the dependence of Tc on the number of CuO2 layers, n, in the unit cell of a crystal. In a given family of these superconductors, Tc rises with the number of layers, reaching a peak at n=3, and then declines: the result is a bell-shaped curve. Despite the ubiquity of this phenomenon, it is still poorly understood and attention has instead been mainly focused on the properties of a single CuO2 plane. Here we show that the quantum tunnelling of Cooper pairs between the layers simply and naturally explains the experimental results, when combined with the recently quantified charge imbalance of the layers and the latest notion of a competing order nucleated by this charge imbalance that suppresses superconductivity. We calculate the bell-shaped curve and show that, if materials can be engineered so as to minimize the charge imbalance as n increases, Tc can be raised further.Comment: 15 pages, 3 figures. The version published in Natur

Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster

Tandemly arranged paralogous genes lbe and lbl are members of the Drosophila NK homeobox family. We analyzed population samples of Drosophila melanogaster from Africa, Europe, North and South America, and single strains of D. sechellia, D. simulans, and D. yakuba within two linked regions encompassing partial sequences of lbe and lbl. The evolution of lbe and lbl is highly constrained due to their important regulatory functions. Despite this, a variety of forces have shaped the patterns of variation in lb genes: recombination, intragenic gene conversion and natural selection strongly influence background variation created by linkage disequilibrium and dimorphic haplotype structure. The two genes exhibited similar levels of nucleotide diversity and positive selection was detected in the noncoding regions of both genes. However, synonymous variability was significantly higher for lbe: no nonsynonymous changes were observed in this gene. We argue that balancing selection impacts some synonymous sites of the lbe gene. Stability of mRNA secondary structure was significantly different between the lbe (but not lbl) haplotype groups and may represent a driving force of balancing selection in epistatically interacting synonymous sites. Balancing selection on synonymous sites may be the first, or one of a few such observations, in Drosophila. In contrast, recurrent positive selection on lbl at the protein level influenced evolution at three codon sites. Transcription factor binding-site profiles were different for lbe and lbl, suggesting that their developmental functions are not redundant. Combined with our previous results on nucleotide variation in esterase and other homeobox genes, these results suggest that interplay of balancing and directional selection may be a general feature of molecular evolution in Drosophila and other eukaryote genomes

Evidence and ideology as a rationale for light-therapy in Russia: from the Soviet Union to the present day.

Light therapy is still used to treat a number of common diseases in Russia. The practice is firmly anchored in history: Soviet clinical practice was divorced from the emerging field of evidence-based medicine. Medical researchers were cut off from international medical research and scientific literature, with much Soviet scientific activity based on a particular socialist ideology. In this study, the use of light therapy serves as a case study to explore tensions between international evidence-based medicine and practices developed in isolation under the Soviet Union, the legacy of which is to the detriment of many patients today. We used four different search methods to uncover scientific and grey literature, both historical and contemporary. We assessed the changing frequency of publications over time and contrasted the volume of literature on light therapy with more orthodox treatments such as statins and painkillers. Our search found an increasing number and comparatively large body of scientific publications on light therapy in the Russian language, and many publications emanating from prestigious Russian institutions. Combined with our analysis of the historical literature and our appraisal of 22 full text articles, this leads us to suggest that light therapy entered mainstream Soviet medical practice before the Stalinist period and still occupies an important position in contemporary Russian clinical practice. We propose that this outdated treatment survives in Russia in part due to the political, economic and social forces that helped to popularize it during Soviet times, and by the seeming justification offered by poorly executed studies

Symbiotic Associations in the Phenotypically-Diverse Brown Alga Saccharina japonica

The brown alga Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is a highly polymorphic representative of the family Laminariaceae, inhabiting the northwest Pacific region. We have obtained 16S rRNA sequence data in symbiont microorganisms of the typical form (TYP) of S. japonica and its common morphological varieties, known as “longipes” (LON) and “shallow-water” (SHA), which show contrasting bathymetric distribution and sharp morphological, life history traits, and ecological differences. Phylogenetic analysis of the 16S rRNA sequences shows that the microbial communities are significantly different in the three forms studied and consist of mosaic sets of common and form-specific bacterial lineages. The divergence in bacterial composition is substantial between the TYP and LON forms in spite of their high genetic similarity. The symbiont distribution in the S. japonica forms and in three other laminarialean species is not related to the depth or locality of the algae settlements. Combined with our previous results on symbiont associations in sea urchins and taking into account the highly specific character of bacteria-algae associations, we propose that the TYP and LON forms may represent incipient species passing through initial steps of reproductive isolation. We suggest that phenotype differences between genetically similar forms may be caused by host-symbiont interactions that may be a general feature of evolution in algae and other eukaryote organisms. Bacterial symbionts could serve as sensitive markers to distinguish genetically similar algae forms and also as possible growth-promoting inductors to increase algae productivity

Comparative Genomics of Bordetella pertussis Reveals Progressive Gene Loss in Finnish Strains

BACKGROUND: Bordetella pertussis is a gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. pertussis circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years. METHODOLOGY/PRINCIPAL FINDINGS: The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of 3,816 ORFs of Tohama I, the strain of which the genome has been sequenced. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, e.g. the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared with the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to inorganic ion transport and metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS481. CONCLUSION/SIGNIFICANCE: Our results showed that the progressive gene loss occurred in Finnish B. pertussis strains isolated during a period of 50 years and confirmed that B. pertussis is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations

Regional Selection Acting on the OFD1 Gene Family

The OFD1 (oral-facial-digital, type 1) gene is implicated in several developmental disorders in humans. The X-linked OFD1 (OFD1X) is conserved in Eutheria. Knowledge about the Y-linked paralog (OFD1Y) is limited. In this study, we identified an OFD1Y on the bovine Y chromosome, which is expressed differentially from the bovine OFD1X. Phylogenetic analysis indicated that: a) the eutherian OFD1X and OFD1Y were derived from the pair of ancestral autosomes during sex chromosome evolution; b) the autosomal OFD1 pseudogenes, present in Catarrhini and Murinae, were derived from retropositions of OFD1X after the divergence of primates and rodents; and c) the presence of OFD1Y in the ampliconic region of the primate Y chromosome is an indication that the expansion of the ampliconic region may initiate from the X-degenerated sequence. In addition, we found that different regions of OFD1/OFD1X/OFD1Y are under differential selection pressures. The C-terminal half of OFD1 is under relaxed selection with an elevated Ka/Ks ratio and clustered positively selected sites, whereas the N-terminal half is under stronger constraints. This study provides some insights into why the OFD1X gene causes OFD1 (male-lethal X-linked dominant) and SGBS2 & JSRDs (X-linked recessive) syndromes in humans, and reveals the origin and evolution of the OFD1 family, which will facilitate further clinical investigation of the OFD1-related syndromes

Trichomonas Transmembrane Cyclases Result from Massive Gene Duplication and Concomitant Development of Pseudogenes

Trichomonas vaginalis is the only medically important protist (single-cell eukaryote) that is sexually transmitted. The ∼160-Mb Trichomonas genome contains more predicted protein-encoding genes (∼60,000) than the human genome. To begin to understand why there are so many copies of some genes, we chose here to study a large family of genes encoding unique transmembrane cyclases. Our most important results include the following. More than 100 transmembrane cyclase genes do not result from chromosomal duplications, because for the most part only the coding regions of the genes, rather than flanking sequences, are duplicated. Almost half of the transmembrane cyclase genes are pseudogenes, and these pseudogenes are polymorphic among laboratory strains of Trichomonas. Messenger RNAs for numerous transmembrane cyclases are expressed simultaneously, and representative cyclase domains have adenylyl cyclase activity. In summary, the large family of Trichomonas genes encoding transmembrane adenylyl cyclases results from massive gene duplication and concomitant development of pseudogenes

PTMs in Conversation: Activity and Function of Deubiquitinating Enzymes Regulated via Post-Translational Modifications

Deubiquitinating enzymes (DUBs) constitute a diverse protein family and their impact on numerous biological and pathological processes has now been widely appreciated. Many DUB functions have to be tightly controlled within the cell, and this can be achieved in several ways, such as substrate-induced conformational changes, binding to adaptor proteins, proteolytic cleavage, and post-translational modifications (PTMs). This review is focused on the role of PTMs including monoubiquitination, sumoylation, acetylation, and phosphorylation as characterized and putative regulative factors of DUB function. Although this aspect of DUB functionality has not been yet thoroughly studied, PTMs represent a versatile and reversible method of controlling the role of DUBs in biological processes. In several cases PTMs might constitute a feedback mechanism insuring proper functioning of the ubiquitin proteasome system and other DUB-related pathways