The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

Peer reviewedPublisher PD

Frustration and the Kondo effect in heavy fermion materials

The observation of a separation between the antiferromagnetic phase boundary and the small-large Fermi surface transition in recent experiments has led to the proposal that frustration is an important additional tuning parameter in the Kondo lattice model of heavy fermion materials. The introduction of a Kondo (K) and a frustration (Q) axis into the phase diagram permits us to discuss the physics of heavy fermion materials in a broader perspective. The current experimental situation is analysed in the context of this combined "QK" phase diagram. We discuss various theoretical models for the frustrated Kondo lattice, using general arguments to characterize the nature of the $f$-electron localization transition that occurs between the spin liquid and heavy Fermi liquid ground-states. We concentrate in particular on the Shastry--Sutherland Kondo lattice model, for which we establish the qualitative phase diagram using strong coupling arguments and the large-$N$ expansion. The paper closes with some brief remarks on promising future theoretical directions.Comment: To appear in a special issue of JLT

Trouble at the top: The construction of a tenant identity in the governance of social housing organizations

The project of citizen governance has transformed the social housing sector in England where 20,000 tenants now sit as directors on the boards of housing associations, but the entrance of social housing tenants to the boardroom has aroused opposition from the chief executives of housing companies and triggered regulatory intervention from government inspectors. This paper investigates the cause of these tensions through a theoretical framework drawn from the work of feminist philosopher Judith Butler. It interprets housing governance as an identificatory project with the power to constitute tenant directors as regulated subjects, and presents evidence to suggest that this project of identity fails to completely enclose its subject, allowing tenant directors to engage in ‘identity work’ that threatens the supposed unity of the board. The paper charts the development of antagonism and political tension in the board rooms of housing companies to present an innovative account of the construction and contestation of identities in housing governance

Photometry and Spectroscopy of GRB 030329 and Its Associated Supernova 2003dh: The First Two Months

We present extensive optical and infrared photometry of the afterglow of gamma-ray burst (GRB) 030329 and its associated supernova (SN) 2003dh over the first two months after detection (2003 March 30-May 29 UT). Optical spectroscopy from a variety of telescopes is shown and, when combined with the photometry, allows an unambiguous separation between the afterglow and supernova contributions. The optical afterglow of the GRB is initially a power-law continuum but shows significant color variations during the first week that are unrelated to the presence of a supernova. The early afterglow light curve also shows deviations from the typical power-law decay. A supernova spectrum is first detectable ~7 days after the burst and dominates the light after ~11 days. The spectral evolution and the light curve are shown to closely resemble those of SN 1998bw, a peculiar Type Ic SN associated with GRB 980425, and the time of the supernova explosion is close to the observed time of the GRB. It is now clear that at least some GRBs arise from core-collapse SNe.Comment: 57 pages, 13 figures, accepted by ApJ, revised per referee's comments, includes full photometry table. Data available at ftp://cfa-ftp.harvard.edu/pub/kstanek/GRB030329 or through WWW at http://cfa-www.harvard.edu/cfa/oir/Research/GRB

Childhood sexual abuse and the risk for recurrent major depression in Chinese women

BACKGROUND: Studies in Western countries have repeatedly shown that women with a history of childhood sexual abuse (CSA) are at increased risk for developing major depression (MD). Would this relationship be found in China? METHOD: Three levels of CSA (non-genital, genital, and intercourse) were assessed by self-report in two groups of Han Chinese women: 1970 clinically ascertained with recurrent MD and 2597 matched controls. Diagnostic and other risk factor information was assessed at personal interview. Odds ratios (ORs) were calculated by logistic regression and regression coefficients by linear or Poisson regression. RESULTS: Any form of CSA was significantly associated with recurrent MD [OR 3.26, 95% confidence interval (CI) 1.95-5.45]. This association strengthened with increasing CSA severity: non-genital (OR 2.47, 95% CI 1.17-5.23), genital (OR 2.77, 95% CI 1.32-5.83) and intercourse (OR 13.35, 95% CI 1.83-97.42). The association between any form of CSA and MD remained significant after accounting for parental history of depression, childhood emotional neglect (CEN), childhood physical abuse (CPA) and parent-child relationship. Among the depressed women, those with CSA had an earlier age of onset, longer depressive episodes and an increased risk for generalized anxiety disorder (GAD; OR 1.92, 95% CI 1.39-2.66) and dysthymia (OR 2.16, 95% CI 1.52-3.09). CONCLUSIONS: In Chinese women CSA is strongly associated with MD and this association increases with greater severity of CSA. Depressed women with CSA have an earlier age of onset, longer depressive episodes and increased co-morbidity with GAD and dysthymia. Although reporting biases cannot be ruled out, our results are consistent with the hypothesis that, as in Western countries, CSA substantially increases the risk for MD in China

Dissolved noble gases and stable isotopes as tracers of preferential fluid flow along faults in the Lower Rhine Embayment, Germany

Groundwater in shallow unconsolidated sedimentary aquifers close to the Bornheim fault in the Lower Rhine Embayment (LRE), Germany, has relatively low δ2H and δ18O values in comparison to regional modern groundwater recharge, and 4He concentrations up to 1.7 × 10−4 cm3 (STP) g–1 ± 2.2 % which is approximately four orders of magnitude higher than expected due to solubility equilibrium with the atmosphere. Groundwater age dating based on estimated in situ production and terrigenic flux of helium provides a groundwater residence time of ∼107 years. Although fluid exchange between the deep basal aquifer system and the upper aquifer layers is generally impeded by confining clay layers and lignite, this study’s geochemical data suggest, for the first time, that deep circulating fluids penetrate shallow aquifers in the locality of fault zones, implying  that sub-vertical fluid flow occurs along faults in the LRE. However, large hydraulic-head gradients observed across many faults suggest that they act as barriers to lateral groundwater flow. Therefore, the geochemical data reported here also substantiate a conduit-barrier model of fault-zone hydrogeology in unconsolidated sedimentary deposits, as well as corroborating the concept that faults in unconsolidated aquifer systems can act as loci for hydraulic connectivity between deep and shallow aquifers. The implications of fluid flow along faults in sedimentary basins worldwide are far reaching and of particular concern for carbon capture and storage (CCS) programmes, impacts of deep shale gas recovery for shallow groundwater aquifers, and nuclear waste storage sites where fault zones could act as potential leakage pathways for hazardous fluids

The Genomic Signature of Crop-Wild Introgression in Maize

The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes were particularly resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies

Commercially Available Outbred Mice for Genome-Wide Association Studies

Genome-wide association studies using commercially available outbred mice can detect genes involved in phenotypes of biomedical interest. Useful populations need high-frequency alleles to ensure high power to detect quantitative trait loci (QTLs), low linkage disequilibrium between markers to obtain accurate mapping resolution, and an absence of population structure to prevent false positive associations. We surveyed 66 colonies for inbreeding, genetic diversity, and linkage disequilibrium, and we demonstrate that some have haplotype blocks of less than 100 Kb, enabling gene-level mapping resolution. The same alleles contribute to variation in different colonies, so that when mapping progress stalls in one, another can be used in its stead. Colonies are genetically diverse: 45% of the total genetic variation is attributable to differences between colonies. However, quantitative differences in allele frequencies, rather than the existence of private alleles, are responsible for these population differences. The colonies derive from a limited pool of ancestral haplotypes resembling those found in inbred strains: over 95% of sequence variants segregating in outbred populations are found in inbred strains. Consequently it is possible to impute the sequence of any mouse from a dense SNP map combined with inbred strain sequence data, which opens up the possibility of cataloguing and testing all variants for association, a situation that has so far eluded studies in completely outbred populations. We demonstrate the colonies' potential by identifying a deletion in the promoter of H2-Ea as the molecular change that strongly contributes to setting the ratio of CD4+ and CD8+ lymphocytes

A Dynamic and Complex Network Regulates the Heterosis of Yield-Correlated Traits in Rapeseed (Brassica napus L.)

Although much research has been conducted, the genetic architecture of heterosis remains ambiguous. To unravel the genetic architecture of heterosis, a reconstructed F2 population was produced by random intercross among 202 lines of a double haploid population in rapeseed (Brassica napus L.). Both populations were planted in three environments and 15 yield-correlated traits were measured, and only seed yield and eight yield-correlated traits showed significant mid-parent heterosis, with the mean ranging from 8.7% (branch number) to 31.4% (seed yield). Hundreds of QTL and epistatic interactions were identified for the 15 yield-correlated traits, involving numerous variable loci with moderate effect, genome-wide distribution and obvious hotspots. All kinds of mode-of-inheritance of QTL (additive, A; partial-dominant, PD; full-dominant, D; over-dominant, OD) and epistatic interactions (additive × additive, AA; additive × dominant/dominant × additive, AD/DA; dominant × dominant, DD) were observed and epistasis, especially AA epistasis, seemed to be the major genetic basis of heterosis in rapeseed. Consistent with the low correlation between marker heterozygosity and mid-parent heterosis/hybrid performance, a considerable proportion of dominant and DD epistatic effects were negative, indicating heterozygosity was not always advantageous for heterosis/hybrid performance. The implications of our results on evolution and crop breeding are discussed

Identification of Equid herpesvirus 2 in tissue-engineered equine tendon

Background: Incidental findings of virus-like particles were identified following electron microscopy of tissue-engineered tendon constructs (TETC) derived from equine tenocytes. We set out to determine the nature of these particles, as there are few studies which identify virus in tendons per se, and their presence could have implications for tissue-engineering using allogenic grafts. Methods: Virus particles were identified in electron microscopy of TETCs. Virion morphology was used to initially hypothesise the virus identity.  Next generation sequencing was implemented to identify the virus. A pan herpesvirus PCR was used to validate the RNASeq findings using an independent platform. Histological analysis and biochemical analysis was undertaken on the TETCs. Results: Morphological features suggested the virus to be either a retrovirus or herpesvirus. Subsequent next generation sequencing mapped reads to Equid herpesvirus 2 (EHV2). Histological examination and biochemical testing for collagen content revealed no significant differences between virally affected TETCs and non-affected TETCs. An independent set of equine superficial digital flexor tendon tissue (n=10) examined using designed primers for specific EHV2 contigs identified at sequencing were negative. These data suggest that EHV is resident in some equine tendon. Conclusions: EHV2 was demonstrated in equine tenocytes for the first time; likely from in vivo infection. The presence of EHV2 could have implications to both tissue-engineering and tendinopathy