Unique intrahepatic transcriptomics profiles discriminate the clinical phases of a chronic HBV infection

Chronic hepatitis B is a highly heterogeneous liver disease characterized by phases with fluctuations in viral replication and progressive liver damage in some, but not all infected individuals. Despite four decades of research, insight into host determinants underlying these distinct clinical phases-immunotolerant, immune active, inactive carrier, and HBeAg-negative hepatitis±remains elusive. We performed an in-depth transcriptome analysis of archived FFPE liver biopsies of each clinical phase to address host determinants associated with the natural history. Therefore, we determined, for the first time, intrahepatic global expression profiles of well-characterized chronic HBV patients at different clinical phases. Our data, obtained by microarray, demonstrate that B cells and NK/cytotoxicrelated genes in the liver, including CD19, TNFRSF13C, GZMH, and KIR2DS3, were differentially expressed across the clinical HBV phases, which was confirmed by modular analysis and also Nanostring arrays in an independent cohort. Compared to the immunotolerant phase, 92 genes were differentially expressed in the liver during the immune active phase, 46 in the inactive carrier phase, and 71 in the HBeAg-negative phase. Furthermore, our study also revealed distinctive transcription of genes associated with cell cycle activity, NF-κB signaling, cytotoxic function and mitochondrial respiration between clinical phases. Our data define for the first time using microarray unique transcriptomes in the HBV-infected liver during consecutive clinical phases. We demonstrate that fluctuations of viral loads and liver damage coincide with fluctuations in the liver transcriptome and point to functionalimmune and non-immune-components contributing to the clinical phenotype in patients

Bosonic Excitations in Random Media

We consider classical normal modes and non-interacting bosonic excitations in disordered systems. We emphasise generic aspects of such problems and parallels with disordered, non-interacting systems of fermions, and discuss in particular the relevance for bosonic excitations of symmetry classes known in the fermionic context. We also stress important differences between bosonic and fermionic problems. One of these follows from the fact that ground state stability of a system requires all bosonic excitation energy levels to be positive, while stability in systems of non-interacting fermions is ensured by the exclusion principle, whatever the single-particle energies. As a consequence, simple models of uncorrelated disorder are less useful for bosonic systems than for fermionic ones, and it is generally important to study the excitation spectrum in conjunction with the problem of constructing a disorder-dependent ground state: we show how a mapping to an operator with chiral symmetry provides a useful tool for doing this. A second difference involves the distinction for bosonic systems between excitations which are Goldstone modes and those which are not. In the case of Goldstone modes we review established results illustrating the fact that disorder decouples from excitations in the low frequency limit, above a critical dimension $d_c$, which in different circumstances takes the values $d_c=2$ and $d_c=0$. For bosonic excitations which are not Goldstone modes, we argue that an excitation density varying with frequency as $\rho(\omega) \propto \omega^4$ is a universal feature in systems with ground states that depend on the disorder realisation. We illustrate our conclusions with extensive analytical and some numerical calculations for a variety of models in one dimension

Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts

Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progression has not been fully defined and tools aiding the deconvolution of complex patient virus profiles is an unmet clinical need. Vari

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

The genetic architecture of the human cerebral cortex

INTRODUCTION The cerebral cortex underlies our complex cognitive capabilities. Variations in human cortical surface area and thickness are associated with neurological, psychological, and behavioral traits and can be measured in vivo by magnetic resonance imaging (MRI). Studies in model organisms have identified genes that influence cortical structure, but little is known about common genetic variants that affect human cortical structure. RATIONALE To identify genetic variants associated with human cortical structure at both global and regional levels, we conducted a genome-wide association meta-analysis of brain MRI data from 51,665 individuals across 60 cohorts. We analyzed the surface area and average thickness of the whole cortex and 34 cortical regions with known functional specializations. RESULTS We identified 306 nominally genome-wide significant loci (P < 5 × 10−8) associated with cortical structure in a discovery sample of 33,992 participants of European ancestry. Of the 299 loci for which replication data were available, 241 loci influencing surface area and 14 influencing thickness remained significant after replication, with 199 loci passing multiple testing correction (P < 8.3 × 10−10; 187 influencing surface area and 12 influencing thickness). Common genetic variants explained 34% (SE = 3%) of the variation in total surface area and 26% (SE = 2%) in average thickness; surface area and thickness showed a negative genetic correlation (rG = −0.32, SE = 0.05, P = 6.5 × 10−12), which suggests that genetic influences have opposing effects on surface area and thickness. Bioinformatic analyses showed that total surface area is influenced by genetic variants that alter gene regulatory activity in neural progenitor cells during fetal development. By contrast, average thickness is influenced by active regulatory elements in adult brain samples, which may reflect processes that occur after mid-fetal development, such as myelination, branching, or pruning. When considered together, these results support the radial unit hypothesis that different developmental mechanisms promote surface area expansion and increases in thickness. To identify specific genetic influences on individual cortical regions, we controlled for global measures (total surface area or average thickness) in the regional analyses. After multiple testing correction, we identified 175 loci that influence regional surface area and 10 that influence regional thickness. Loci that affect regional surface area cluster near genes involved in the Wnt signaling pathway, which is known to influence areal identity. We observed significant positive genetic correlations and evidence of bidirectional causation of total surface area with both general cognitive functioning and educational attainment. We found additional positive genetic correlations between total surface area and Parkinson’s disease but did not find evidence of causation. Negative genetic correlations were evident between total surface area and insomnia, attention deficit hyperactivity disorder, depressive symptoms, major depressive disorder, and neuroticism. CONCLUSION This large-scale collaborative work enhances our understanding of the genetic architecture of the human cerebral cortex and its regional patterning. The highly polygenic architecture of the cortex suggests that distinct genes are involved in the development of specific cortical areas. Moreover, we find evidence that brain structure is a key phenotype along the causal pathway that leads from genetic variation to differences in general cognitive function

An updated check list of the ichthyofaunal species assemblage of the Tsitsikamma National Park, South Africa

This work summarises ichthyological research in the Tsitsikamma National Park (TNP) over the past 20 years, and an updated species check list of fishes has been compiled. A total of 202 species of fishes from 84 families has been recorded within the boundaries of the national park. All species which have been included were identified from visual transects, rotenone collections, estuarine surveys, ichthyoplankton surveys, mark/recapture studies and personal observations. The ichthyofauna is a diverse assemblage of chondrichthyans and teleosts, 75 (37.1) of which are components of commercial and recreational fisheries along the east coast. Surveys also indicate that the TNP provides refuge to all life history stages for 17 of the commercial and recreational teleost species. The need for more detailed collections of previously neglected teleost and chondrichthyan groups is recognised. The number of species and diversity demonstrates that the TNP appears not only to afford protection to exploited fish species, but also fulfills one of the basic requirements of Marine Protected Areas@that of conserving biodiversity (of fishes)

CO2 fluxes at leaf and canopy scale in millet, fallow and tiger bush vegetation at the HAPEX-Sahel southern super-site.

Measurements of canopy and leaf scale CO2 flux from the three sub-sites at the HAPEX-Sahel Southern supersite are presented. These are analysed in relation to biological and environmental variables. At leaf scale, the flux is most strongly influenced by photosynthetic photon flux density (PPFD) and stomatal conductance. Together with measurements of canopy structure at each site, the measurements of leaf photosynthesis, stomatal conductance and stem respiration were used to parameterise sub-models within the canopy model MAESTRO, which predicts canopy net CO2 flux. Comparison of the independent canopy flux measurements with predictions is informative, as the model represents an integration of our knowledge of the system, and so differences highlight weak points in our understanding as well as measurement artefacts. These differences are largest in tiger bush and smallest in millet, and are attributed to the effect of canopy heterogeneity on measurements rather than biological processes. Generally, good agreement was found at all three sites and the model can be regarded as validated. The model was used to extrapolate measurements in time, and, using a year's weather data, predicted a value for carbon sequestration at the millet site over the growing season very close to harvest measurement

SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder.

N-linked glycosylation is the most frequent modification of secreted and membrane-bound proteins in eukaryotic cells, disruption of which is the basis of the congenital disorders of glycosylation (CDGs). We describe a new type of CDG caused by mutations in the steroid 5a-reductase type 3 (SRD5A3) gene. Patients have mental retardation and ophthalmologic and cerebellar defects. We found that SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols, required for synthesis of dolichol-linked monosaccharides, and the oligosaccharide precursor used for N-glycosylation. The presence of residual dolichol in cells depleted for this enzyme suggests the existence of an unexpected alternative pathway for dolichol de novo biosynthesis. Our results thus suggest that SRD5A3 is likely to be the long-sought polyprenol reductase and reveal the genetic basis of one of the earliest steps in protein N-linked glycosylation