High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome

Peer reviewedPublisher PD

An integrable modification of the critical Chalker-Coddington network model

We consider the Chalker-Coddington network model for the Integer Quantum Hall Effect, and examine the possibility of solving it exactly. In the supersymmetric path integral framework, we introduce a truncation procedure, leading to a series of well-defined two-dimensional loop models, with two loop flavours. In the phase diagram of the first-order truncated model, we identify four integrable branches related to the dilute Birman-Wenzl-Murakami braid-monoid algebra, and parameterised by the loop fugacity $n$. In the continuum limit, two of these branches (1,2) are described by a pair of decoupled copies of a Coulomb-Gas theory, whereas the other two branches (3,4) couple the two loop flavours, and relate to an $SU(2)_r \times SU(2)_r / SU(2)_{2r}$ Wess-Zumino-Witten (WZW) coset model for the particular values $n= -2\cos[\pi/(r+2)]$ where $r$ is a positive integer. The truncated Chalker-Coddington model is the $n=0$ point of branch 4. By numerical diagonalisation, we find that its universality class is neither an analytic continuation of the WZW coset, nor the universality class of the original Chalker-Coddington model. It constitutes rather an integrable, critical approximation to the latter.Comment: 34 pages, 18 figures, 3 appendice

Analytical solution for capacitance calculation of a curved patch capacitor that conforms to the curvature of a homogeneous cylindrical dielectric rod

This Letter presents an analytical expression for the capacitance of a curved patch capacitor whose electrodes conform to the curvature of a long, homogeneous, cylindrical dielectric rod. The capacitor is composed of two infinitely long curved electrodes, symmetrically placed about a diameter of the cylinder cross-section. The resulting capacitance per unit length depends on both the dielectric properties of the material under test and the capacitor configuration. A practical capacitance measurement is also presented, with appropriately guarded finite electrodes. Very good agreement between measured and theoretically predicted capacitances were observed, to within 2.4 percent. The analytical result presented in this Letter can be applied for extremely rapid evaluation of rod permittivity from measured capacitance

Randomized multicentre pilot study of sacubitril/valsartan versus irbesartan in patients with chronic kidney disease: United Kingdom Heart and Renal Protection (HARP)- III—rationale, trial design and baseline data

BACKGROUND: Patients with chronic kidney disease (CKD) are at risk of progression to end-stage renal disease and cardiovascular disease. Data from other populations and animal experiments suggest that neprilysin inhibition (which augments the natriuretic peptide system) may reduce these risks, but clinical trials among patients with CKD are required to test this hypothesis. METHODS: UK Heart and Renal Protection III (HARP-III) is a multicentre, double-blind, randomized controlled trial comparing sacubitril/valsartan 97/103 mg two times daily (an angiotensin receptor-neprilysin inhibitor) with irbesartan 300 mg one time daily among 414 patients with CKD. Patients ≥18 years of age with an estimated glomerular filtration rate (eGFR) of ≥45 but <60 mL/min/1.73 m2 and urine albumin:creatinine ratio (uACR) >20 mg/mmol or eGFR ≥20 but <45 mL/min/1.73 m2 (regardless of uACR) were invited to be screened. Following a 4- to 7-week pre-randomization single-blind placebo run-in phase (during which any current renin-angiotensin system inhibitors were stopped), willing and eligible participants were randomly assigned either sacubitril/valsartan or irbesartan and followed-up for 12 months. The primary aim was to compare the effects of sacubitril/valsartan and irbesartan on measured GFR after 12 months of therapy. Important secondary outcomes include effects on albuminuria, change in eGFR over time and the safety and tolerability of sacubitril/valsartan in CKD. RESULTS: Between November 2014 and January 2016, 620 patients attended a screening visit and 566 (91%) entered the pre-randomization run-in phase. Of these, 414 (73%) participants were randomized (mean age 63 years; 72% male). The mean eGFR was 34.0 mL/min/1.73 m2 and the median uACR was 58.5 mg/mmol. CONCLUSIONS: UK HARP-III will provide important information on the short-term effects of sacubitril/valsartan on renal function, tolerability and safety among patients with CKD

Entanglement and boundary critical phenomena

We investigate boundary critical phenomena from a quantum information perspective. Bipartite entanglement in the ground state of one-dimensional quantum systems is quantified using the Renyi entropy S_alpha, which includes the von Neumann entropy (alpha=1) and the single-copy entanglement (alpha=infinity) as special cases. We identify the contribution from the boundary entropy to the Renyi entropy, and show that there is an entanglement loss along boundary renormalization group (RG) flows. This property, which is intimately related to the Affleck-Ludwig g-theorem, can be regarded as a consequence of majorization relations between the spectra of the reduced density matrix along the boundary RG flows. We also point out that the bulk contribution to the single-copy entanglement is half of that to the von Neumann entropy, whereas the boundary contribution is the same.Comment: 4 pages, 2 figure

An Unrecognized Source of PCB Contamination in Schools and Other Buildings

An investigation of 24 buildings in the Greater Boston Area revealed that one-third (8 of 24) contained caulking materials with polychlorinated biphenyl (PCB) content exceeding 50 ppm by weight, which is the U.S. Environmental Protection Agency (U.S. EPA) specified limit above which this material is considered to be PCB bulk product waste. These buildings included schools and other public buildings. In a university building where similar levels of PCB were found in caulking material, PCB levels in indoor air ranged from 111 to 393 ng/m(3); and in dust taken from the building ventilation system, < 1 ppm to 81 ppm. In this building, the U.S. EPA mandated requirements for the removal and disposal of the PCB bulk product waste as well as for confirmatory sampling to ensure that the interior and exterior of the building were decontaminated. Although U.S. EPA regulations under the Toxic Substances Control Act stipulate procedures by which PCB-contaminated materials must be handled and disposed, the regulations apparently do not require that materials such as caulking be tested to determine its PCB content. This limited investigation strongly suggests that were this testing done, many buildings would be found to contain high levels of PCBs in the building materials and potentially in the building environment. The presence of PCBs in schools is of particular concern given evidence suggesting that PCBs are developmental toxins

Corepressor/coactivator paradox: potential constitutive coactivation by corepressor splice variants

The functional consequences of the interaction of transcriptional coregulators with the human thyroid hormone receptor (TR) in mammalian cells are complex. We have used the yeast, Saccharomyces cerevisiae, which lack endogenous nuclear receptors (NRs) and NR coregulators, as a model to decipher mechanisms regulating transcriptional activation by TR. In effect, this system allows the reconstitution of TR mediated transcription complexes by the expression of specific combinations of mammalian proteins in yeast. In this yeast system, human adenovirus 5 early region 1A (E1A), a natural N-CoR splice variant (N-CoR(I)) or an artificial N-CoR truncation (N-CoR(C)) coactivate unliganded TRs and these effects are inhibited by thyroid hormone (TH). E1A contains a short peptide sequence that resembles known corepressor-NR interaction motifs (CoRNR box motif, CBM), and this motif is required for TR binding and coactivation. N-CoR(I) and N-CoR(C) contain three CBMs, but only the C-terminal CBM1 is critical for coactivation. These observations in a yeast model system suggest that E1A and N-CoR(I) are naturally occurring TR coactivators that bind in the typical corepressor mode. These findings also raise the possibility that alternative splicing events which form corepressor proteins containing only C-terminal CBM motifs could represent a novel mechanism in mammalian cells for regulating constitutive transcriptional activation by TRs

Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ~20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr

Sex Differences in Rhesus Monkeys’ Digit Ratio (2D:4D Ratio) and Its Association With Maternal Social Dominance Rank

Prenatal androgen exposure (PAE) plays a pivotal role in masculinizing the developing body and brain, and extreme exposure may contribute to autism, anxiety disorder and schizophrenia. One commonly used biomarker for PAE is the pointer-to-ring-finger digit length (2D:4D) ratio. Although this biomarker is widely used in human studies, relatively few studies have investigated 2D:4D ratio in nonhuman primates, particularly rhesus macaques (Macaca mulatta), one of the most commonly used animals in biomedical research. Thus far, data suggest that sexual dimorphism in 2D:4D ratio may be in the opposite direction in some monkey species, when compared to the pattern exhibited by humans and great apes. Using a large sample size, we investigated whether rhesus monkeys’ 2D:4D ratio shows the same sex-differentiated pattern present in other Old World monkey species. We also investigated whether individual differences in 2D:4D ratio are associated with the social dominance rank of subjects’ mothers during pregnancy, and the social dominance rank the subjects attained as adults. Subjects were 335 rhesus monkeys between 3 years and 24 years of age (M = 6.6). Maternal dominance rank during pregnancy and subjects’ adult dominance rank were categorized into tertiles (high, middle and low). Results showed that, across both hands, male rhesus monkeys exhibited higher 2D:4D ratio than females, a pattern consistent with other monkey species and a reversal from the pattern typically observed in humans and apes. This sex difference was modulated by maternal dominance rank, with female offspring of high-ranking and middle-ranking mothers exhibiting masculinized 2D:4D ratio, indicating that maternal dominance rank during pregnancy may influence levels of PAE. There was no association between subjects’ 2D:4D ratio and the social dominance rank they attained as adults. These findings show a consistent sex difference in Old World monkeys’ 2D:4D ratio that diverges from the pattern observed in apes and humans, and suggest maternal social dominance rank modulates PAE in rhesus monkeys