Selective effects of fatty acids upon cell growth and metabolic regulation

Positional isomers ofcis‐methyleneoctadecanoic acid differed greatly in their efficiency for growth of an unsaturated fatty acid auxotroph ofEscherichia coli upon glucose as a carbon source. The 8, 9, and 11 isomers were more efficient in producing cells (60–70 cells/fmole) than the others (0–7 cells/fmole), although all isomers were found esterified to a similar extent into cellular lipid. WithSaccharomyces cerevisiae mutants, all isomers between 6 and 12 supported some growth of the eukaryotic cells, and the 7 and 9 isomers were slightly more efficient than the 8‐isomer. WhenE. coli were grown with glycerol, all isomers from 5 to 14 supported growth, and those with the substituent near the center of the acyl chain had the greatest efficiency (70 cells/fmole). With the glycerol medium, the pattern of efficiencies for the variouscis‐methylene acyl chains resembled the broad selectivity reported earlier for thecis‐ethylenic isomers in glucose medium, which agreed closely with predictions based upon the physical property of their phospholipid derivatives. Thus, metabolism of glycerol appeared to allow the cyclopropane acyl chains to support cell functions to the limits expected for bulk phase chain‐chain fluidity considerations. This broad specificity was also obtained when cells were grown on glucose with cyclic AMP added to the culture. Therefore, the selective inadequacies of the 5, 6, 7, 10, 12 and 13 isomers in supporting cell growth on glucose may occur through an interaction modified by cAMP and dependent upon reduced cellular levels of cyclic AMP. The highly selective pattern of efficiency of thecis‐methylene acids forE. coli growth on glucose resembles that with the acetylenic acids, but was shifted one carbon atom toward the methyl terminus. This observed selectivity pattern seems due to interactions of the individual acyl chains with cellular protein(s) rather than to chain‐chain interactions in a bulk phase. The ability of certain positional isomers to support cell function equally well in both nutrient conditions suggests that the role of those acyl chain isomers may be independent of metabolite flux or cyclic nucleotide contents of the cell, whereas the actions of other isomeric fatty acids seem closely related to the metabolic status of the cell. A highly selective role for different fatty acids in modulating cellular function seems possible on the basis of the current evidence.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141577/1/lipd0878.pd

Nodal liquid and s-wave superconductivity in transition metal dichalcogenides

We explore the physical properties of a unified microscopic theory for the coexistence of superconductivity and charge density waves in two-dimensional transition metal dichalcogenides. In the case of particle-hole symmetry the elementary particles are Dirac fermions at the nodes of the charge density wave gap. When particle-hole symmetry is broken electron (hole) pockets are formed around the Fermi surface. The superconducting ground state emerges from the pairing of nodal quasi-particles mediated by acoustic phonons via a piezoelectric coupling. We calculate several properties in the s-wave superconducting phase, including specific heat, ultra-sound absorption, nuclear magnetic relaxation, thermal, and optical conductivities. In the case with particle-hole symmetry, the specific heat jump at the transition deviates strongly from ordinary superconductors. The nuclear magnetic response shows an anomalous anisotropy due to the broken time-reversal symmetry of the superconducting gap, induced by the triple charge density wave state. The loss of lattice inversion symmetry in the charge density wave phase leads to anomalous coherence factors in the optical conductivity and to the appearance of an absorption edge at the optical gap energy. Furthermore, optical and thermal conductivities display anomalous peaks in the infrared when particle-hole symmetry is broken.Comment: 23 pages, 16 figures. Published versio

Leishmania sexual reproductive strategies as resolved through computational methods designed for aneuploid genomes

A cryptic sexual reproductive cycle i

The Disunity of Consciousness

It is commonplace for both philosophers and cognitive scientists to express their allegiance to the "unity of consciousness". This is the claim that a subject’s phenomenal consciousness, at any one moment in time, is a single thing. This view has had a major influence on computational theories of consciousness. In particular, what we call single-track theories dominate the literature, theories which contend that our conscious experience is the result of a single consciousness-making process or mechanism in the brain. We argue that the orthodox view is quite wrong: phenomenal experience is not a unity, in the sense of being a single thing at each instant. It is a multiplicity, an aggregate of phenomenal elements, each of which is the product of a distinct consciousness-making mechanism in the brain. Consequently, cognitive science is in need of a multi-track theory of consciousness; a computational model that acknowledges both the manifold nature of experience, and its distributed neural basis

Gene expression in Leishmania is regulated predominantly by gene dosage

ABSTRACT Leishmania tropica, a unicellular eukaryotic parasite present in North and East Africa, the Middle East, and the Indian subcontinent, has been linked to large outbreaks of cutaneous leishmaniasis in displaced populations in Iraq, Jordan, and Syria. Here, we report the genome sequence of this pathogen and 7,863 identified protein-coding genes, and we show that the majority of clinical isolates possess high levels of allelic diversity, genetic admixture, heterozygosity, and extensive aneuploidy. By utilizing paired genome-wide high-throughput DNA sequencing (DNA-seq) with RNA-seq, we found that gene dosage, at the level of individual genes or chromosomal “somy” (a general term covering disomy, trisomy, tetrasomy, etc.), accounted for greater than 85% of total gene expression variation in genes with a 2-fold or greater change in expression. High gene copy number variation (CNV) among membrane-bound transporters, a class of proteins previously implicated in drug resistance, was found for the most highly differentially expressed genes. Our results suggest that gene dosage is an adaptive trait that confers phenotypic plasticity among natural Leishmania populations by rapid down- or upregulation of transporter proteins to limit the effects of environmental stresses, such as drug selection. IMPORTANCE Leishmania is a genus of unicellular eukaryotic parasites that is responsible for a spectrum of human diseases that range from cutaneous leishmaniasis (CL) and mucocutaneous leishmaniasis (MCL) to life-threatening visceral leishmaniasis (VL). Developmental and strain-specific gene expression is largely thought to be due to mRNA message stability or posttranscriptional regulatory networks for this species, whose genome is organized into polycistronic gene clusters in the absence of promoter-mediated regulation of transcription initiation of nuclear genes. Genetic hybridization has been demonstrated to yield dramatic structural genomic variation, but whether such changes in gene dosage impact gene expression has not been formally investigated. Here we show that the predominant mechanism determining transcript abundance differences (>85%) in Leishmania tropica is that of gene dosage at the level of individual genes or chromosomal somy

Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania

Hybrid genotypes have been repeatedly described among natural isolates of Leishmania, and the recovery of experimental hybrids from sand flies co-infected with different strains or species of Leishmania has formally demonstrated that members of the genus possess the machinery for genetic exchange. As neither gamete stages nor cell fusion events have been directly observed during parasite development in the vector, we have relied on a classical genetic analysis to determine if Leishmania has a true sexual cycle. Here, we used whole genome sequencing to follow the chromosomal inheritance patterns of experimental hybrids generated within and between different strains of L. major and L. infantum. We also generated and sequenced the first experimental hybrids in L. tropica. We found that in each case the parental somy and allele contributions matched the inheritance patterns expected under meiosis 97–99% of the time. The hybrids were equivalent to F1 progeny, heterozygous throughout most of the genome for the markers that were homozygous and different between the parents. Rare, non-Mendelian patterns of chromosomal inheritance were observed, including a gain or loss of somy, and loss of heterozygosity, that likely arose during meiosis or during mitotic divisions of the progeny clones in the fly or culture. While the interspecies hybrids appeared to be sterile, the intraspecies hybrids were able to produce backcross and outcross progeny. Analysis of 5 backcross and outcross progeny clones generated from an L. major F1 hybrid, as well as 17 progeny clones generated from backcrosses involving a natural hybrid of L. tropica, revealed genome wide patterns of recombination, demonstrating that classical crossing over occurs at meiosis, and allowed us to construct the first physical and genetic maps in Leishmania. Altogether, the findings provide strong evidence for meiosis-like sexual recombination in Leishmania, presenting clear opportunities for forward genetic analysis and positional cloning of important genes.</div

Racial differences between African-American and white women in insulin resistance and visceral adiposity are associated with differences in apoCIII containing apoAI and apoB lipoproteins

Background: African-Americans have higher HDL, less visceral adipose tissue (VAT) and lower triglyceride (TG) and apoCIII concentrations than whites, despite being more insulin-resistant. We studied in African-American and white women the influences of insulin resistance and VAT on the apoAI concentrations of two HDL subspecies, one that contains apoCIII that is associated with increased risk of coronary heart disease (CHD) and one that does not have apoCIII that is associated with decreased CHD; and on the apoCIII concentrations of HDL and of the apoB lipoproteins. Methods: The participants were 32 women (14 African-Americans, 18 white) of similar age (39 ± 12 vs. 42 ± 11y). Mean BMI was 34 kg/m2 in the African-Americans compared to 30 in the whites. A standard diet (33% fat, 52% carbohydrate, 15% protein) was provided for 7 days followed by a test meal (40% fat, 40% carbohydrate, 20% protein) on Day 8. Insulin sensitivity index (SI) was calculated from the minimal model. Results: After controlling for SI, African-Americans have a higher mean apoAI level in HDL with apoCIII compared with whites (12.9 ± 2.8 and 10.9 ± 2.9 mg/dL, respectively, P = 0.05). SI was associated with higher apoAI in HDL with apoCIII, whereas VAT was not associated with this HDL subspecies. This pattern of results was reversed for apoCIII concentrations in apoB lipoproteins. After adjusting for SI, African-Americans had lower apoCIII in apoB lipoproteins. SI was associated with lower apoCIII in total apoB lipoproteins, whereas VAT was associated with higher apoCIII in all the apoB lipoproteins. Additional adjustment for VAT tended to reduce the difference in apoCIII between the groups. Conclusions: African-American women have a higher HDL with apoCIII level than whites when controlled for insulin sensitivity. African-Americans have lower insulin sensitivity. Insulin sensitivity is associated with higher levels of HDL with apoCIII. ApoCIII levels in VLDL are lower in African-American women than whites, also affected by insulin sensitivity which is associated with low apoCIII in VLDL. VAT has a strong association with apoCIII in apoB lipoproteins but not with apoAI in HDL with apoCIII. Trial registration ClinicalTrials.gov Identifier: NCT0048486

Interactional Structure Applied to the Identification and Generation of Visual Interactive Behavior: Robots that (Usually) Follow the Rules

Peer reviewe

Quasiparticle spectrum of the cuprate BiSrCaCuO: Possible connection to the phase diagram

We previously introduced [T. Cren et al., Europhys. Lett. 52, 203 (2000)] an energy-dependant gap function, $\Delta(E)$, that fits the unusual shape of the quasiparticle (QP) spectrum for both BiSrCaCuO and YBaCuO. A simple anti-resonance in $\Delta(E)$ accounts for the pronounced QP peaks in the density of states, at an energy $\Delta_p$, and the dip feature at a higher energy, $E_{dip}$. Here we go a step further : our gap function is consistent with the ($T, p$) phase diagram, where $p$ is the carrier density. For large QP energies ($E >> \Delta_p$), the total spectral gap is $\Delta(E) \simeq \Delta_p + \Delta_\phi$, where $\Delta_\phi$ is tied to the condensation energy. From the available data, a simple $p$-dependance of $\Delta_p$ and $\Delta_\phi$ is found, in particular $\Delta_\phi(p) \simeq 2.3 k_B T_c(p)$. These two distinct energy scales of the superconducting state are interpreted by comparing with the normal and pseudogap states. The various forms of the QP density of states, as well as the spectral function $A(k,E)$, are discussed

A comparison of statistical emulation methodologies for multi-wave calibration of environmental models

Expensive computer codes, particularly those used simulating environmental or geological processes such as climate models, require calibration (sometimes called tuning). When calibrating expensive simulators using uncertainty quantification methods, it is usually necessary to use a statistical model called an emulator in place of the computer code when running the calibration algorithm. Though emulators based on Gaussian processes are typically many orders of magnitude faster to evaluate than the simulator they mimic, many applications have sought to speed up the computations by using regression-only emulators within the calculations instead, arguing that the extra sophistication brought using the Gaussian process is not worth the extra computational power. This was the case for the analysis that produced the UK climate projections in 2009. In this paper we compare the effectiveness of both emulation approaches upon a multi-wave calibration framework that is becoming popular in the climate modelling community called \history matching". We find that Gaussian processes offer significant benefits to the reduction of parametric uncertainty over regression-only approaches. We find that in a multi-wave experiment, a combination of regression-only emulators initially, followed by Gaussian process emulators for refocussing experiments can be nearly as effective as using Gaussian processes throughout for a fraction of the computational cost. We also discover a number of design and emulator-dependent features of the multi-wave history matching approach that can cause apparent, yet premature, convergence of our estimates of parametric uncertainty. We compare these approaches to calibration in idealised examples and apply it to a well-known geological reservoir mode