Ranking ligand affinity for the DNA minor groove by experiment and simulation

The structural and thermodynamic basis for the strength and selectivity of the interactions of minor-groove binders (MGBs) with DNA is not fully understood. In 2003 we reported the first example of a thiazole containing MGB that bound in a phase shifted pattern that spanned 6 base-pairs rather than the usual 4 (for tricyclic distamycin-like compounds). Since then, using DNA footprinting, nuclear magnetic resonance spectroscopy, isothermal titration calorimetry and molecular dynamics, we have established that the flanking bases around the central 4 being read by the ligand have subtle effects on recognition. We have investigated the effect of these flanking sequences on binding and the reasons for the differences and established a computational method to rank ligand affinity against varying DNA sequences

Flattening of Single-Particle Spectra in Strongly Correlated Electron Systems and the Violation of the Wiedemann-Franz Law

The renormalization of the Wiedemann-Franz (WF) ratio in strongly correlated electron systems is analyzed within the Landau quasiparticle picture. We demonstrate that the WF law is violated: (i) at the quantum critical point, where the effective mass diverges, and (ii) beyond a point of fermion condensation, where the single-particle spectrum $\epsilon(p)$ becomes flat. Results of the analysis are compared with available experimental data.Comment: 6 pages, 5 figures, added reference

Phonon drag thermopower and weak localization

Previous experimental work on a two-dimensional (2D) electron gas in a Si-on-sapphire device led to the conclusion that both conductivity and phonon drag thermopower $S^g$ are affected to the same relative extent by weak localization. The present paper presents further experimental and theoretical results on these transport coefficients for two very low mobility 2D electron gases in $\delta-$doped GaAs/Ga$_x$Al$_{1-x}$As quantum wells. The experiments were carried out in the temperature range 3-7K where phonon drag dominates the thermopower and, contrary to the previous work, the changes observed in the thermopower due to weak localization were found to be an order of magnitude less than those in the conductivity. A theoretical framework for phonon drag thermopower in 2D and 3D semiconductors is presented which accounts for this insensitivity of $S^g$ to weak localization. It also provides transparent physical explanations of many previous experimental and theoretical results.Comment: 19 page Revtex file, 3 Postscript figur

Effect of Cyclooxygenase(COX)-1 and COX-2 inhibition on furosemide-induced renal responses and isoform immunolocalization in the healthy cat kidney

BACKGROUND: The role of cyclooxygenase(COX)-1 and COX-2 in the saluretic and renin-angiotensin responses to loop diuretics in the cat is unknown. We propose in vivo characterisation of isoform roles in a furosemide model by administering non-steroidal anti-inflammatory drugs (NSAIDs) with differing selectivity profiles: robenacoxib (COX-2 selective) and ketoprofen (COX-1 selective). RESULTS: In this four period crossover study, we compared the effect of four treatments: placebo, robenacoxib once or twice daily and ketoprofen once daily concomitantly with furosemide in seven healthy cats. For each period, urine and blood samples were collected at baseline and within 48 h of treatment starting. Plasma renin activity (PRA), plasma and urinary aldosterone concentrations, glomerular filtration rate (GFR) and 24 h urinary volumes, electrolytes and eicosanoids (PGE(2), 6-keto-PGF1(α,) TxB(2)), renal injury biomarker excretions [N-acetyl-beta-D-glucosaminidase (NAG) and Gamma-Glutamyltransferase] were measured. Urine volume (24 h) and urinary sodium, chloride and calcium excretions increased from baseline with all treatments. Plasma creatinine increased with all treatments except placebo, whereas GFR was significantly decreased from baseline only with ketoprofen. PRA increased significantly with placebo and once daily robenacoxib and the increase was significantly higher with placebo compared to ketoprofen (10.5 ± 4.4 vs 4.9 ± 5.0 ng ml(−1) h(−1)). Urinary aldosterone excretion increased with all treatments but this increase was inhibited by 75 % with ketoprofen and 65 % with once daily robenacoxib compared to placebo. Urinary PGE(2) excretion decreased with all treatments and excretion was significantly lower with ketoprofen compared to placebo. Urinary TxB(2) excretion was significantly increased from baseline only with placebo. NAG increased from baseline with all treatments. Immunohistochemistry on post-mortem renal specimens, obtained from a different group of cats that died naturally of non-renal causes, suggested constitutive COX-1 and COX-2 co-localization in many renal structures including the macula densa (MD). CONCLUSIONS: These data suggest that both COX-1 and COX-2 could generate the signal from the MD to the renin secreting cells in cats exposed to furosemide. Co-localization of COX isoenzymes in MD cells supports the functional data reported here. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0598-z) contains supplementary material, which is available to authorized users

ExoMol line lists - XLIV. IR and UV line list for silicon monoxide (SiO)

A new silicon monoxide (28Si16O) line list covering infrared, visible and ultraviolet regions called SiOUVenIR is presented. This line list extends the infrared EBJT ExoMol line list by including vibronic transitions to the A 1Π and E 1Σ+ electronic states. Strong perturbations to the A 1Π band system are accurately modelled through the treatment of 6 dark electronic states: C 1Σ−, D 1Δ, a 3Σ+, b 3Π, e 3Σ− and d 3Δ. Along with the X 1Σ+ ground state, these 9 electronic states were used to build a comprehensive spectroscopic model of SiO using a combination of empirical and ab initio curves, including the potential energy (PE), spin-orbit (SO), electronic angular momentum (EAM) and (transition) dipole moment curves. The ab initio PE and coupling curves, computed at the multireference configuration interaction (MRCI) level of theory, were refined by fitting their analytical representations to 2617 experimentally derived SiO energy levels determined from 97 vibronic bands belonging to the X–X, E–X and A–X electronic systems through the MARVEL procedure. 112 observed forbidden transitions from the C–X, D–X, e–X, and d–X bands were assigned using our predictions, and these could be fed back into the MARVEL procedure. The SiOUVenIR line list was computed using published ab initio transition dipole moments for the E–X and A–X bands; the line list is suitable for temperatures up to 10 000 K and for wavelengths longer than 140 nm. SiOUVenIR is available from www.exomol.com and the CDS database

ExoMol line lists - XLIV. IR and UV line list for silicon monoxide (SiO)

A new silicon monoxide (28Si16O) line list covering infrared, visible and ultraviolet regions called SiOUVenIR is presented. This line list extends the infrared EBJT ExoMol line list by including vibronic transitions to the A 1Π and E 1Σ+ electronic states. Strong perturbations to the A 1Π band system are accurately modelled through the treatment of 6 dark electronic states: C 1Σ−, D 1Δ, a 3Σ+, b 3Π, e 3Σ− and d 3Δ. Along with the X 1Σ+ ground state, these 9 electronic states were used to build a comprehensive spectroscopic model of SiO using a combination of empirical and ab initio curves, including the potential energy (PE), spin-orbit (SO), electronic angular momentum (EAM) and (transition) dipole moment curves. The ab initio PE and coupling curves, computed at the multireference configuration interaction (MRCI) level of theory, were refined by fitting their analytical representations to 2617 experimentally derived SiO energy levels determined from 97 vibronic bands belonging to the X–X, E–X and A–X electronic systems through the MARVEL procedure. 112 observed forbidden transitions from the C–X, D–X, e–X, and d–X bands were assigned using our predictions, and these could be fed back into the MARVEL procedure. The SiOUVenIR line list was computed using published ab initio transition dipole moments for the E–X and A–X bands; the line list is suitable for temperatures up to 10 000 K and for wavelengths longer than 140 nm. SiOUVenIR is available from www.exomol.com and the CDS database

Characterisation of feline renal cortical fibroblast cultures and their transcriptional response to transforming growth factor beta 1

Chronic kidney disease (CKD) is common in geriatric cats, and the most prevalent pathology is chronic tubulointerstitial inflammation and fibrosis. The cell type predominantly responsible for the production of extra-cellular matrix in renal fibrosis is the myofibroblast, and fibroblast to myofibroblast differentiation is probably a crucial event. The cytokine TGF-β1 is reportedly the most important regulator of myofibroblastic differentiation in other species. The aim of this study was to isolate and characterise renal fibroblasts from cadaverous kidney tissue of cats with and without CKD, and to investigate the transcriptional response to TGF-β1

Calcium and Vitamin D increase mRNA levels for the growth control hIK1 channel in human epidermal keratinocytes but functional channels are not observed

BACKGROUND: Intermediate-conductance, calcium-activated potassium channels (IKs) modulate proliferation and differentiation in mesodermal cells by enhancing calcium influx, and they contribute to the physiology of fluid movement in certain epithelia. Previous reports suggest that IK channels stimulate proliferative growth in a keratinocyte cell line; however, because these channels indirectly promote calcium influx, a critically unique component of the keratinocyte differentiation program, an alternative hypothesis is that they would be anti-proliferative and pro-differentiating. This study addresses these hypotheses. METHODS: Real-time PCR, patch clamp electrophysiology, and proliferation assays were used to determine if human IK1 (hIK1) expression and function are correlated with either proliferation or differentiation in cultured human skin epidermal keratinocytes, and skin biopsies grown in explant culture. RESULTS: hIK1 mRNA expression in human keratinocytes and skin was increased in response to anti-proliferative/pro-differentiating stimuli (elevated calcium and Vitamin D). Correspondingly, the hIK1 agonist 1-EBIO inhibited keratinocyte proliferation suggesting that the channel could be anti-proliferative and pro-differentiating. However, this proliferative inhibition by 1-EBIO was not reversed by a panel of hIK1 blockers, calling into question the mechanism of 1-EBIO action. Subsequent patch clamp electrophysiological analysis failed to detect hIK1 channel currents in keratinocytes, even those expressing substantial hIK1 mRNA in response to calcium and Vitamin D induced differentiation. Identical electrophysiological recording conditions were then used to observe robust IK1 currents in fibroblasts which express IK1 mRNA levels comparable to those of keratinocytes. Thus, the absence of observable hIK1 currents in keratinocytes was not a function of the electrophysiological techniques. CONCLUSION: Human keratinocyte differentiation is stimulated by calcium mobilization and influx, and differentiation stimuli coordinately upregulate mRNA levels of the calcium-activated hIK1 channel. This upregulation is paradoxical in that functional hIK1 channels are not observed in cultured keratinocytes. It appears, therefore, that hIK1 does not contribute to the functional electrophysiology of primary human keratinocytes, nor intact human skin. Further, the results indicate caution is required when interpreting experiments utilizing pharmacological hIK1 modulators in human keratinocytes

Expression of UDP-glucuronosyltransferase 1A4 in human placenta at term

The placenta contains a large variety of metabolizing enzymes, among them UDP-glucuronosyltransferase (UGT). Several UGT2B isozymes have so far been detected in human placenta, but little is known on placental expression of UGT1A isozymes. The antiepileptic drug lamotrigine (LTG) is a UGT1A4-substrate, and its serum concentration falls by over 50% during pregnancy, leading to impaired seizure control. The placenta may be involved in this. Microsomes from term placentas of 4 LTG-users and 10 healthy control subjects were prepared. Western blot analysis detected UGT1A proteins in all placentas. The presence of UGT1A4 in placenta from LTG users was confirmed with UGT1A4 commercial standard and a specific UGT1A4 primary antibody. Since LTG is primarily metabolized by UGT1A4 and this isozyme is shown to be present in placenta at term, it may be hypothesized that the placenta is involved in the fall of LTG serum concentrations during pregnancy