Simulation of the phase diagram of magnetic vortices in two-dimensional superconductors: evidence for vortex chain formation

We study the superconducting vortex states induced by the interplay of long-range Pearl repulsion and short-range intervortex attraction using Langevin dynamics simulations. We show that at low temperatures the vortices form an ordered Abrikosov lattice both in low and high fields. The vortices show distinctive modulated structures at intermediate fields depending on the effective intervortex attraction: ordered vortex chain and kagome-like vortex structures for weak attraction; bubble, stripe and antibubble lattices for strong attraction. Moreover, in the regime of the chain state, the vortices display structural transitions from chain to labyrinthine (or disordered chain) and/or to disordered states depending on the strength of the disorder.

Pharmacokinetics and ex-vivo pharmacodynamics of cefquinome against Klebsiella pneumonia in healthy dogs

A two-period cross-over study was carried to investigate the pharmacokinetics (PK) and ex-vivo pharmacodynamics (PD) of cefquinome when administrated intravenously (IV) and intramuscularly (IM) in seven healthy dogs at a dose of 2 mg/kg of body weight. Serum concentrations were determined by HPLC-MS/MS assay and cefquinome concentration vs. time data after IV and IM were best fit to a two-compartment open model. Cefquinome mean values of area under concentration-time curve (AUC) were 5.15 μg · h/mL for IV dose and 4.59 μg · h/mL for IM dose. Distribution half-lives and elimination half-lives after IV dose and IM dose were 0.27 and 0.44 h, 1.53 and 1.94 h, respectively. Values of total body clearance (ClB ) and volume of distribution at steady-state (Vss ) were 0.49 L · kg/h and 0.81 L/kg, respectively. After IM dose, Cmax was 2.53 μg/mL and the bioavailability was 89.13%. For PD profile, the determined MIC and MBC values against K. pneumonia were 0.030 and 0.060 μg/mL in MHB and 0.032 and 0.064 μg/mL in serum. The ex vivo time-kill curves also were established in serum. In conjunction with the data on MIC, MBC values and the ex vivo bactericidal activity in serum, the present results allowed prediction that a single cefquinome dosage of 2 mg/kg may be effective in dogs against K. pneumonia infection.

Recurrent nasopharyngeal carcinoma: a clinical dilemma and challenge

Recurrent nasopharyngeal carcinoma, which represents a small proportion of head-and-neck cancers, has a unique set of patho-clinical characteristics. The management of recurrent nasopharyngeal carcinoma remains a challenging clinical problem. Traditional treatments offer limited local control and survival benefits; more seriously, they frequently induce severe late complications. Recently, novel treatment techniques and strategies-including precision radiotherapy, endoscopic surgery or transoral robotic resection, third-generation chemotherapy regimens, and targeted therapies and immunotherapy-have provided new hope for patients with recurrent nasopharyngeal carcinoma. Some of these patients can potentially be cured with modern treatments. However, a lack of adequate evidence makes it difficult for clinicians to apply these powerful techniques and strategies. Individualized management guidelines, full evaluation of quality of life in these patients, and a further understanding of the mechanisms underlying recurrence are future directions for research into recurrent nasopharyngeal carcinoma.

A novel chemical uncoupler ameliorates obesity and related phenotypes in mice with diet-induced obesity by modulating energy expenditure and food intake

AIMS/HYPOTHESIS

Decreasing mitochondrial coupling efficiency has been shown to be an effective therapy for obesity and related metabolic symptoms. Here we identified a novel mitochondrial uncoupler that promoted uncoupled respiration in a cell type-specific manner and investigated its effects on modulation of energy metabolism in vivo and in vitro.

METHODS

We screened a collection of mitochondrial membrane potential depolarising compounds for a novel chemical uncoupler on isolated skeletal muscle mitochondria using a channel oxygen system. The effect on respiration of metabolic cells (L6 myotubes, 3T3-L1 adipocytes and rat primary hepatocytes) was examined and metabolic pathways sensitive to cellular ATP content were also evaluated. The chronic metabolic effects were investigated in high-fat diet-induced obese mice and standard diet-fed (SD) lean mice.

RESULTS

The novel uncoupler, CZ5, promoted uncoupled respiration in a cell type-specific manner. It stimulated fuel oxidation in L6 myotubes and reduced lipid accumulation in 3T3-L1 adipocytes but did not affect gluconeogenesis or the triacylglycerol content in hepatocytes. The administration of CZ5 to SD mice increased energy expenditure (EE) but did not affect body weight or adiposity. Chronic studies in mice on high-fat diet showed that CZ5 reduced body weight and improved glucose and lipid metabolism via both increased EE and suppressed energy intake. The reduced adiposity was associated with the restoration of expression of key metabolic genes in visceral adipose tissue.

CONCLUSIONS/INTERPRETATION

This work demonstrates that a cell type-specific mitochondrial chemical uncoupler may have therapeutic potential for treating high-fat diet-induced metabolic diseases.

Reduction of osteopontin in vivo inhibits tubular epithelial to mesenchymal transition in rats with chronic allograft nephropathy

OBJECTIVE

Chronic allograft nephropathy (CAN) is an important etiological factor causing graft loss. However, the mechanism of CAN is unclear. Osteopontin (OPN), a proinflammatory and profibrosis molecule, plays a key role in late stages of renal diseases. We investigated the potential role of OPN in the pathogenesis of CAN.

METHODS

Using a F344 to Lewis rat CAN model, we injected short hairpin RNA (shRNA) constructs targeting OPN or negative control plasmids through the renal vein following electroporation. At 12 weeks after the transplantation, we determined interstitial fibrosis (IF) and tubular atrophy (TA) of the tubular epithelial cells (TECs). OPN expression was examined using Western blots and immunohistochemistry (IHC). Molecules involved in epithelial to mesenchymal transition (EMT) of TECs were examined using IHC and Western blots.

RESULTS

OPN expression in kidney grafts was decreased by the RNA interference (RNAi) group. Histology observations showed IF and TA to be mild with stable renal function in the RNAi-treated group. EMT of TECs was significantly lessened after reducing OPN.

CONCLUSION

Reduction of OPN in vivo inhibited progression of CAN. OPN may be of therapeutic value in transplantation settings.

Resonant soft-X-ray emission as a bulk probe of correlated electron behavior in metallic SrxCa1-xVO3

The evolution of electron correlation in SrxCa1-xVO3 has been studied using a combination of bulk-sensitive resonant soft x-ray emission spectroscopy, surface-sensitive photoemission spectroscopy, and ab initio band structure calculations. We show that the effect of electron correlation is enhanced at the surface. Strong incoherent Hubbard subbands are found to lie ∼20% closer in energy to the coherent quasiparticle features in surface-sensitive photoemission spectroscopy measurements compared with those from bulk-sensitive resonant soft x-ray emission spectroscopy, and a ∼10% narrowing of the overall bandwidth at the surface is also observed.

Insight into the sporulation phosphorelay: crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD

The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligand-binding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per-Arnt-Sim (PAS)-like domains. The KinD ligand-binding site is located on the membrane distal PAS-like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinD-dependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.

Interfacial ferromagnetism and exchange bias in CaRuO3/CaMnO3 superlattices

We have found ferromagnetism in epitaxially grown superlattices of CaRuO(3)/CaMnO(3) that arises in one unit cell at the interface. Scanning transmission electron microscopy and electron energy loss spectroscopy indicate that the difference in magnitude of the Mn valence states between the center of the CaMnO(3) layer and the interface region is consistent with double exchange interaction among the Mn ions at the interface. Polarized neutron reflectivity and the CaMnO(3) thickness dependence of the exchange bias field together indicate that the interfacial ferromagnetism is only limited to one unit cell of CaMnO(3) at each interface. The interfacial moment alternates between the 1 μ(B)/interface Mn ion for even CaMnO(3) layers and the 0.5 μ(B)/interface Mn ion for odd CaMnO(3) layers. This modulation, combined with the exchange bias, suggests the presence of a modulating interlayer coupling between neighboring ferromagnetic interfaces via the antiferromagnetic CaMnO(3) layers.

Expression of putative stem marker nestin and CD133 in advanced serous ovarian cancer

It is hypothesized that "cancer stem cells" are responsible for the resistance to chemotherapy of cancer cells in ovarian cancers. The objective of the studies was to explore if the stem cell biomarkers could be used to predict the tumor chemotherapy-resistance in serous ovarian cancer patients. Expression of two putative stem cell markers CD133 and nestin, and vascular epithelial growth factor (VEGF) and epidermal growth factor receptor (EGFR) were detected in 123 cases of advanced serous ovarian cancer specimens by immunohistochemistry. To estimate intra-tumoral microvessel density (MVD), CD34 immunostaining was also performed. CD133 and nestin were defined to be positive in 35.0% and 32.5% of the serous ovarian carcinoma tissues, respectively. It was observed that overexpression of nestin but not CD133 was associated with the cisplatin-based chemotherapy resistance and shorter overall survival of the patients, and nestin was found to be an independent prognostic factor. Moreover, positive nestin expression also correlated to increased expression of EGFR and VEGF, and elevated MVD in tumors. The results of this study suggest that serous ovarian cancers with high expression level of nestin represent an aggressive malignant phenotype associated with poor prognosis, and treatment targeted the nestin positive cancer cells might be a promising therapeutic strategy for this subgroups.

The polymorphisms in the VHL and HIF1A genes are associated with the prognosis but not the development of renal cell carcinoma

BACKGROUND

The von Hippel-Lindau (VHL) tumor suppressor gene and hypoxia-inducible factor-1α (HIF1A) play a pivotal role in renal carcinogenesis. This study was aimed to clarify the influence of VHL and HIF1A polymorphisms on renal cell cancer (RCC) susceptibility and survival.

SUBJECTS AND METHODS

We genotyped four potentially functional single-nucleotide polymorphisms (rs779805 in VHL and rs11549465, rs11549467, and rs2057482 in HIF1A) and assessed their associations with RCC risk, clinicopathologic parameters in a case-control study of 620 patients and 623 controls, and the prognosis of RCC in a cohort of 311 patients.

RESULTS

No significant differences in VHL or HIF1A genotypes were observed between RCC cases and controls. However, individuals with ≥2 variant alleles of the four polymorphisms were associated with less frequent lymph node metastasis and lower clinical stage (P = 0.032 and P = 0.041, respectively). And the number of variant alleles was associated with improved survival in a dose-response manner (P(trend) = 0.013). Furthermore, multivariate Cox regression analysis showed that the number of variant alleles (≥1 versus 0) was an independent prognostic factor for RCC survival (P = 0.036) together with clinical stage and tumor grade.

CONCLUSION

The VHL and HIF1A polymorphisms may not influence RCC susceptibility but may jointly influence RCC progression and survival.

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression levels, and to be able to interpret it mechanistically and functionally. Here we use RNA sequencing (RNA-seq) of mouse Th2 cells, coupled with a range of other techniques, to show that all genes can be separated, based on their expression abundance, into two distinct groups: one group comprised of lowly expressed and putatively non-functional mRNAs, and the other of highly expressed mRNAs with active chromatin marks at their promoters. These observations are confirmed in many other microarray and RNA-seq data sets of metazoan cell types.

Circular dichroism in biological photonic crystals and cubic chiral nets

Nature provides impressive examples of chiral photonic crystals, with the notable example of the cubic so-called srs network (the label for the chiral degree-three network modeled on SrSi2) or gyroid structure realized in wing scales of several butterfly species. By a circular polarization analysis of the band structure of such networks, we demonstrate strong circular dichroism effects: The butterfly srs microstructure, of cubic I4(1)32 symmetry, shows significant circular dichroism for blue to ultraviolet light, that warrants a search for biological receptors sensitive to circular polarization. A derived synthetic structure based on four like-handed silicon srs nets exhibits a large circular polarization stop band of a width exceeding 30%. These findings offer design principles for chiral photonic devices.

Interplay of cAMP and MAPK pathways in hCG secretion and fusogenic gene expression in a trophoblast cell line

Differentiation of human placental mononuclear trophoblasts into a multinucleate syncytium involves up-regulation of key proteins promoting cell fusion and increased capacity for placental hormonogenesis. It is well established that the activation of adenylyl cyclase leads to increased expression of trophoblast fusogenic gene machinery and human chorionic gonadotropin (hCG) secretion. We used the forskolin-induced syncytialisation of BeWo choriocarcinoma cells as a model to characterise in detail the signalling pathway downstream of adenylyl cyclase. Forskolin treatment induced a rapid and potent ERK1/2 and p38MAPK phosphorylation; this cascade required PKA-AKAP interactions and led to downstream CREB-1/ATF-1 phosphorylation via ERK1/2-dependent but p38MAPK-independent mechanisms. Interestingly both p38MAPK and ERK1/2 were involved in forskolin-induced hCG-secretion, suggesting the presence of additional p38MAPK-dependent but CREB-1/ATF-1-independent pathways. Forskolin treatment of BeWo cells significantly up-regulated the expression of various fusogenic gene mRNAs, including syncytin-1 and -2 (by 3- and 10-fold, respectively) the transcription factors old astrocyte specifically induced substance (OASIS) and glial cells missing a (GCMa) (by 3- and 6-fold, respectively) and the syncytin-2 receptor, major facilitator superfamily domain containing 2 (MFSD2) (by 2-fold). Up-regulation of AKAP79 and AKAP250 (by 2.5- and 4-fold, respectively) was also identified in forskolin-treated BeWo cells. Forskolin effects on all these genes were suppressed by chemical inhibition of p38MAPK whereas only specific genes were sensitive to ERK1/2 inhibition. This data provide novel insights into the signalling molecules and mechanisms regulating fusogenic gene expression by the adenylyl cyclase pathway.

EpiChIP: gene-by-gene quantification of epigenetic modification levels

The combination of chromatin immunoprecipitation with next-generation sequencing technology (ChIP-seq) is a powerful and increasingly popular method for mapping protein-DNA interactions in a genome-wide fashion. The conventional way of analyzing this data is to identify sequencing peaks along the chromosomes that are significantly higher than the read background. For histone modifications and other epigenetic marks, it is often preferable to find a characteristic region of enrichment in sequencing reads relative to gene annotations. For instance, many histone modifications are typically enriched around transcription start sites. Calculating the optimal window that describes this enrichment allows one to quantify modification levels for each individual gene. Using data sets for the H3K9/14ac histone modification in Th cells and an accompanying IgG control, we present an analysis strategy that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal. Curve fitting permits false discovery rate-based classification of genes as modified versus unmodified. We have developed a software package called EpiChIP that carries out this type of analysis, including integration with and visualization of gene expression data.

Calculation of the Johann error for spherically bent x-ray imaging crystal spectrometers

New x-ray imaging crystal spectrometers, currently operating on Alcator C-Mod, NSTX, EAST, and KSTAR, record spectral lines of highly charged ions, such as Ar(16+), from multiple sightlines to obtain profiles of ion temperature and of toroidal plasma rotation velocity from Doppler measurements. In the present work, we describe a new data analysis routine, which accounts for the specific geometry of the sightlines of a curved-crystal spectrometer and includes corrections for the Johann error to facilitate the tomographic inversion. Such corrections are important to distinguish velocity induced Doppler shifts from instrumental line shifts caused by the Johann error. The importance of this correction is demonstrated using data from Alcator C-Mod.

Comparative microarray analysis reveals that the core biofilm-associated transcriptome of Pseudomonas aeruginosa comprises relatively few genes

Pseudomonas aeruginosa is a model organism for the study of intercellular communication and biofilm formation. As such, P. aeruginosa has been the subject of several microarray analyses comparing gene expression in biofilms and planktonic cultures. In the current work, we carried out a meta-analysis of these data sets to try and identify genes that are generically associated with biofilm formation in all of the conditions examined. Although the total number of transcripts modulated in the biofilms was large within the individual studies, the overlap between the data sets was small. Indeed, only five transcripts were upregulated and six transcripts were downregulated by more than twofold in the three data sets analysed. However, when the threshold modulation was relaxed to less than twofold, the overlap between the data sets increased, revealing a set of transcripts common to all of the studies. Transcriptional fusions and quantitative real-time PCR were used to independently confirm a selection of the observed modulations. Notably, we found that the expression profile of genes encoding the catabolic pathways for branched chain and aromatic amino acids was altered in biofilms, and that these alterations correlated with the onset of anaerobic growth. These findings were confirmed by quantitative amino acid analysis of culture supernatants. A mutant in one of the genes that we identified showed diminished biofilm formation in an attachment assay. The relatively small number of common biofilm-specific endpoint transcripts throws doubt on the suggestion that biofim formation proceeds through a pre-determined developmental pathway.