Electronic Structure of Metallophlorins: Lessons from Iridium and Gold Phlorin Derivatives.

Phlorins have long remained underexplored relative to their fully conjugated counterparts, such as porphyrins, hydroporphyrins, and corroles. Herein, we have attempted to bridge that knowledge gap with a scalar-relativistic density functional theory (DFT) study of unsubstituted iridium and gold phlorin derivatives and a multitechnique experimental study of iridium-bispyridine and gold complexes of 5,5-dimethyl-10,15,20-tris(pentafluorophenyl)phlorin. Theory and experiments concur that the phlorin derivatives exhibit substantially smaller HOMO-LUMO gaps, as reflected in a variety of observable properties. Thus, the experimentally studied Ir and Au complexes absorb strongly in the near-infrared (NIR), with absorption maxima at 806 and 770 nm, respectively. The two complexes are also weakly phosphorescent with emission maxima at 950 and 967 nm, respectively. They were also found to photosensitize singlet oxygen formation, with quantum yields of 40 and 28%, respectively. The near-infrared (NIR) absorption and emission are consonants with smaller electrochemical HOMO-LUMO gaps of ∼1.6 V, compared to values of ∼2.1 V, for electronically innocent porphyrins and corroles. Interestingly, both the first oxidation and reduction potentials of the Ir complex are some 600 mV shifted to more negative potentials relative to those of the Au complex, indicating an exceptionally electron-rich macrocycle in the case of the Ir complex.

Transition-Metal Isocorroles as Singlet Oxygen Sensitizers.

Building on a highly efficient synthesis of pyrrole-appended isocorroles, we have worked out conditions for manganese, palladium, and platinum insertion into free-base 5/10-(2-pyrrolyl)-5,10,15-tris(4-methylphenyl)isocorrole, H2[5/10-(2-py)TpMePiC]. Platinum insertion proved exceedingly challenging but was finally accomplished with cis-Pt(PhCN)2Cl2. All the complexes proved weakly phosphorescent in the near-infrared under ambient conditions, with a maximum phosphorescence quantum yield of 0.1% observed for Pd[5-(2-py)TpMePiC]. The emission maximum was found to exhibit a strong metal ion dependence for the 5-regioisomeric complexes but not for the 10-regioisomers. Despite the low phosphorescence quantum yields, all the complexes were found to sensitize singlet oxygen formation with moderate to good efficiency, with singlet oxygen quantum yields ranging over 21-52%. With significant absorption in the near-infrared and good singlet oxygen-sensitizing ability, metalloisocorroles deserve examination as photosensitizers in the photodynamic therapy of cancer and other diseases.

Revealing the Magnetic Structure and Properties of Mn(Co,Ge)2.

The atomic and magnetic structures of Mn(Co,Ge)2 are reported herein. The system crystallizes in the space group P63/mmc as a superstructure of the MgZn2-type structure. The system exhibits two magnetic transitions with associated magnetic structures, a ferromagnetic (FM) structure around room temperature, and an incommensurate structure at lower temperatures. The FM structure, occurring between 193 and 329 K, is found to be a member of the magnetic space group P63/mm'c'. The incommensurate structure found below 193 K is helical with propagation vector k = (0 0 0.0483). Crystallographic results are corroborated by magnetic measurements and ab initio calculations.

DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling of protein-RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to RNA nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods for modeling RNA-protein binding. Importantly, we demonstrate that DeepCLIP predictions correlate with the functional outcomes of nucleotide variants in independent wet lab experiments. Furthermore, we show how DeepCLIP binding profiles can be used in the design of therapeutically relevant antisense oligonucleotides, and to uncover possible position-dependent regulation in a tissue-specific manner. DeepCLIP is freely available as a stand-alone application and as a webtool at http://deepclip.compbio.sdu.dk.

From single drug targets to synergistic network pharmacology in ischemic stroke.

Drug discovery faces an efficacy crisis to which ineffective mainly single-target and symptom-based rather than mechanistic approaches have contributed. We here explore a mechanism-based disease definition for network pharmacology. Beginning with a primary causal target, we extend this to a second using guilt-by-association analysis. We then validate our prediction and explore synergy using both cellular in vitro and mouse in vivo models. As a disease model we chose ischemic stroke, one of the highest unmet medical need indications in medicine, and reactive oxygen species forming NADPH oxidase type 4 (Nox4) as a primary causal therapeutic target. For network analysis, we use classical protein-protein interactions but also metabolite-dependent interactions. Based on this protein-metabolite network, we conduct a gene ontology-based semantic similarity ranking to find suitable synergistic cotargets for network pharmacology. We identify the nitric oxide synthase (Nos1 to 3) gene family as the closest target to Nox4 Indeed, when combining a NOS and a NOX inhibitor at subthreshold concentrations, we observe pharmacological synergy as evidenced by reduced cell death, reduced infarct size, stabilized blood-brain barrier, reduced reoxygenation-induced leakage, and preserved neuromotor function, all in a supraadditive manner. Thus, protein-metabolite network analysis, for example guilt by association, can predict and pair synergistic mechanistic disease targets for systems medicine-driven network pharmacology. Such approaches may in the future reduce the risk of failure in single-target and symptom-based drug discovery and therapy.

Whole-Exome Sequencing of Patients With Recurrent HSV-2 Lymphocytic Mollaret Meningitis.

Recurrent lymphocytic meningitis, also referred to as Mollaret meningitis, is a rare neurological disease characterized mainly by reactivation of herpes simplex virus 2 (HSV-2) from sensory ganglia. However, the underlying host immune determinants and viral factors rendering some individuals unable to maintain HSV-2 latency are largely unknown. We collected a cohort of 15 patients diagnosed with Mollaret meningitis. By whole-exome sequencing we identified rare host genetic variants predicted to be deleterious in molecules involved in (1) ubiquitin-proteasome pathways, (2) the autophagy machinery, and (3) cell proliferation/apoptosis. Moreover, infection of patient cells with HSV-2 or stimulation by virus-derived double-stranded DNA ligands revealed reduced antiviral interferon responses in most patients. These findings may contribute to a better understanding of disease pathogenesis and protective immunity to HSV in the central nervous system, and may ultimately be of importance for identification of targets for development of improved prophylaxis and treatment of this disease.

E. coli gene regulatory networks are inconsistent with gene expression data.

Gene regulatory networks (GRNs) and gene expression data form a core element of systems biology-based phenotyping. Changes in the expression of transcription factors are commonly believed to have a causal effect on the expression of their targets. Here we evaluated in the best researched model organism, Escherichia coli, the consistency between a GRN and a large gene expression compendium. Surprisingly, a modest correlation was observed between the expression of transcription factors and their targets and, most noteworthy, both activating and repressing interactions were associated with positive correlation. When evaluated using a sign consistency model we found the regulatory network was not more consistent with measured expression than random network models. We conclude that, at least in E. coli, one cannot expect a causal relationship between the expression of transcription and factors their targets, and that the current static GRN does not adequately explain transcriptional regulation. The implications of this are profound as they question what we consider established knowledge of the systemic biology of cells and point to methodological limitations with respect to single omics analysis, static networks and temporality.

Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes.

BACKGROUND: Ovarian carcinomas presenting homologous recombination deficiency (HRD), which is observed in about 50% of cases, are more sensitive to platinum and PARP inhibitor therapies. Although platinum resistant disease has a low chance to be responsive to platinum-based chemotherapy, a set of patients is retreated with platinum and some of them are responsive. In this study, we evaluated copy number alterations, HR gene mutations and HR deficiency scores in ovarian cancer patients with prolonged platinum sensitivity. METHODS: In this retrospective study (2005 to 2014), we selected 31 patients with platinum resistant ovarian cancer retreated with platinum therapy. Copy number alterations and HR scores were evaluated using the OncoScan® FFPE platform in 15 cases. The mutational profile of 24 genes was investigated by targeted-NGS. RESULTS: The median values of the four HRD scores were higher in responders (LOH = 15, LST = 28, tAI = 33, CS = 84) compared with non-responders (LOH = 7.5, LST = 17.5, tAI = 23, CS = 47). Patients with high LOH, LST, tAI and CS scores had better response rates, although these differences were not statistically significant. Response rate to platinum retreatment was 22% in patients with CCNE1 gains and 83.5% in patients with no CCNE1 gains (p = 0.041). Furthermore, response rate was 54.5% in patients with RB1 loss and 25% in patients without RB1 loss (p = 0.569). Patients with CCNE1 gains showed a worse progression free survival (PFS = 11.1 months vs 3.7 months; p = 0.008) and a shorter overall survival (OS = 39.3 months vs 7.1 months; p = 0.007) in comparison with patients with no CCNE1 gains. Patients with RB1 loss had better PFS (9.0 months vs 2.6 months; p = 0.093) and OS (27.4 months vs 3.6 months; p = 0.025) compared with cases with no RB1 loss. Four tumor samples were BRCA mutated and tumor mutations were not associated with response to treatment. CONCLUSIONS: HR deficiency was found in 60% of our cases and HRD medium values were higher in responders than in non-responders. Despite the small number of patients tested, CCNE1 gain and RB1 loss discriminate patients with tumors extremely sensitive to platinum retreatment.

Rapid one-pot synthesis of pyrrole-appended isocorroles.

Free-base meso-triarylcorroles have been found to undergo oxidative coupling with an excess of pyrrole in dichloromethane in the presence of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) affording 5/10-pyrrole-appended isocorroles in reasonable yields (35-60%) and in a matter of seconds. The free-base isocorrole ligands could all be complexed to copper with Cu(OAc)2·H2O in chloroform/methanol in 55-80% yields. Single-crystal X-ray structures of two of the new compounds (H2[5-pyr-TpOMePiC] and Cu[10-pyr-TpOMePiC]) revealed planar macrocycles with rms atomic displacements of only 0.02 and 0.06 Å relative to their respective best-fit C19N4 planes. Both free-base and Cu(ii)-complexed isocorroles exhibit richly featured UV-vis-NIR spectra with red/NIR absorption maxima at ∼650 nm and ∼725 nm for the free-bases and ∼800-850 nm for the copper complexes, suggesting potential applications in photodynamic therapy. Cyclic voltammetric analyses of five of the Cu complexes revealed fully reversible redox cycles with multiple oxidation and reduction features.

Comprehensive Genomic Profiling of Androgen-Receptor-Negative Canine Prostate Cancer.

Canine carcinomas have been considered natural models for human diseases; however, the genomic profile of canine prostate cancers (PCs) has not been explored. In this study, 14 PC androgen-receptor-negative cases, 4 proliferative inflammatory atrophies (PIA), and 5 normal prostate tissues were investigated by array-based comparative genomic hybridization (aCGH). Copy number alterations (CNAs) were assessed using the Canine Genome CGH Microarray 4 × 44K (Agilent Technologies). Genes covered by recurrent CNAs were submitted to enrichment and cross-validation analysis. In addition, the expression levels of TP53, MDM2 and ZBTB4 were evaluated in an independent set of cases by qPCR. PC cases presented genomic complexity, while PIA samples had a small number of CNAs. Recurrent losses covering well-known tumor suppressor genes, such as ATM, BRCA1, CDH1, MEN1 and TP53, were found in PC. The in silico functional analysis showed several cancer-related genes associated with canonical pathways and interaction networks previously described in human PC. The MDM2, TP53, and ZBTB4 copy number alterations were translated into altered expression levels. A cross-validation analysis using The Cancer Genome Atlas (TCGA) database for human PC uncovered similarities between canine and human PCs. Androgen-receptor-negative canine PC is a complex disease characterized by high genomic instability, showing a set of genes with similar alterations to human cancer.

CoNVaQ: a web tool for copy number variation-based association studies.

BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies. The web service allows users to upload two sets of CNV segments and search for genomic regions where the occurrence of CNVs is significantly associated with the phenotype. CoNVaQ provides two models: a simple statistical model using Fisher's exact test and a novel query-based model matching regions to user-defined queries. For each region, the method computes a global q-value statistic by repeated permutation of samples among the populations. We demonstrate our platform by using it to analyze a data set of HPV-positive and HPV-negative penile cancer patients. CONCLUSIONS: CoNVaQ provides a simple workflow for performing CNV-based association studies. It is made available as a web platform in order to provide a user-friendly workflow for biologists and clinicians to carry out CNV data analysis without installing any software. Through the web interface, users are also able to analyze their results to find overrepresented GO terms and pathways. In addition, our method is also available as a package for the R programming language. CoNVaQ is available at https://convaq.compbio.sdu.dk .

Sample cell for studying liquid interfaces with an in situ electric field using X-ray reflectivity and application to clay particles at oil-oil interfaces.

Commissioning results of a liquid sample cell for X-ray reflectivity studies with an in situ applied electrical field are presented. The cell consists of a Plexiglas container with lateral Kapton windows for air-liquid and liquid-liquid interface studies, and was constructed with grooves to accept plate electrodes on the walls parallel to the direction of the beam. Both copper and ITO plate electrodes have been used, the latter being useful for simultaneous optical studies. Commissioning tests were made at the I07 beamline of the Diamond Light Source.

Local versus global aromaticity in azuliporphyrin and benziporphyrin derivatives.

Carbaporphyrinoids afford fascinating examples of competition between local and global aromaticity in conjugated, polycyclic systems. Thus, whereas density functional theory calculations reveal only a modest effect of metal complexation on the current density profiles of true carbaporphyrins and azuliporphyrins, the impact is much greater for benziporphyrins, underscoring a strong competition between local and global aromaticity in the latter system. Furthermore, the calculations shed light on the remarkable efficacy of suitably placed electron-donating substituents on the benzene ring in boosting the global diatropic currents in a metallobenziporphyrin.

Selection of cell-type specific antibodies on tissue-sections using phage display.

With the advent of modern technologies enabling single cell analysis, it has become clear that small sub-populations of cells or even single cells can drive the phenotypic appearance of tissue, both diseased and normal. Nucleic acid based technologies allowing single cell analysis has been faster to mature, while technologies aimed at analysing the proteome at a single cell level is still lacking behind, especially technologies which allow single cell analysis in tissue. Introducing methods, that allows such analysis, will pave the way for discovering new biomarkers with more clinical relevance, as these may be unique for microenvironments only present in tissue and will avoid artifacts introduced by in vitro studies. Here, we introduce a technology enabling biomarker identification on small sub-populations of cells within a tissue section. Phage antibody libraries are applied to the tissue sections, followed by washing to remove non-bound phage particles. To eliminate phage antibodies binding to antigens ubiquitously expressed and retrieve phage antibodies binding specifically to antigens expressed by the sub-population of cells, the area of interest is protected by a 'shadow stick'. The phage antibodies on the remaining areas on the slide are exposed to UV light, which introduces cross-links in the phage genome, thus rendering them non-replicable. In this work we applied the technology, guided by CD31 expressing endothelial cells, to isolate recombinant antibodies specifically binding biomarkers expressed either by the cell or in the microenvironment surrounding the endothelial cell.

Computer-assisted training as a complement in rehabilitation of patients with chronic vestibular dizziness--a randomized controlled trial.

OBJECTIVE: To compare a computer-assisted home exercise program with conservative home-training following printed instructions in the rehabilitation of elderly patients with vestibular dysfunction. DESIGN: Single-blind, randomized, controlled trial. SETTING: Geriatric department of a university hospital. PARTICIPANTS: Patients with chronic dizziness due to vestibular dysfunction (N=63) were randomly assigned to either rehabilitation in the clinic followed by computer-assisted home exercises (intervention group: n=32) or rehabilitation in the clinic followed by home exercises according to printed instructions (control group: n=31). INTERVENTIONS: Patients in the intervention group received assisted rehabilitation by a computer program. MAIN OUTCOME MEASURES: Measurements at baseline and at 8 and 16 weeks were compared. These included the One Leg Stand Test, Dynamic Gait Index, Chair Stand Test, Motion Sensitivity Test, Short Form-12, Dizziness Handicap Inventory, and visual analog scale. RESULTS: Both groups improved significantly during 16 weeks of rehabilitation. However, neither t tests nor repeated-measures analysis of variance demonstrated any significant differences between the 2 groups. The overall compliance rate to computer program exercises during 16 weeks was 57%. CONCLUSIONS: A computer-assisted program to support the home training of elderly patients with vestibular dysfunction did not improve rehabilitation more than did printed instructions.

Structure irregularity impedes drop roll-off at superhydrophobic surfaces.

We study water drop roll-off at superhydrophobic surfaces with different surface patterns. Superhydrophobic microcavity surfaces were fabricated in silicon and coated with 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS). For the more irregular surface patterns, the observed increase in roll-off angles is found to be caused by a decrease of the receding contact angle, which in turn is caused by an increase of the triple phase contact line of the drops for those more irregular surfaces. To understand the observation, we propose to treat the microdrops as rigid bodies and apply a torque balance between the torque exerted by the projected gravity force and the torque exerted by the adhesion force acting along the triple line on the receding side of the drop. This simple model provides a proper order of magnitude estimate of the measured effects.

Study of transitions between wetting states on microcavity arrays by optical transmission microscopy.

In this article, we present a simple and fast optical method based on transmission microscopy to study the stochastic wetting transitions on micro- and nanostructured polymer surfaces immersed in water. We analyze the influence of immersion time and the liquid pressure on the degree of water intrusion in individual microcavities on these surfaces as well as the lifespan of their superhydrophobicity. We show that transitions among the three wetting states (Cassie, Cassie-impregnating, and Wenzel) occur with a certain pressure threshold (300 mbar for a microcavity diameter of 7.5 µm). Below this threshold, the transitions between the Cassie and the Cassie-impregnating states are reversible, whereas above this threshold, irreversible transitions to the Wenzel state start to occur. The transitions between the different wetting states can be explained by taking into account both the Young-Laplace equation for the water menisci in the cavities and the diffusion of dissolved gas molecules in the water. In addition, the wetting transitions had a stochastic nature, which resulted from the short diffusion distance for dissolved gas molecules in the water between neighboring cavities. Furthermore, we compared the contact angle properties of two polymeric materials (COC and PP) with moderate hydrophobicity. We attributed the difference in the water repellency of the two materials to a difference in the wetting of their nanostructures. Our experimental observations thus indicate that both the diffusion of gas molecules in water and the wetting properties of nanostructures are important for understanding the sustainability of superhydrophobicity of surfaces under water and for improving the structural design of superhydrophobic surfaces.

Hierarchical association of COPD to principal genetic components of biological systems.

Many disease-causing genetic variants converge on common biological functions and pathways. Precisely how to incorporate pathway knowledge in genetic association studies is not yet clear, however. Previous approaches employ a two-step approach, in which a regular association test is first performed to identify variants associated with the disease phenotype, followed by a test for functional enrichment within the genes implicated by those variants. Here we introduce a concise one-step approach, Hierarchical Genetic Analysis (Higana), which directly computes phenotype associations against each function in the large hierarchy of biological functions documented by the Gene Ontology. Using this approach, we identify risk genes and functions for Chronic Obstructive Pulmonary Disease (COPD), highlighting microtubule transport, muscle adaptation, and nicotine receptor signaling pathways. Microtubule transport has not been previously linked to COPD, as it integrates genetic variants spread over numerous genes. All associations validate strongly in a second COPD cohort.

Amperometric noise at thin film band electrodes.

Background current noise is often a significant limitation when using constant-potential amperometry for biosensor application such as amperometric recordings of transmitter release from single cells through exocytosis. In this paper, we fabricated thin-film electrodes of gold and conductive polymers and measured the current noise in physiological buffer solution for a wide range of different electrode areas. The noise measurements could be modeled by an analytical expression, representing the electrochemical cell as a resistor and capacitor in series. The studies revealed three domains; for electrodes with low capacitance, the amplifier noise dominated, for electrodes with large capacitances, the noise from the resistance of the electrochemical cell was dominant, while in the intermediate region, the current noise scaled with electrode capacitance. The experimental results and the model presented here can be used for choosing an electrode material and dimensions and when designing chip-based devices for low-noise current measurements.

All polymer chip for amperometric studies of transmitter release from large groups of neuronal cells.

We present an all polymer electrochemical chip for simple detection of transmitter release from large groups of cultured PC 12 cells. Conductive polymer PEDOT:tosylate microelectrodes were used together with constant potential amperometry to obtain easy-to-analyze oxidation signals from potassium-induced release of transmitter molecules. The nature of the resulting current peaks is discussed, and the time for restoring transmitter reservoirs is studied. The relationship between released transmitters and potassium concentration was found to fit to a sigmoidal dose-response curve. Finally, we demonstrate how the presented device can be used for simple drug screening purposes, by measuring the increase of transmitter release due to short-term treatment with L-DOPA.