bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel giardicidal compounds bearing proton pump inhibitor scaffold proceeding through triosephosphate isomerase inactivation
Authors: Hernández-Ochoa B. , Navarrete-Vázquez G. , Nava-Zuazo C. , Castillo-Villanueva A. , Méndez S. T. , Torres-Arroyo A. , Gómez-Manzo S. , Marcial-Quino J. , Ponce-Macotela M. , Rufino-González Y. , Martínez-Gordillo M. , Palencia-Hernández G. , Esturau-Escofet N. , Calderon-Jaimes E. , Oria-Hernández J. , Reyes-Vivas H.
Published: August 2017

Giardiasis is a worldwide parasitic disease that affects mainly children and immunosuppressed people. Side effects and the emergence of resistance over current used drugs make imperative looking for new antiparasitics through discovering of new biological targets and designing of novel drugs. Recently, it has determined that gastric proton-pump inhibitors (PPI) have anti-giardiasic activity. The glycolytic enzyme, triosephosphate isomerase (GlTIM), is one of its potential targets. Therefore, we employed the scaffold of PPI to design new compounds aimed to increase their antigiardial capacity by inactivating GlTIM. Here we demonstrated that two novel PPI-derivatives (BHO2 and BHO3), have better anti-giardiasic activity than omeprazole in concentrations around 120–130 µM, without cytotoxic effect on mammal cell cultures. The derivatives inactivated GlTIM through the chemical modification of Cys222 promoting local structural changes in the enzyme. Furthermore, derivatives forms adducts linked to Cys residues through a C-S bond. We demonstrated that PPI can be used as scaffolds to design better antiparasitic molecules; we also are proposing a molecular mechanism of reaction for these novel derivatives.
New findings in a 400 million-year-old Devonian placoderm shed light on jaw structure and function in basal gnathostomes
Authors: Hu Yuzhi , Lu Jing , Young Gavin C.
Published: August 2017

Arthodire placoderms have been proposed as the sister group of Chinese ‘maxillate’ placoderms plus all the more crownward gnathostomes. These basal groups provide key information for understanding the early evolution of jaws. Here, we test previous assumptions about placoderm jaw structure and function by using high-resolution computed tomography, digital dissection, and enlarged 3D printouts on a unique articulated 400 million-year-old buchanosteid arthrodire. The upper jaw has a double ethmoid and a palatobasal connection, but no otic connection; the dermal bone attachment for the quadrate is different to other placoderms. A separately ossified cartilage behind the mandibular joint is comparable to the interhyal of osteichthyans. Two articular facets on the braincase associated with the hyomandibular nerve foramen supported a possible epihyal element and a separate opercular cartilage. Reassembling and manipulating 3D printouts demonstrates the limits of jaw kenetics. The new evidence indicates unrecognized similarities in jaw structure between arthrodires and osteichthyans, and will help to clarify the sequence of character acquisition in the evolution of basal gnathostome groups. New details on the hyoid arch will help to reformulate characters that are key in the heated debate of placoderm monophyly or paraphyly.
Acclimation to prolonged hypoxia alters hemoglobin isoform expression and increases hemoglobin oxygen affinity and aerobic performance in a marine fish
Authors: Pan Yihang K. , Ern Rasmus , Morrison Phillip R. , Brauner Colin J. , Esbaugh Andrew J.
Published: August 2017

Hemoglobin (Hb) multiplicity is common in fish, yet despite its ubiquitous nature, the functional significance is unclear. Here we explore the hypothesis that Hb multiplicity plays a role in hypoxia tolerance using the red drum (Sciaenops ocellatus). Red drum is an economically and ecologically important species native to coastal regions and estuaries of the Gulf of Mexico – habitats that routinely experience pronounced hypoxic events. Using a transcriptomic approach, we demonstrate that red drum red blood cells express 7 and 5 Hbα and Hbβ isoforms, respectively. Phylogenetic analysis grouped these isoforms into distinct isoHb clades, and provided evidence of lineage specific expression of particular isoHbs. In normoxia, three isoHbs predominated (Hbα-3.1, -3.2, and Hbβ-3.1). A three-week hypoxia acclimation (48 mmHg) resulted in significant up-regulation of Hbα-2, Hbα-3.2, and Hbβ-3.1, effectively switching the predominantly expressed isoforms. Changes in subunit expression were correlated with a decrease in non-stripped hemolysate P50. Similarly, hypoxia acclimation resulted in a 20% reduction in whole animal critical oxygen threshold (Pcrit). Hypoxia acclimation was not associated with changes in gill morphology, hematocrit, or relative ventricular mass. Overall, these data provide support for the hypothesis that Hb isoform switching can provide a physiological benefit to counteract environmental stress in fishes.
Wet tropical climate in SE Tibet during the Late Eocene
Authors: Sorrel Philippe , Eymard Ines , Leloup Philippe-Herve , Maheo Gweltaz , Olivier Nicolas , Sterb Mary , Gourbet Loraine , Wang Guocan , Jing Wu , Lu Haijian , Li Haibing , Yadong Xu , Zhang Kexin , Cao Kai , Chevalier Marie-Luce , Replumaz Anne
Published: August 2017

Cenozoic climate cooling at the advent of the Eocene-Oligocene transition (EOT), ~33.7 Ma ago, was stamped in the ocean by a series of climatic events albeit the impact of this global climatic transition on terrestrial environments is still fragmentary. Yet archival constraints on Late Eocene atmospheric circulation are scarce in (tropical) monsoonal Asia, and the paucity of terrestrial records hampers a meaningful comparison of the long-term climatic trends between oceanic and continental realms. Here we report new sedimentological data from the Jianchuan basin (SE Tibet) arguing for wetter climatic conditions in monsoonal Asia at ~35.5 Ma almost coevally to the aridification recognized northwards in the Xining basin. We show that the occurrence of flash-flood events in semi-arid to sub-humid palustrine-sublacustrine settings preceded the development of coal-bearing deposits in swampy-like environments, thus paving the way to a more humid climate in SE Tibet ahead from the EOT. We suggest that this moisture redistribution possibly reflects more northern and intensified ITCZ-induced tropical rainfall in monsoonal Asia around 35.5 Ma, in accordance with recent sea-surface temperature reconstructions from equatorial oceanic records. Our findings thus highlight an important period of climatic upheaval in terrestrial Asian environments ~2–4 millions years prior to the EOT.
Analysis of Factors Influencing Diagnostic Accuracy of T-SPOT.TB for Active Tuberculosis in Clinical Practice
Authors: Zhang Lifan , Shi Xiaochun , Zhang Yueqiu , Zhang Yao , Huo Feifei , Zhou Baotong , Deng Guohua , Liu Xiaoqing
Published: August 2017

T-SPOT.TB didn’t perform a perfect diagnosis for active tuberculosis (ATB), and some factors may influence the results. We did this study to evaluate possible factors associated with the sensitivity and specificity of T-SPOT.TB, and the diagnostic parameters under varied conditions. Patients with suspected ATB were enrolled prospectively. Influencing factors of the sensitivity and specificity of T-SPOT.TB were evaluated using logistic regression models. Sensitivity, specificity, predictive values (PV), and likelihood ratios (LR) were calculated with consideration of relevant factors. Of the 865 participants, 205 (23.7%) had ATB, including 58 (28.3%) microbiologically confirmed TB and 147 (71.7%) clinically diagnosed TB. 615 (71.7%) were non-TB. 45 (5.2%) cases were clinically indeterminate and excluded from the final analysis. In multivariate analysis, serous effusion was the only independent risk factor related to lower sensitivity (OR = 0.39, 95% CI: 0.18–0.81) among patients with ATB. Among non-TB patients, age, TB history, immunosuppressive agents/glucocorticoid treatment and lymphocyte count were the independent risk factors related to specificity of T-SPOT.TB. Sensitivity, specificity, PV+, PV−, LR+ and LR− of T-SPOT.TB for diagnosis of ATB were 78.5%, 74.1%, 50.3%, 91.2%, 3.0 and 0.3, respectively. This study suggests that influencing factors of sensitivity and specificity of T-SPOT.TB should be considered for interpretation of T-SPOT.TB results.
An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system
Authors: Kirchner Marion , Schorpp Kenji , Hadian Kamyar , Schneider Sabine
Published: August 2017

Riboswitches are bacterial RNA elements that regulate gene expression in response to metabolite or ion abundance and are considered as potential drug targets. In recent years a number of methods to find non-natural riboswitch ligands have been described. Here we report a high-throughput in vivo screening system that allows identifying OFF-riboswitch modulators in a 384 well bioluminescence assay format. We use a reverse reporter gene setup in Bacillus subtilis, consisting of a primary screening assay, a secondary assay as well as counter assays to detect compounds in a library of 1,280 molecules that act on the guanine-responsive xpt riboswitch from B. anthracis. With this in vivo high-throughput approach we identified several hit compounds and could validate the impact of one of them on riboswitch-mediated gene regulation, albeit this might not be due to direct binding to the riboswitch. However, our data demonstrate the capability of our screening assay for bigger high-throughput screening campaigns. Furthermore, the screening system described here can not only be generally employed to detect non-natural ligands or compounds influencing riboswitches acting as genetic OFF switches, but it can also be used to investigate natural ligands of orphan OFF-riboswitches.
Crystal Structure of MpPR-1i, a SCP/TAPS protein from Moniliophthora perniciosa, the fungus that causes Witches’ Broom Disease of Cacao
Authors: Baroni Renata M. , Luo Zhipu , Darwiche Rabih , Hudspeth Elissa M. , Schneiter Roger , Pereira Gonçalo A. G. , Mondego Jorge M. C. , Asojo Oluwatoyin A.
Published: August 2017

The pathogenic fungi Moniliophthora perniciosa causes Witches’ Broom Disease (WBD) of cacao. The structure of MpPR-1i, a protein expressed by M. perniciosa when it infects cacao, are presented. This is the first reported de novo structure determined by single-wavelength anomalous dispersion phasing upon soaking with selenourea. Each monomer has flexible loop regions linking the core alpha-beta-alpha sandwich topology that comprise ~50% of the structure, making it difficult to generate an accurate homology model of the protein. MpPR-1i is monomeric in solution but is packed as a high ~70% solvent content, crystallographic heptamer. The greatest conformational flexibility between monomers is found in loops exposed to the solvent channel that connect the two longest strands. MpPR-1i lacks the conserved CAP tetrad and is incapable of binding divalent cations. MpPR-1i has the ability to bind lipids, which may have roles in its infection of cacao. These lipids likely bind in the palmitate binding cavity as observed in tablysin-15, since MpPR-1i binds palmitate with comparable affinity as tablysin-15. Further studies are required to clarify the possible roles and underlying mechanisms of neutral lipid binding, as well as their effects on the pathogenesis of M. perniciosa so as to develop new interventions for WBD.
Molecular Organization Induced Anisotropic Properties of Perylene – Silica Hybrid Nanoparticles
Authors: Sriramulu Deepa , Turaga Shuvan Prashant , Bettiol Andrew Anthony , Valiyaveettil Suresh
Published: August 2017

Optically active silica nanoparticles are interesting owing to high stability and easy accessibility. Unlike previous reports on dye loaded silica particles, here we address an important question on how optical properties are dependent on the aggregation-induced segregation of perylene molecules inside and outside the silica nanoparticles. Three differentially functionalized fluorescent perylene - silica hybrid nanoparticles are prepared from appropriate ratios of perylene derivatives and tetraethyl orthosilicate (TEOS) and investigated the structure property correlation (P-ST, P-NP and P-SF). The particles differ from each other on the distribution, organization and intermolecular interaction of perylene inside or outside the silica matrix. Structure and morphology of all hybrid nanoparticles were characterized using a range of techniques such as electron microscope, optical spectroscopic measurements and thermal analysis. The organizations of perylene in three different silica nanoparticles were explored using steady-state fluorescence, fluorescence anisotropy, lifetime measurements and solid state polarized spectroscopic studies. The interactions and changes in optical properties of the silica nanoparticles in presence of different amines were tested and quantified both in solution and in vapor phase using fluorescence quenching studies. The synthesized materials can be regenerated after washing with water and reused for sensing of amines.
Superparamagnetic colloids in viscous fluids
Authors: Darras A. , Opsomer E. , Vandewalle N. , Lumay G.
Published: August 2017

The influence of a magnetic field on the aggregation process of superparamagnetic colloids has been well known on short time for a few decades. However, the influence of important parameters, such as viscosity of the liquid, has received only little attention. Moreover, the equilibrium state reached after a long time is still challenging on some aspects. Indeed, recent experimental measurements show deviations from pure analytical models in extreme conditions. Furthermore, current simulations would require several years of computing time to reach equilibrium state under those conditions. In the present paper, we show how viscosity influences the characteristic time of the aggregation process, with experimental measurements in agreement with previous theories on transient behaviour. Afterwards, we performed numerical simulations on equivalent systems with lower viscosities. Below a critical value of viscosity, a transition to a new aggregation regime is observed and analysed. We noticed this result can be used to reduce the numerical simulation time from several orders of magnitude, without modifying the intrinsic physical behaviour of the particles. However, it also implies that, for high magnetic fields, granular gases could have a very different behaviour from colloidal liquids.
Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
Authors: Rydzewski J. , Nowak W.
Published: August 2017

Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B′ helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.
Kleptoplast photosynthesis is nutritionally relevant in the sea slug Elysia viridis
Authors: Cartaxana Paulo , Trampe Erik , Kühl Michael , Cruz Sónia
Published: August 2017

Several sacoglossan sea slug species feed on macroalgae and incorporate chloroplasts into tubular cells of their digestive diverticula. We investigated the role of the “stolen” chloroplasts (kleptoplasts) in the nutrition of the sea slug Elysia viridis and assessed how their abundance, distribution and photosynthetic activity were affected by light and starvation. Elysia viridis individuals feeding on the macroalga Codium tomentosum were compared with starved specimens kept in dark and low light conditions. A combination of variable Chl a fluorescence and hyperspectral imaging, and HPLC pigment analysis was used to evaluate the spatial and temporal variability of photopigments and of the photosynthetic capacity of kleptoplasts. We show increased loss of weight and body length in dark-starved E. viridis as compared to low light-starved sea slugs. A more pronounced decrease in kleptoplast abundance and lower photosynthetic electron transport rates were observed in dark-starved sea slugs than in low light-starved animals. This study presents strong evidence of the importance of kleptoplast photosynthesis for the nutrition of E. viridis in periods of food scarcity. Deprived of photosynthates, E. viridis could accelerate the breakdown of kleptoplasts in the dark to satisfy its’ energy requirements.
Sunscreen products impair the early developmental stages of the sea urchin Paracentrotus lividus
Authors: Corinaldesi Cinzia , Damiani Elisabetta , Marcellini Francesca , Falugi Carla , Tiano Luca , Brugè Francesca , Danovaro Roberto
Published: August 2017

Marine ecosystems are increasingly threatened by the release of personal care products. Among them, sunscreens are causing concern either for the effects on skin protection from UV radiation and for the potential impacts on marine life. Here, we assessed the UVA protective efficacy of three sunscreens on human dermal fibroblasts, including two common products in Europe and USA, and an eco-friendly product. The sunscreens’ effects were also tested on Paracentrotus lividus, a marine species possibly threatened by these contaminants. We found that all tested sunscreens had similar efficacy in protecting human fibroblasts from UVA radiation. Conversely, the sunscreens’ effects on embryo-larval development of P. lividus were dependent on the product tested. In particular, the USA sunscreen, containing benzophenone-3, homosalate and preservatives, caused the strongest impact on the sea urchin development, whereas the eco-friendly sunscreen determined the weakest effects. These results suggest that although the tested products protected human skin cells from UVA-induced damage, they might severely affect the success of recruitment and survival of the sea urchin. Our findings underline the importance of developing eco-friendly sunscreens for minimising or avoiding the impact on marine life while protecting human skin from UV damage.
Evidence of robust 2D transport and Efros-Shklovskii variable range hopping in disordered topological insulator (Bi2Se3) nanowires
Authors: Bhattacharyya Biplab , Sharma Alka , Sinha Bhavesh , Shah Kunjal , Jejurikar Suhas , Senguttuvan T. D. , Husale Sudhir
Published: August 2017

We report the experimental observation of variable range hopping conduction in focused-ion-beam (FIB) fabricated ultra-narrow nanowires of topological insulator (Bi2Se3). The value of the exponent (d + 1)−1 in the hopping equation was extracted as $$ \sim \frac{1}{2}\,\,$$
~

1
2

for different widths of nanowires, which is the proof of the presence of Efros-Shklovskii hopping transport mechanism in a strongly disordered system. High localization lengths (0.5 nm, 20 nm) were calculated for the devices. A careful analysis of the temperature dependent fluctuations present in the magnetoresistance curves, using the standard Universal Conductance Fluctuation theory, indicates the presence of 2D topological surface states. Also, the surface state contribution to the conductance was found very close to one conductance quantum. We believe that our experimental findings shed light on the understanding of quantum transport in disordered topological insulator based nanostructures.
ER/K linked GPCR-G protein fusions systematically modulate second messenger response in cells
Authors: Malik Rabia U. , Dysthe Matthew , Ritt Michael , Sunahara Roger K. , Sivaramakrishnan Sivaraj
Published: August 2017

FRET and BRET approaches are well established for detecting ligand induced GPCR-G protein interactions in cells. Currently, FRET/BRET assays rely on co-expression of GPCR and G protein, and hence depend on the stoichiometry and expression levels of the donor and acceptor probes. On the other hand, GPCR-G protein fusions have been used extensively to understand the selectivity of GPCR signaling pathways. However, the signaling properties of fusion proteins are not consistent across GPCRs. In this study, we describe and characterize novel sensors based on the Systematic Protein Affinity Strength Modulation (SPASM) technique. Sensors consist of a GPCR and G protein tethered by an ER/K linker flanked by FRET probes. SPASM sensors are tested for the β2-, α1-, and α2- adrenergic receptors, and adenosine type 1 receptor (A1R), tethered to Gαs-XL, Gαi2, or Gαq subunits. Agonist stimulation of β2-AR and α2-AR increases FRET signal comparable to co-expressed FRET/BRET sensors. SPASM sensors also retain signaling through the endogenous G protein milieu. Importantly, ER/K linker length systematically tunes the GPCR-G protein interaction, with consequent modulation of second messenger signaling for cognate interactions. SPASM GPCR sensors serve the dual purpose of detecting agonist-induced changes in GPCR-G protein interactions, and linking these changes to downstream signaling.
Epicatechin oligomers longer than trimers have anti-cancer activities, but not the catechin counterparts
Authors: Takanashi Kohki , Suda Manato , Matsumoto Kiriko , Ishihara Chisato , Toda Kazuya , Kawaguchi Koichiro , Senga Shogo , Kobayashi Narumi , Ichikawa Mikihiro , Katoh Miyuki , Hattori Yasunao , Kawahara Sei-ichi , Umezawa Koji , Fujii Hiroshi , Makabe Hidefumi
Published: August 2017

Since procyanidins (oligomeric catechin or epicatechin) were reported to exhibit health benefits, much attention has been paid to the synthesis of these compounds, especially those that are longer than trimers. In the present study, syntheses of cinnamtannin A3 (epicatechin pentamer), A4 (epicatechin hexamer), catechin tetramer, pentamer, arecatannin A2 (epicatechin-epicatechin-epicatechin-catechin) and A3 (epicatechin-epicatechin-epicatechin-epicatechin-catechin) were achieved. The key reaction was a Lewis acid mediated equimolar condensation. The antitumor effects of these synthesized compounds against a human prostate cancer cell line (PC-3) were investigated. Among the tested compounds, cinnamtannin A3, A4 and arecatannin A3, which possess epicatechin oligomers longer than tetramers as the basic scaffold, showed significant activities for suppression of cell growth, invasion and FABP5 (fatty acid-binding protein 5) gene expression. Effects on cell cycle distribution showed that cell cycle arrest in the G2 phase was induced. Furthermore, these epicatechin oligomers suppressed significantly the expression of the cancer-promoting gene, FABP5, which is related to cell proliferation and metastasis in various cancer cells. Interestingly, the suppressive activities were associated with the degree of oligomerization of epicatechin. Thus, synthetic studies clearly demonstrate that epicatechin oligomers longer than trimers have significant anti-tumorigenic activities, but not the catechin counterparts.
CYP2C19*2 and CYP2C19*17 variants and effect of tamoxifen on breast cancer recurrence: Analysis of the International Tamoxifen Pharmacogenomics Consortium dataset
Authors: Damkier Per , Kjærsgaard Anders , Barker Kimberly A. , Cronin-Fenton Deidre , Crawford Anatasha , Hellberg Ylva , Janssen Emilius A. M. , Langefeld Carl , Ahern Thomas P. , Lash Timothy L.
Published: August 2017

The role of cytochrome P450 drug metabolizing enzymes in the efficacy of tamoxifen treatment of breast cancer is subject to substantial interest and controversy. CYP2D6 have been intensively studied, but the role of CYP2C19 is less elucidated, and we studied the association of CYPC19 genotype and recurrence of breast cancer. We used outcome and genotyping data from the large publicly available International Tamoxifen Pharmacogenomics Consortium (ITPC) dataset. Cox regression was used to compute the hazard ratios (HRs) for recurrence. CYP2C19 genotype data was available for 2 423 patients and the final sample cohort comprised 2 102 patients. CYP2C19*2 or *19 alleles did not influence DFS. For the CYP2C19*2 allele, the HR was 1.05 (CI 0.78–1.42) and 0.79 (CI 0.32–1.94) for hetero- and homozygote carriers, respectively. The corresponding HR for hetero- and homozygote carriers of the CYP2C19*17 allele were 1.02 (CI 0.71–1.46) and 0.57 (CI 0.26–1.24), respectively. Accounting for CYP2D6 genotype status did not change these estimates. We found no evidence to support a clinically meaningful role of CYP2C19 polymorphisms and response to tamoxifen in breast cancer patients and, consequently, CYP2C19 genotype status should not be included in clinical decisions on tamoxifen treatment.
Assessing cell-nanoparticle interactions by high content imaging of biocompatible iron oxide nanoparticles as potential contrast agents for magnetic resonance imaging
Authors: Hachani Roxanne , Birchall Martin A. , Lowdell Mark W. , Kasparis Georgios , Tung Le D. , Manshian Bella B. , Soenen Stefaan J. , Gsell Willy , Himmelreich Uwe , Gharagouzloo Codi A. , Sridhar Srinivas , Thanh Nguyen T. K.
Published: August 2017

Stem cell tracking in cellular therapy and regenerative medicine is an urgent need, superparamagnetic iron oxide nanoparticles (IONPs) could be used as contrast agents in magnetic resonance imaging (MRI) that allows visualization of the implanted cells ensuring they reach the desired sites in vivo. Herein, we report the study of the interaction of 3,4-dihydroxyhydrocinnamic acid (DHCA) functionalized IONPs that have desirable properties for T2 - weighted MRI, with bone marrow-derived primary human mesenchymal stem cells (hMSCs). Using the multiparametric high-content imaging method, we evaluate cell viability, formation of reactive oxygen species, mitochondrial health, as well as cell morphology and determine that the hMSCs are minimally affected after labelling with IONPs. Their cellular uptake is visualized by transmission electron microscopy (TEM) and Prussian Blue staining, and quantified using an iron specific colourimetric method. In vitro and in vivo studies demonstrate that these IONPs are biocompatible and can produce significant contrast enhancement in T2-weighted MRI. Iron oxide nanoparticles are detected in vivo as hypointense regions in the liver up to two weeks post injection using 9.4 T MRI. These DHCA functionalized IONPs are promising contrast agents for stem cell tracking by T2-weighted MRI as they are biocompatible and show no evidence of cytotoxic effects on hMSCs.
Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs
Authors: Garcia-Elias Anna , Alloza Leonor , Puigdecanet Eulàlia , Nonell Lara , Tajes Marta , Curado Joao , Enjuanes Cristina , Díaz Oscar , Bruguera Jordi , Martí-Almor Julio , Comín-Colet Josep , Benito Begoña
Published: August 2017

MicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq). Our results indicate that the Infinite® 200 PRO Nanoquant and Nanodrop 2000 spectrophotometers magnified the miRNA concentration by detecting contaminants, proteins, and other forms of RNA. The Agilent 2100 Bioanalyzer PicoChip and SmallChip gave valuable information on RNA profile but were not a reliable quantification method for plasma samples. The Qubit® 2.0 Fluorometer provided the most accurate quantification of miRNA content, although RNA-seq confirmed that only ~58% of small RNAs in plasma are true miRNAs. On the other hand, reducing the starting RNA to 70% of the recommended amount for miRNA profiling with arrays yielded results comparable to those obtained with the full amount, whereas a 50% reduction did not. These findings provide important clues for miRNA determination in human plasma samples.
Isoflurane produces antidepressant effects and induces TrkB signaling in rodents
Authors: Antila Hanna , Ryazantseva Maria , Popova Dina , Sipilä Pia , Guirado Ramon , Kohtala Samuel , Yalcin Ipek , Lindholm Jesse , Vesa Liisa , Sato Vinicius , Cordeira Joshua , Autio Henri , Kislin Mikhail , Rios Maribel , Joca Sâmia , Casarotto Plinio , Khiroug Leonard , Lauri Sari , Taira Tomi , Castrén Eero , Rantamäki Tomi
Published: August 2017

A brief burst-suppressing isoflurane anesthesia has been shown to rapidly alleviate symptoms of depression in a subset of patients, but the neurobiological basis of these observations remains obscure. We show that a single isoflurane anesthesia produces antidepressant-like behavioural effects in the learned helplessness paradigm and regulates molecular events implicated in the mechanism of action of rapid-acting antidepressant ketamine: activation of brain-derived neurotrophic factor (BDNF) receptor TrkB, facilitation of mammalian target of rapamycin (mTOR) signaling pathway and inhibition of glycogen synthase kinase 3β (GSK3β). Moreover, isoflurane affected neuronal plasticity by facilitating long-term potentiation in the hippocampus. We also found that isoflurane increased activity of the parvalbumin interneurons, and facilitated GABAergic transmission in wild type mice but not in transgenic mice with reduced TrkB expression in parvalbumin interneurons. Our findings strengthen the role of TrkB signaling in the antidepressant responses and encourage further evaluation of isoflurane as a rapid-acting antidepressant devoid of the psychotomimetic effects and abuse potential of ketamine.
2D surface optical lattice formed by plasmon polaritons with application to nanometer-scale molecular deposition
Authors: Yin Yanning , Xu Supeng , Li Tao , Yin Yaling , Xia Yong , Yin Jianping
Published: August 2017

Surface plasmon polaritons, due to their tight spatial confinement and high local intensity, hold great promises in nanofabrication which is beyond the diffraction limit of conventional lithography. Here, we demonstrate theoretically the 2D surface optical lattices based on the surface plasmon polariton interference field, and the potential application to nanometer-scale molecular deposition. We present the different topologies of lattices generated by simple configurations on the substrate. By explicit theoretical derivations, we explain their formation and characteristics including field distribution, periodicity and phase dependence. We conclude that the topologies can not only possess a high stability, but also be dynamically manipulated via changing the polarization of the excitation laser. Nanometer-scale molecular deposition is simulated with these 2D lattices and discussed for improving the deposition resolution. The periodic lattice point with a width resolution of 33.2 nm can be obtained when the fullerene molecular beam is well-collimated. Our study can offer a superior alternative method to fabricate the spatially complicated 2D nanostructures, with the deposition array pitch serving as a reference standard for accurate and traceable metrology of the SI length standard.
Responses of crop yield growth to global temperature and socioeconomic changes
Authors: Iizumi Toshichika , Furuya Jun , Shen Zhihong , Kim Wonsik , Okada Masashi , Fujimori Shinichiro , Hasegawa Tomoko , Nishimori Motoki
Published: August 2017

Although biophysical yield responses to local warming have been studied, we know little about how crop yield growth—a function of climate and technology—responds to global temperature and socioeconomic changes. Here, we present the yield growth of major crops under warming conditions from preindustrial levels as simulated by a global gridded crop model. The results revealed that global mean yields of maize and soybean will stagnate with warming even when agronomic adjustments are considered. This trend is consistent across socioeconomic assumptions. Low-income countries located at low latitudes will benefit from intensive mitigation and from associated limited warming trends (1.8 °C), thus preventing maize, soybean and wheat yield stagnation. Rice yields in these countries can improve under more aggressive warming trends. The yield growth of maize and soybean crops in high-income countries located at mid and high latitudes will stagnate, whereas that of rice and wheat will not. Our findings underpin the importance of ambitious climate mitigation targets for sustaining yield growth worldwide.
Understanding the molecular basis of agonist/antagonist mechanism of human mu opioid receptor through gaussian accelerated molecular dynamics method
Authors: Wang Yeng-Tseng , Chan Yang-Hsiang
Published: August 2017

The most powerful analgesic and addictive properties of opiate alkaloids are mediated by the μ opioid receptor (MOR). The MOR has been extensively investigated as a drug target in the twentieth century, with numerous compounds of varying efficacy being identified. We employed molecular dynamics and Gaussian accelerated molecular dynamics techniques to identify the binding mechanisms of MORs to BU72 (agonist) and β-funaltrexamine (antagonist). Our approach theoretically suggests that the 34 residues (Lys209–Phe221 and Ile301–Cys321) of the MORs were the key regions enabling the two compounds to bind to the active site of the MORs. When the MORs were in the holo form, the key region was in the open conformation. When the MORs were in the apo form, the key region was in the closed conformation. The key region might be responsible for the selectivity of new MOR agonists and antagonists.
Constructing ordinal partition transition networks from multivariate time series
Authors: Zhang Jiayang , Zhou Jie , Tang Ming , Guo Heng , Small Michael , Zou Yong
Published: August 2017

A growing number of algorithms have been proposed to map a scalar time series into ordinal partition transition networks. However, most observable phenomena in the empirical sciences are of a multivariate nature. We construct ordinal partition transition networks for multivariate time series. This approach yields weighted directed networks representing the pattern transition properties of time series in velocity space, which hence provides dynamic insights of the underling system. Furthermore, we propose a measure of entropy to characterize ordinal partition transition dynamics, which is sensitive to capturing the possible local geometric changes of phase space trajectories. We demonstrate the applicability of pattern transition networks to capture phase coherence to non-coherence transitions, and to characterize paths to phase synchronizations. Therefore, we conclude that the ordinal partition transition network approach provides complementary insight to the traditional symbolic analysis of nonlinear multivariate time series.
Measurement of caveolin-1 densities in the cell membrane for quantification of caveolar deformation after exposure to hypotonic membrane tension
Authors: Tachikawa Masashi , Morone Nobuhiro , Senju Yosuke , Sugiura Tadao , Hanawa-Suetsugu Kyoko , Mochizuki Atsushi , Suetsugu Shiro
Published: August 2017

Caveolae are abundant flask-shaped invaginations of plasma membranes that buffer membrane tension through their deformation. Few quantitative studies on the deformation of caveolae have been reported. Each caveola contains approximately 150 caveolin-1 proteins. In this study, we estimated the extent of caveolar deformation by measuring the density of caveolin-1 projected onto a two-dimensional (2D) plane. The caveolin-1 in a flattened caveola is assumed to have approximately one-quarter of the density of the caveolin-1 in a flask-shaped caveola. The proportion of one-quarter-density caveolin-1 increased after increasing the tension of the plasma membrane through hypo-osmotic treatment. The one-quarter-density caveolin-1 was soluble in detergent and formed a continuous population with the caveolin-1 in the caveolae of cells under isotonic culture. The distinct, dispersed lower-density caveolin-1 was soluble in detergent and increased after the application of tension, suggesting that the hypo-osmotic tension induced the dispersion of caveolin-1 from the caveolae, possibly through flattened caveolar intermediates.
Comparison of Pathogenicity-Related Genes in the Current Pseudorabies Virus Outbreak in China
Authors: Tang Yan-Dong , Liu Ji-Ting , Wang Tong-Yun , Sun Ming-Xia , Tian Zhi-Jun , Cai Xue-Hui
Published: August 2017

There is currently a pandemic of pseudorabies virus (PRV) variant strains in China. Despite extensive research on PRV variant strains in the past two years, few studies have investigated PRV pathogenicity-related genes. To determine which gene(s) is/are linked to PRV virulence, ten putative virulence genes were knocked out using clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 technology. The pathogenicity of these mutants was evaluated in a mouse model. Our results demonstrated that of the ten tested genes, the thymidine kinase (TK) and glycoprotein M (gM) knockout mutants displayed significantly reduced virulence. However, mutants of other putative virulence genes, such as glycoprotein E (gE), glycoprotein I (gI), Us2, Us9, Us3, glycoprotein G (gG), glycoprotein N (gN) and early protein 0 (EP0), did not exhibit significantly reduced virulence compared to that of the wild-type PRV. To our knowledge, this study is the first to compare virulence genes from the current pandemic PRV variant strain. This study will provide a valuable reference for scientists to design effective live attenuated vaccines in the future.
NEDD4-family E3 ligase dysfunction due to PKHD1/Pkhd1 defects suggests a mechanistic model for ARPKD pathobiology
Authors: Kaimori Jun-ya , Lin Cheng-Chao , Outeda Patricia , Garcia-Gonzalez Miguel A. , Menezes Luis F. , Hartung Erum A. , Li Ao , Wu Guanqing , Fujita Hideaki , Sato Yasunori , Nakanuma Yasuni , Yamamoto Satoko , Ichimaru Naotsugu , Takahara Shiro , Isaka Yoshitaka , Watnick Terry , Onuchic Luiz F. , Guay-Woodford Lisa M. , Germino Gregory G.
Published: August 2017

Autosomal recessive polycystic kidney disease (ARPKD) is an important childhood nephropathy, occurring 1 in 20,000 live births. The major clinical phenotypes are expressed in the kidney with dilatation of the collecting ducts, systemic hypertension, and progressive renal insufficiency, and in the liver with biliary dysgenesis, portal tract fibrosis, and portal hypertension. The systemic hypertension has been attributed to enhanced distal sodium reabsorption in the kidney, the structural defects have been ascribed to altered cellular morphology, and fibrosis to increased TGF-β signaling in the kidney and biliary tract, respectively. The pathogenic mechanisms underlying these abnormalities have not been determined. In the current report, we find that disrupting PKHD1 results in altered sub-cellular localization and function of the C2-WWW-HECT domain E3 family of ligases regulating these processes. We also demonstrate altered activity of RhoA and increased TGF-β signaling and ENaC activity. Linking these phenomena, we found that vesicles containing the PKHD1/Pkhd1 gene product, FPC, also contain the NEDD4 ubiquitin ligase interacting protein, NDFIP2, which interacts with multiple members of the C2-WWW-HECT domain E3 family of ligases. Our results provide a mechanistic explanation for both the cellular effects and in vivo phenotypic abnormalities in mice and humans that result from Pkhd1/PKHD1 mutation.
A novel signature for stratifying the molecular heterogeneity of the tissue-infiltrating T-cell receptor repertoire reflects gastric cancer prognosis
Authors: Kuang Manchao , Cheng Jieyao , Zhang Chengli , Feng Lin , Xu Xue , Zhang Yajing , Zu Ming , Cui Jianfang , Yu Hang , Zhang Kaitai , Yang Aiming , Cheng Shujun
Published: August 2017

Many basic properties of the T-cell receptor (TCR) repertoire require clarification, and the changes occurring in the TCR repertoire during carcinogenesis, especially during precancerous stages, remain unclear. This study used deep sequencing analyses to examine 41 gastric tissue samples at different pathological stages, including low-grade intraepithelial neoplasia, high-grade intraepithelial neoplasia, early gastric cancer and matched adjacent tissues, to define the characteristics of the infiltrating TCRβ repertoire during gastric carcinogenesis. Moreover, to illustrate the relationship between the local molecular phenotype and TCR repertoire of the microenvironment, whole-genome gene expression microarray analysis of the corresponding gastric precancerous lesions and early gastric cancer tissues was conducted. Our results showed that the degree of variation in the TCR repertoire gradually increased during tumourigenesis. Integrative analysis of microarray data and the TCR repertoire variation index using the network-based Clique Percolation Method identified an 11-gene module related to the inflammatory response that can predict the overall survival of gastric cancer (GC) patients. In conclusion, our results revealed the multistage heterogeneity of tissue-infiltrating TCR repertoire during carcinogenesis. We report a novel way for identifying prognostic biomarkers for GC patients and improves our understanding of immune responses during gastric carcinogenesis.
Triglycerides and Open Angle Glaucoma – A Meta-analysis with meta-regression
Authors: Pertl Laura , Mossböck Georg , Wedrich Andreas , Weger Martin , Königsbrügge Oliver , Silbernagel Günther , Posch Florian
Published: August 2017

Although intraocular pressure is the main the risk factor for the development of glaucoma, other risk factors such as vascular dysfunction might play an additional pathogenic role. Hypertriglyceridemia, which may lead to vascular dysfunction, has been implicated in the development of glaucoma. The objective of this meta-analysis was to investigate the association of triglyceride levels with the risk of glaucoma in case-control studies. Seventeen case-control studies were included investigating the difference in triglyceride levels in patients with glaucoma (N = 1 391) compared to subjects without glaucoma (N = 25 575). In random effects meta-analysis, the pooled mean triglyceride level across all studies and patients with and without glaucoma was 132.9 mg/dL (95%CI: 124.0–141.7). Patients with glaucoma had significantly higher mean triglyceride levels than patients without glaucoma (absolute difference = 14.2 mg/dL, 95%CI: 5.8–22.5, p < 0.0001). A considerable amount of heterogeneity of included studies was observed (I2 = 66.2%, heterogeneity χ2 = 47.4 on 16 degrees of freedom, p < 0.0001). In conclusion, this meta-analysis of case-control studies found that patients with glaucoma had higher mean triglyceride levels than patients without glaucoma. This finding is consistent with the concept that hypertriglyceridemia represents an additional risk factor for glaucoma. Whether this association is causal and/or might be modified by glaucoma medications remains to be investigated.
Magnesium Chloride promotes Osteogenesis through Notch signaling activation and expansion of Mesenchymal Stem Cells
Authors: Díaz-Tocados Juan M. , Herencia Carmen , Martínez-Moreno Julio M. , Montes de Oca Addy , Rodríguez-Ortiz Maria E. , Vergara Noemi , Blanco Alfonso , Steppan Sonja , Almadén Yolanda , Rodríguez Mariano , Muñoz-Castañeda Juan R.
Published: August 2017

Mesenchymal stem cells (MSC) are osteoblasts progenitors and a variety of studies suggest that they may play an important role for the health in the field of bone regeneration. Magnesium supplementation is gaining importance as adjuvant treatment to improve osteogenesis, although the mechanisms involving this process are not well understood. The objective of this study was to investigate the effects of magnesium on MSC differentiation. Here we show that in rat bone marrow MSC, magnesium chloride increases MSC proliferation in a dose-dependent manner promoting osteogenic differentiation and mineralization. These effects are reduced by 2-APB administration, an inhibitor of magnesium channel TRPM7. Of note, magnesium supplementation did not increase the canonical Wnt/β-catenin pathway, although it promoted the activation of Notch1 signaling, which was also decreased by addition of 2-APB. Electron microscopy showed higher proliferation, organization and maturation of osteoblasts in bone decellularized scaffolds after magnesium addition. In summary, our results demonstrate that magnesium chloride enhances MSC proliferation by Notch1 signaling activation and induces osteogenic differentiation, shedding light on the understanding of the role of magnesium during bone regeneration.
Sexual conflict and the evolution of genitalia: male damselflies remove more sperm when mating with a heterospecific female
Authors: Cordero-Rivera Adolfo
Published: August 2017

In Calopteryx damselflies, males remove rivals’ sperm stored by the female, thereby reducing sperm competition. This behaviour may create a sexual conflict, because females could lose the sperm stored in the spermatheca, used for long-term storage. Comparative evidence suggested antagonistic coevolution between sexes, which might prompt the evolution of narrow spermathecal ducts, or longer spermathecae, hindering sperm removal. Calopteryx haemorrhoidalis and C. splendens coexist and sometimes hybridize. Therefore, here I predicted that if females coevolve with conspecific males, heterospecific males should have an advantage when interspecific matings occur because females will show less resistance to them than to conspecific males. By hand-pairing females to males of both species, I found that in intraspecific and interspecific matings, sperm was almost completely removed from the bursa (97–100%), but only partially from the spermathecae, with more spermathecal removal in interspecific (63–71%) than intraspecific matings (14–33%). This suggests that heterospecific males are more efficient in sperm removal as predicted by a sexually-antagonistic coevolutionary scenario. Furthermore, in most cases, only the left spermatheca was emptied, suggesting that the evolution of more than one spermatheca might also be a female counter-adaptation to regain control over fertilization.