bluuebunny/crossref_metadata_2025 huggingface dataset:
Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen
Authors: Kwak Won-Jin , Kim Hun , Petit Yann K. , Leypold Christian , Nguyen Trung Thien , Mahne Nika , Redfern Paul , Curtiss Larry A. , Jung Hun-Gi , Borisov Sergey M. , Freunberger Stefan A. , Sun Yang-Kook
Published: March 2019

Non-aqueous lithium-oxygen batteries cycle by forming lithium peroxide during discharge and oxidizing it during recharge. The significant problem of oxidizing the solid insulating lithium peroxide can greatly be facilitated by incorporating redox mediators that shuttle electron-holes between the porous substrate and lithium peroxide. Redox mediator stability is thus key for energy efficiency, reversibility, and cycle life. However, the gradual deactivation of redox mediators during repeated cycling has not conclusively been explained. Here, we show that organic redox mediators are predominantly decomposed by singlet oxygen that forms during cycling. Their reaction with superoxide, previously assumed to mainly trigger their degradation, peroxide, and dioxygen, is orders of magnitude slower in comparison. The reduced form of the mediator is markedly more reactive towards singlet oxygen than the oxidized form, from which we derive reaction mechanisms supported by density functional theory calculations. Redox mediators must thus be designed for stability against singlet oxygen.
Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
Authors: Matheus Carnevali Paula B. , Schulz Frederik , Castelle Cindy J. , Kantor Rose S. , Shih Patrick M. , Sharon Itai , Santini Joanne M. , Olm Matthew R. , Amano Yuki , Thomas Brian C. , Anantharaman Karthik , Burstein David , Becraft Eric D. , Stepanauskas Ramunas , Woyke Tanja , Banfield Jillian F.
Published: March 2019

The original version of this Article contained errors in Fig. 4. In panel a, the labels ‘F420-reducing NiFe hydrogenase (group 3a)’ and ‘Group 2 NiFe hydrogenase’ were misplaced. These errors have been corrected in both the PDF and HTML versions of the Article.
Author Correction: Loss of BCL9/9l suppresses Wnt driven tumourigenesis in models that recapitulate human cancer
Authors: Gay David M. , Ridgway Rachel A. , Müller Miryam , Hodder Michael C. , Hedley Ann , Clark William , Leach Joshua D. , Jackstadt Rene , Nixon Colin , Huels David J. , Campbell Andrew D. , Bird Thomas G. , Sansom Owen J.
Published: March 2019

The original version of this Article contained an error in the spelling of the author Miryam Müller, which was incorrectly given as Miryam Müeller. This has now been corrected in both the PDF and HTML versions of the Article.
Characterization of putative DD-carboxypeptidase-encoding genes in Mycobacterium smegmatis
Authors: Ealand Christopher S. , Asmal Rukaya , Mashigo Lethabo , Campbell Lisa , Kana Bavesh D.
Published: March 2019

Penicillin binding proteins (PBPs) are the target of numerous antimicrobial agents that disrupt bacterial cell wall synthesis. In mycobacteria, cell elongation occurs through insertion of nascent cell wall material in the sub-polar region, a process largely driven by High Molecular Weight PBPs. In contrast, the function of DD-carboxypeptidases (DD-CPases), which are Low Molecular Weight Class 1C PBPs, in mycobacteria remains poorly understood. Mycobacterium smegmatis encodes four putative DD-CPase homologues, which display homology to counterparts in Escherichia coli. Herein, we demonstrate that these are expressed in varying abundance during growth. Deletion of MSMEG_1661, MSMEG_2433 or MSMEG_2432, individually resulted in no defects in growth, cell morphology, drug susceptibility or spatial incorporation of new peptidoglycan. In contrast, deletion of MSMEG_6113 (dacB) was only possible in a merodiploid strain expressing the homologous M. tuberculosis operon encoding Rv3627c (dacB), Rv3626c, Rv3625c (mesJ) and Rv3624c (hpt), suggestive of essentiality. To investigate the role of this operon in mycobacterial growth, we depleted gene expression using anhydrotetracycline-responsive repressors and noted reduced bipolar peptidoglycan synthesis. These data point to a possible role for this four gene operon, which is highly conserved across all mycobacterial species, in regulating spatial localization of peptidoglycan synthesis.
Utilizing general human movement models to predict the spread of emerging infectious diseases in resource poor settings
Authors: Kraemer M. U. G. , Golding N. , Bisanzio D. , Bhatt S. , Pigott D. M. , Ray S. E. , Brady O. J. , Brownstein J. S. , Faria N. R. , Cummings D. A. T. , Pybus O. G. , Smith D. L. , Tatem A. J. , Hay S. I. , Reiner R. C.
Published: March 2019

Human mobility is an important driver of geographic spread of infectious pathogens. Detailed information about human movements during outbreaks are, however, difficult to obtain and may not be available during future epidemics. The Ebola virus disease (EVD) outbreak in West Africa between 2014–16 demonstrated how quickly pathogens can spread to large urban centers following one cross-species transmission event. Here we describe a flexible transmission model to test the utility of generalised human movement models in estimating EVD cases and spatial spread over the course of the outbreak. A transmission model that includes a general model of human mobility significantly improves prediction of EVD’s incidence compared to models without this component. Human movement plays an important role not only to ignite the epidemic in locations previously disease free, but over the course of the entire epidemic. We also demonstrate important differences between countries in population mixing and the improved prediction attributable to movement metrics. Given their relative rareness, locally derived mobility data are unlikely to exist in advance of future epidemics or pandemics. Our findings show that transmission patterns derived from general human movement models can improve forecasts of spatio-temporal transmission patterns in places where local mobility data is unavailable.
Keggin-type polyoxotungstates as mushroom tyrosinase inhibitors - A speciation study
Authors: Breibeck Joscha , Gumerova Nadiia I. , Boesen Benedikt B. , Galanski Mathea Sophia , Rompel Annette
Published: March 2019

Mushroom tyrosinase abPPO4 is a commercially relevant polyphenol oxidase and has been being targeted for numerous inhibition studies including polyoxometalates (POMs). In the present work, its diphenolase activity was inhibited at pH 6.8 by a series of structurally related polyoxotungstates (POTs) of the α-Keggin archetype, exhibiting the general formula [Xn+W12O40](8−n)− in order to elucidate charge-dependent activity correlations. Kinetic data were obtained from the dopachrome assay and 183W NMR was applied to obtain crucial insights into the actual Keggin POT speciation in solution, facilitating a straightforward assignment of inhibition effects to the identified POT species. While [PW12O40]3− was completely hydrolyzed to its moderately active lacunary form Hx[PW11O39](7−x)− (Ki = 25.6 mM), [SiW12O40]4− showed the most pronounced inhibition effects with a Ki of 4.7 mM despite of partial hydrolysis to its ineffective lacunary form Hx[SiW11O39](8−x)−. More negative Keggin cluster charges of 5− and 6− generally resulted in preclusion of inhibitory efficacy as well as hydrolysis, but with the Ni-substituted cluster [PW11O39{Ni(H2O)}]5− enzymatic inhibition was clearly restored (Ki = 9.7 mM). The inhibitory capacity of the structurally intact Keggin POTs was found to be inversely correlated to their net charge. The here applied speciation strategy is of utmost importance for any biological POM application to identify the actually active POM species.
Reverse-Correlation Analysis of the Mechanosensation Circuit and Behavior in C. elegans Reveals Temporal and Spatial Encoding
Authors: Porto Daniel A. , Giblin John , Zhao Yiran , Lu Hang
Published: March 2019

Animals must integrate the activity of multiple mechanoreceptors to navigate complex environments. In Caenorhabditis elegans, the general roles of the mechanosensory neurons have been defined, but most studies involve end-point or single-time-point measurements, and thus lack dynamic information. Here, we formulate a set of unbiased quantitative characterizations of the mechanosensory system by using reverse correlation analysis on behavior. We use a custom tracking, selective illumination, and optogenetics platform to compare two mechanosensory systems: the gentle-touch (TRNs) and harsh-touch (PVD) circuits. This method yields characteristic linear filters that allow for the prediction of behavioral responses. The resulting filters are consistent with previous findings and further provide new insights on the dynamics and spatial encoding of the systems. Our results suggest that the tiled network of the gentle-touch neurons has better resolution for spatial encoding than the harsh-touch neurons. Additionally, linear-nonlinear models can predict behavioral responses based only on sensory neuron activity. Our results capture the overall dynamics of behavior induced by the activation of sensory neurons, providing simple transformations that quantitatively characterize these systems. Furthermore, this platform can be extended to capture the behavioral dynamics induced by any neuron or other excitable cells in the animal.
Differential Diffusion of Helium Isotopes in Glass, Quantum-tunneling 3He Enrichment, and Portable 3He/4He Monitoring of Mantle Processes
Authors: McMurtry Gary M. , DeLuze James R. , Hilton David R. , Blessing James E.
Published: March 2019

While studying the scientific and engineering aspects of a field-portable 3He/4He ratio detector, we found elevated ratios at comparatively lower temperatures that appear to result from differential diffusion of these isotopes in pure quartz glass. The 3He enrichment relative to 4He in lab air, expressed as the ratio R and normalized to the accepted 3He/4He ratio of 1.40 E-06 (Ra), ranges from peak values of about 200 to 600 in dry static samples. Even at the maximum classical 3He/4He diffusivity ratio of 1.15, the expected R would be only 1.61 E-06. Within a narrow temperature window, the air value in our experimental set up with pure quartz glass can range from about 2.70 to 8.20 E-04, or nearly 1000 times the expected enrichment based upon classical fractionation. When plotted versus temperature, the narrow 3He net partial pressure peak reveals at least three sharper embedded peaks that may be quantized vibrational entrance states in quartz glass which are temperature specific. This discovery has implications for relatively low-energy industrial enrichment of scarce 3He from natural sources on Earth, and for radiogenic and cosmogenic helium dating assumptions in natural glasses. It also has bearing upon designs for field portable 3He/4He ratio detectors aimed at earthquake and volcanic eruption studies, and monitoring of nuclear sites.
The M1 muscarinic acetylcholine receptor subtype is important for retinal neuron survival in aging mice
Authors: Laspas Panagiotis , Zhutdieva Mayagozel B. , Brochhausen Christoph , Musayeva Aytan , Zadeh Jenia Kouchek , Pfeiffer Norbert , Xia Ning , Li Huige , Wess Juergen , Gericke Adrian
Published: March 2019

Muscarinic acetylcholine receptors have been implicated as potential neuroprotective targets for glaucoma. We tested the hypothesis that the lack of a single muscarinic receptor subtype leads to age-dependent neuron reduction in the retinal ganglion cell layer. Mice with targeted disruption of single muscarinic acetylcholine receptor subtype genes (M1 to M5) and wild-type controls were examined at two age categories, 5 and 15 months, respectively. We found no differences in intraocular pressure between individual mouse groups. Remarkably, in 15-month-old mice devoid of the M1 receptor, neuron number in the retinal ganglion cell layer and axon number in the optic nerve were markedly reduced. Moreover, mRNA expression for the prooxidative enzyme, NOX2, was increased, while mRNA expression for the antioxidative enzymes, SOD1, GPx1 and HO-1, was reduced in aged M1 receptor-deficient mice compared to age-matched wild-type mice. In line with these findings, the reactive oxygen species level was also elevated in the retinal ganglion cell layer of aged M1 receptor-deficient mice. In conclusion, M1 receptor deficiency results in retinal ganglion cell loss in aged mice via involvement of oxidative stress. Based on these findings, activation of M1 receptor signaling may become therapeutically useful to promote retinal ganglion cell survival.
Simulation and design of folded perovskite x-ray detectors
Authors: Mescher Henning , Hamann Elias , Lemmer Uli
Published: March 2019

A variety of medical, industrial, and scientific applications requires highly sensitive and cost-effective x-ray detectors for photon energies ranging from keV to MeV. Adapting the thickness of polycrystalline or single crystal conversion layers especially to high-energy applications increases the complexity of fabrication and potentially decreases the performance of conventional direct conversion x-ray detectors. To tackle the challenges with respect to the active layer thickness and to combine the superior performance of single crystal materials with the low-cost nature of polycrystalline conversion layers, we investigate thin film x-ray detector technologies based on a folded device architecture. Analytical models simulating the sensitivity and the detective quantum efficiency (DQE) are used to evaluate the performance of folded detectors based on polycrystalline organic-inorganic perovskite semiconductors in various layout configurations and for different photon energies. Simulations of folded perovskite devices show high sensitivities. The DQE analysis introduces additional noise related boundary conditions for the folding length. A comparison with conventional detectors based on state of the art conversion materials at different photon energies demonstrates the potential of the folded detector layout as simulated sensitivities are comparable to single crystal detectors.
Nanoscale structure of amyloid-β plaques in Alzheimer’s disease
Authors: Querol-Vilaseca Marta , Colom-Cadena Martí , Pegueroles Jordi , Nuñez-Llaves Raúl , Luque-Cabecerans Joan , Muñoz-Llahuna Laia , Andilla Jordi , Belbin Olivia , Spires-Jones Tara L. , Gelpi Ellen , Clarimon Jordi , Loza-Alvarez Pablo , Fortea Juan , Lleó Alberto
Published: March 2019

Soluble amyloid-β (Aβ) is considered to be a critical component in the pathogenesis of Alzheimer’s disease (AD). Evidence suggests that these non-fibrillar Aβ assemblies are implicated in synaptic dysfunction, neurodegeneration and cell death. However, characterization of these species comes mainly from studies in cellular or animal models, and there is little data in intact human samples due to the lack of adequate optical microscopic resolution to study these small structures. Here, to achieve super-resolution in all three dimensions, we applied Array Tomography (AT) and Stimulated Emission Depletion microscopy (STED), to characterize in postmortem human brain tissue non-fibrillar Aβ structures in amyloid plaques of cases with autosomal dominant and sporadic AD. Ultrathin sections scanned with super-resolution STED microscopy allowed the detection of small Aβ structures of the order of 100 nm. We reconstructed a whole human amyloid plaque and established that plaques are formed by a dense core of higher order Aβ species (~0.022 µm3) and a peripheral halo of smaller Aβ structures (~0.003 µm3). This work highlights the potential of AT-STED for human neuropathological studies.
Calcitonin native prefibrillar oligomers but not monomers induce membrane damage that triggers NMDA-mediated Ca2+-influx, LTP impairment and neurotoxicity
Authors: Belfiore Marcello , Cariati Ida , Matteucci Andrea , Gaddini Lucia , Macchia Gianfranco , Fioravanti Raoul , Frank Claudio , Tancredi Virginia , D’Arcangelo Giovanna , Diociaiuti Marco
Published: March 2019

Amyloid protein misfolding results in a self-assembling aggregation process, characterized by the formation of typical aggregates. The attention is focused on pre-fibrillar oligomers (PFOs), formed in the early stages and supposed to be neurotoxic. PFOs structure may change due to their instability and different experimental protocols. Consequently, it is difficult to ascertain which aggregation species are actually neurotoxic. We used salmon Calcitonin (sCT) as an amyloid model whose slow aggregation rate allowed to prepare stable samples without photochemical cross-linking. Intracellular Ca2+ rise plays a fundamental role in amyloid protein-induced neurodegerations. Two paradigms have been explored: (i) the “membrane permeabilization” due to the formation of amyloid pores or other types of membrane damage; (ii) “receptor-mediated” modulation of Ca2+ channels. In the present paper, we tested the effects of native sCT PFOs- with respect to Monomer-enriched solutions in neurons characterized by an increasing degree of differentiation, in terms of -Ca2+-influx, cellular viability, -Long-Term Potentiation impairment, Post-Synaptic Densities and synaptophysin expression. Results indicated that PFOs-, but not Monomer-enriched solutions, induced abnormal -Ca2+-influx, which could only in part be ascribed to NMDAR activation. Thus, we propose an innovative neurotoxicity mechanism for amyloid proteins where “membrane permeabilization” and “receptor-mediated” paradigms coexist.
Bromeliaceae subfamilies show divergent trends of genome size evolution
Authors: Müller Lilian-Lee B. , Zotz Gerhard , Albach Dirk C.
Published: March 2019

Genome size is known to vary widely across plants. Yet, the evolutionary drivers and consequences of genome size variation across organisms are far from understood. We investigated genome size variation and evolution in two major subfamilies of the Neotropical family Bromeliaceae by determining new genome size values for 83 species, testing phylogenetic signal in genome size variation, and assessing the fit to different evolutionary models. For a subset of epiphytic bromeliad species, we also evaluated the relationship of genome size with thermal traits and relative growth rate (RGR), respectively. Genome size variation in Bromelioideae appears to be evolutionary conserved, while genome size among Tillandsioideae varies considerably, not just due to polyploidy but arguably also due to environmental factors. The subfamilies show fundamental differences in genome size and RGR: Bromelioideae have, on average, lower genome sizes than Tillandsioideae and at the same time exhibit higher RGR. We attribute this to different resource use strategies in the subfamilies. Analyses among subfamilies, however, revealed unexpected positive relationships between RGR and genome size, which might be explained by the nutrient regime during cultivation. Future research should test whether there is indeed a trade-off between genome size and growth efficiency as a function of nutrient supply.
Friction factor for turbulent open channel flow covered by vegetation
Authors: Wang Wei-Jie , Peng Wen-Qi , Huai Wen-Xin , Katul Gabriel G. , Liu Xiao-Bo , Qu Xiao-Dong , Dong Fei
Published: March 2019

The need for operational models describing the friction factor f in streams remains undisputed given its utility across a plethora of hydrological and hydraulic applications concerned with shallow inertial flows. For small-scale roughness elements uniformly covering the wetted parameter of a wide channel, the Darcy-Weisbach f = 8(u*/Ub)2 is widely used at very high Reynolds numbers, where u* is friction velocity related to the surface kinematic stress, Ub = Q/A is bulk velocity, Q is flow rate, and A is cross-sectional area orthogonal to the flow direction. In natural streams, the presence of vegetation introduces additional complications to quantifying f, the subject of the present work. Turbulent flow through vegetation are characterized by a number of coherent vortical structures: (i) von Karman vortex streets in the lower layers of vegetated canopies, (ii) Kelvin-Helmholtz as well as attached eddies near the vegetation top, and (iii) attached eddies well above the vegetated layer. These vortical structures govern the canonical mixing lengths for momentum transfer and their influence on f is to be derived. The main novelty is that the friction factor of vegetated flow can be expressed as fv = 4Cd(Uv/Ub)2 where Uv is the spatially averaged velocity within the canopy volume, and Cd is a local drag coefficient per unit frontal area derived to include the aforemontioned layer-wise effects of vortical structures within and above the canopy along with key vegetation properties. The proposed expression is compared with a number of empirical relations derived for vegetation under emergent and submerged conditions as well as numerous data sets covering a wide range of canopy morphology, densities, and rigidity. It is envisaged that the proposed formulation be imminently employed in eco-hydraulics where the interaction between flow and vegetation is being sought.
Developing a blood-based gene mutation assay as a novel biomarker for oesophageal adenocarcinoma
Authors: Haboubi Hasan N. , Lawrence Rachel L. , Rees Benjamin , Williams Lisa , Manson James M. , Al-Mossawi Neam , Bodger Owen , Griffiths Paul , Thornton Catherine , Jenkins Gareth J.
Published: March 2019

The Phosphatidylinositol glycan class A (PIG-A)gene mutation assay phenotypically measures erythrocyte mutations, assessed here for their correlation to neoplastic progression in the gastro-oesophageal reflux disease (GORD)-Barrett’s metaplasia (BM)-oesophageal adenocarcinoma (OAC) model. Endoscopy patients underwent venipuncture and erythrocytes fluorescently stained for glycosyl phosphatidylinositol (GPI)–anchored proteins; CD55 and CD59. Using flow cytometry, GPI–anchor negative erythrocytes (mutants) were scored and compared amongst groups. The study enlisted 200 patients and 137 healthy volunteers. OAC patients had a three–fold increase in erythrocyte mutant frequency (EMF) compared to GORD patients (p < 0.001) and healthy volunteers (p < 0.001). In OAC patients, higher EMF was associated with worsening tumour staging (p = 0.014), nodal involvement (p = 0.019) and metastatic disease (p = 0.008). Chemotherapy patients demonstrated EMF’s over 19–times higher than GORD patients. Patients were further classified into groups containing those with non-neoplastic disease and those with high-grade dysplasia/cancer with 72.1% of cases correctly classified by high EMF. Within the non-neoplastic group, aspirin users had lower EMF (p = 0.001) and there was a positive correlation between body mass index (p = 0.03) and age (p < 0.001) and EMF. Smokers had EMF’s over double that of non-smokers (p = 0.011). Results suggest this test could help detect OAC and may be a useful predictor of disease progression.
Liberibacter crescens biofilm formation in vitro: establishment of a model system for pathogenic ‘Candidatus Liberibacter spp.’
Authors: Naranjo Eber , Merfa Marcus V. , Ferreira Virginia , Jain Mukesh , Davis Michael J. , Bahar Ofir , Gabriel Dean W. , De La Fuente Leonardo
Published: March 2019

The Liberibacter genus comprises insect endosymbiont bacterial species that cause destructive plant diseases, including Huanglongbing in citrus and zebra chip in potato. To date, pathogenic ‘Candidatus Liberibacter spp.’ (CLs) remain uncultured, therefore the plant-associated Liberibacter crescens (Lcr), only cultured species of the genus, has been used as a biological model for in vitro studies. Biofilm formation by CLs has been observed on the outer midgut surface of insect vectors, but not in planta. However, the role of biofilm formation in the life cycle of these pathogens remains unclear. Here, a model system for studying CLs biofilms was developed using Lcr. By culture media modifications, bovine serum albumin (BSA) was identified as blocking initial cell-surface adhesion. Removal of BSA allowed for the first time observation of Lcr biofilms. After media optimization for biofilm formation, we demonstrated that Lcr attaches to surfaces, and form cell aggregates embedded in a polysaccharide matrix both in batch cultures and under flow conditions in microfluidic chambers. Biofilm structures may represent excellent adaptive advantages for CLs during insect vector colonization helping with host retention, immune system evasion, and transmission. Future studies using the Lcr model established here will help in the understanding of the biology of CLs.
Improving in-silico normalization using read weights
Authors: Durai Dilip A. , Schulz Marcel H.
Published: March 2019

Specialized de novo assemblers for diverse datatypes have been developed and are in widespread use for the analyses of single-cell genomics, metagenomics and RNA-seq data. However, assembly of large sequencing datasets produced by modern technologies is challenging and computationally intensive. In-silico read normalization has been suggested as a computational strategy to reduce redundancy in read datasets, which leads to significant speedups and memory savings of assembly pipelines. Previously, we presented a set multi-cover optimization based approach, ORNA, where reads are reduced without losing important k-mer connectivity information, as used in assembly graphs. Here we propose extensions to ORNA, named ORNA-Q and ORNA-K, which consider a weighted set multi-cover optimization formulation for the in-silico read normalization problem. These novel formulations make use of the base quality scores obtained from sequencers (ORNA-Q) or k-mer abundances of reads (ORNA-K) to improve normalization further. We devise efficient heuristic algorithms for solving both formulations. In applications to human RNA-seq data, ORNA-Q and ORNA-K are shown to assemble more or equally many full length transcripts compared to other normalization methods at similar or higher read reduction values. The algorithm is implemented under the latest version of ORNA (v2.0, https://github.com/SchulzLab/ORNA).
HSV-1\EGFP stimulates miR-146a expression in a NF-κB-dependent manner in monocytic THP-1 cells
Authors: Venuti Assunta , Musarra-Pizzo Maria , Pennisi Rosamaria , Tankov Stoyan , Medici Maria Antonietta , Mastino Antonio , Rebane Ana , Sciortino Maria Teresa
Published: March 2019

The nuclear factor κB (NF-κB) pathway plays a key role in innate and adaptive immunity, cell proliferation and survival, inflammation and tumors development. MiR-146a is an immune system regulator that has anti-inflammatory function in multiple cell types and conditions. Here we demonstrate activation of canonical NF-κB pathway in monocytic cells upon HSV-1 replication. By constructing and using a recombinant HSV-1\EGFP virus, we monitored the capability of the virus to recruit NF-κB and we report that the phosphorylation of p65 protein correlates with an active virus replication at single-cell level. In addition, we found that upregulation of miR-146a during viral replication is strictly dependent on NF-κB activation and correlates with tight control of the interleukin-1 receptor-associate kinase 1 (IRAK1). Accordingly, THP-1 DN IκBα cells, expressing a dominant negative mIκBα, did not show upregulation of miR-146a upon HSV-1 infection. Our data suggest that the expression of miRNA-146a modulates NF-κB activation through targeting IRAK1 during HSV-1 replication in THP-1 cells.
High glucose level and angiotensin II type 1 receptor stimulation synergistically amplify oxidative stress in renal mesangial cells
Authors: Akaishi Tetsuya , Abe Michiaki , Okuda Hiroshi , Ishizawa Kota , Abe Takaaki , Ishii Tadashi , Ito Sadayoshi
Published: March 2019

Oxidative stress in renal mesangial cell causes diabetic glomerular changes. High glucose levels and angiotensin II (Ang II) are known to stimulate superoxide production in renal mesangial cells. However, it has been unclear whether Ang II stimulation and pre-conditioning with high glucose affects the same pathway of superoxide production in renal mesangial cells or not. In this study, we examined the levels of oxidative stress under Ang II stimulation in renal mesangial cells preincubated for six hours at various glucose levels. Intracellular levels of reactive oxidative species (ROS) were measured using dihydroethidium or 5′,6′-chloromethyl- 2′,7′ dichlorodihydro-fluorescein diacetate, which facilitates the detection of intracellular ROS under real-time fluorescent microscope. Ang II-induced elevated intracellular ROS levels were detected only when the cells were pre-incubated with high levels of glucose (13.5 mM, 27.8 mM), but was not detected under normal glucose condition (5.5 mM). Production of Ang II-induced intracellular ROS was higher under pre-treatment with 27.8 mM glucose compared to pretreatment with 13.5 mM glucose level. This ROS production in mesangial cells was induced within several minutes of the initiation of Ang II stimulation under high glucose levels. The production of intracellular ROS was significantly reduced in the presence of angiotensin II type1-receptor (AT1R) antagonist, whereas it was augmented in the presence of angiotensin II type2-receptor antagonist. In conclusion, Ang II-induced oxidative stress was augmented by high glucose levels and ROS levels were further alleviated in the presence of AT1R antagonists.
Physiological Association between Limb Ballistocardiogram and Arterial Blood Pressure Waveforms: A Mathematical Model-Based Analysis
Authors: Yousefian Peyman , Shin Sungtae , Mousavi Azin Sadat , Kim Chang-Sei , Finegan Barry , McMurtry M. Sean , Mukkamala Ramakrishna , Jang Dae-Geun , Kwon Uikun , Kim Youn Ho , Hahn Jin-Oh
Published: March 2019

By virtue of its direct association with the cardiovascular (CV) functions and compatibility to unobtrusive measurement during daily activities, the limb ballistocardiogram (BCG) is receiving an increasing interest as a viable means for ultra-convenient CV health and disease monitoring. However, limited insights on its physical implications have hampered disciplined interpretation of the BCG and systematic development of the BCG-based approaches for CV health monitoring. In this study, a mathematical model that can predict the limb BCG in responses to the arterial blood pressure (BP) waves in the aorta was developed and experimentally validated. The validated mathematical model suggests that (i) the limb BCG waveform reveals the timings and amplitudes associated with the aortic BP waves; (ii) mechanical filtering exerted by the musculoskeletal properties of the body can obscure the manifestation of the arterial BP waves in the limb BCG; and (iii) the limb BCG exhibits meaningful morphological changes in response to the alterations in the CV risk predictors. The physical insights garnered by the analysis of the mathematical model may open up new opportunities toward next generation of the BCG-based CV healthcare techniques embedded with transparency, interpretability, and robustness against the external variability.
Causal relationship between local field potential and intrinsic optical signal in epileptiform activity in vitro
Authors: Benkő Zsigmond , Moldován Kinga , Szádeczky-Kardoss Katalin , Zalányi László , Borbély Sándor , Világi Ildikó , Somogyvári Zoltán
Published: March 2019

The directed causal relationship were examined between the local field potential (LFP) and the intrinsic optical signal (IOS) during induced epileptiform activity in in vitro cortical slices by the convergent cross-mapping causality analysis method. Two components of the IOS signal have been distinguished: a faster, activity dependent component (IOSh) which changes its sign between transmitted and reflected measurement, thus it is related to the reflectance or the scattering of the tissue and a slower component (IOSl), which is negative in both cases, thus it is resulted by the increase of the absorption of the tissue. We have found a strong, unidirectional, delayed causal effect from LFP to IOSh with 0.5-1s delay, without signs of feedback from the IOSh to the LFP, while the correlation was small and the peaks of the cross correlation function did not reflect the actual causal dependency. Based on these observations, a model has been set up to describe the dependency of the IOSh on the LFP power and IOSh was reconstructed, based on the LFP signal. This study demonstrates that causality analysis can lead to better understanding the physiological interactions, even in case of two data series with drastically different time scales.
The small GTPase RhoG regulates microtubule-mediated focal adhesion disassembly
Authors: Zinn Ashtyn , Goicoechea Silvia M. , Kreider-Letterman Gabriel , Maity Debonil , Awadia Sahezeel , Cedeno-Rosario Luis , Chen Yun , Garcia-Mata Rafael
Published: March 2019

Focal adhesions (FA) are a complex network of proteins that allow the cell to form physical contacts with the extracellular matrix (ECM). FA assemble and disassemble in a dynamic process, orchestrated by a variety of cellular components. However, the underlying mechanisms that regulate adhesion turnover remain poorly understood. Here we show that RhoG, a Rho GTPase related to Rac, modulates FA dynamics. When RhoG expression is silenced, FA are more stable and live longer, resulting in an increase in the number and size of adhesions, which are also more mature and fibrillar-like. Silencing RhoG also increases the number and thickness of stress fibers, which are sensitive to blebbistatin, suggesting contractility is increased. The molecular mechanism by which RhoG regulates adhesion turnover is yet to be characterized, but our results demonstrate that RhoG plays a role in the regulation of microtubule-mediated FA disassembly.
Distinct mechanical properties in homologous spectrin-like repeats of utrophin
Authors: Rajaganapathy Sivaraman , McCourt Jackie L. , Ghosal Sayan , Lindsay Angus , McCourt Preston M. , Lowe Dawn A. , Ervasti James M. , Salapaka Murti V.
Published: March 2019

Patients with Duchenne muscular dystrophy (DMD) lack the protein dystrophin, which is a critical molecular component of the dystrophin-glycoprotein complex (DGC). Dystrophin is hypothesized to function as a molecular shock absorber that mechanically stabilizes the sarcolemma of striated muscle through interaction with the cortical actin cytoskeleton via its N-terminal half and with the transmembrane protein β-dystroglycan via its C-terminal region. Utrophin is a fetal homologue of dystrophin that can subserve many dystrophin functions and is therefore under active investigation as a dystrophin replacement therapy for DMD. Here, we report the first mechanical characterization of utrophin using atomic force microscopy (AFM). Our data indicate that the mechanical properties of spectrin-like repeats in utrophin are more in line with the PEVK and Ig-like repeats of titin rather than those reported for repeats in spectrin or dystrophin. Moreover, we measured markedly different unfolding characteristics for spectrin repeats within the N-terminal actin-binding half of utrophin compared to those in the C-terminal dystroglycan-binding half, even though they exhibit identical thermal denaturation profiles. Our results demonstrate dramatic differences in the mechanical properties of structurally homologous utrophin constructs and suggest that utrophin may function as a stiff elastic element in series with titin at the myotendinous junction.
Sediment replenishment combined with an artificial flood improves river habitats downstream of a dam
Authors: Stähly Severin , Franca Mário J. , Robinson Christopher T. , Schleiss Anton J.
Published: March 2019

River reaches downstream dams where a constant residual flow discharge is imposed, often lack sediment supply and periodic inundation due to the absence of natural flood events. In this study, a two-year return flood was released from an upstream reservoir and combined with sediment replenishment to enhance instream habitat conditions downstream of Rossens hydropower dam on the Sarine River in western Switzerland. Sediment replenishment consisted of four sediment deposits distributed as alternate bars along the river banks, a solution which was previously tested in laboratory. The morphological evolution of the replenishment and of the downstream riverbed were surveyed including pre- and post-flood topography. A hydro-morphological index to evaluate the quality of riverine habitats, based on the variability of flow depth and flow velocity in the analyzed reach, was investigated. The combination of the artificial flood with sediment replenishment proved to be a robust measure to supply a river with sediment and to enhance hydraulic habitat suitability.
Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability
Authors: Jayaraman Bhargavi , Fernandes Jason D. , Yang Shumin , Smith Cynthia , Frankel Alan D.
Published: March 2019

HIV-1 Rev is an essential viral regulatory protein that facilitates the nuclear export of intron-containing viral mRNAs. It is organized into structured, functionally well-characterized motifs joined by less understood linker regions. Our recent competitive deep mutational scanning study confirmed many known constraints in Rev’s established motifs, but also identified positions of mutational plasticity, most notably in surrounding linker regions. Here, we probe the mutational limits of these linkers by testing the activities of multiple truncation and mass substitution mutations. We find that these regions possess previously unknown structural, functional or regulatory roles, not apparent from systematic point mutational approaches. Specifically, the N- and C-termini of Rev contribute to protein stability; mutations in a turn that connects the two main helices of Rev have different effects in different contexts; and a linker region which connects the second helix of Rev to its nuclear export sequence has structural requirements for function. Thus, Rev function extends beyond its characterized motifs, and is tuned by determinants within seemingly plastic portions of its sequence. Additionally, Rev’s ability to tolerate many of these massive truncations and substitutions illustrates the overall mutational and functional robustness inherent in this viral protein.
Longitudinal development of the airway microbiota in infants with cystic fibrosis
Authors: Ahmed Bushra , Cox Michael J. , Cuthbertson Leah , James Phillip , Cookson William O. C. , Davies Jane C. , Moffatt Miriam F. , Bush Andrew
Published: March 2019

The pathogenesis of airway infection in cystic fibrosis (CF) is poorly understood. We performed a longitudinal study coupling clinical information with frequent sampling of the microbiota to identify changes in the airway microbiota in infancy that could underpin deterioration and potentially be targeted therapeutically. Thirty infants with CF diagnosed on newborn screening (NBS) were followed for up to two years. Two hundred and forty one throat swabs were collected as a surrogate for lower airway microbiota (median 35 days between study visits) in the largest longitudinal study of the CF oropharyngeal microbiota. Quantitative PCR and Illumina sequencing of the 16S rRNA bacterial gene were performed. Data analyses were conducted in QIIME and Phyloseq in R. Streptococcus spp. and Haemophilus spp. were the most common genera (55% and 12.5% of reads respectively) and were inversely related. Only beta (between sample) diversity changed with age (Bray Curtis r2 = 0.15, P = 0.03). Staphylococcus and Pseudomonas were rarely detected. These results suggest that Streptococcus spp. and Haemophilus spp., may play an important role in early CF. Whether they are protective against infection with more typical CF micro-organisms, or pathogenic and thus meriting treatment needs to be determined.
Assessment and Clinical Relevance of Serum IL-19 Levels in Psoriasis and Atopic Dermatitis Using a Sensitive and Specific Novel Immunoassay
Authors: Konrad Robert J. , Higgs Richard E. , Rodgers George H. , Ming Wenyu , Qian Yue-Wei , Bivi Nicoletta , Mack Justin K. , Siegel Robert W. , Nickoloff Brian J.
Published: March 2019

Because development of reliable biomarkers in psoriasis and atopic dermatitis has lagged behind therapeutic progress, we created a blood-based test to fill the void in objective methods available for dermatological assessments. Our novel interleukin-19 (IL-19) immunoassay was initially tested to determine concentrations of IL-19 serum levels, then correlated with the psoriasis activity and severity index (PASI) in psoriasis, and the eczema area and severity index (EASI) in atopic dermatitis. Not only was IL-19 increased in psoriasis and correlated to PASI, but ixekizumab administration led to rapid, sustained IL-19 decreases to normal levels, with decreases at 2-weeks correlating with PASI improvement at 16-weeks. IL-19 increased upon ixekizumab withdraw, prior to relapse, and decreased following re-treatment. In baricitinib- and etanercept-treated psoriasis patients, IL-19 decreases also correlated with improvement. Many patients with limited skin disease, including genital psoriasis and psoriatic arthritis patients, also had increased IL-19, which was reduced to normal levels upon ixekizumab treatment, correlating with PASI improvement. We also measured IL-19 in baricitinib-treated atopic dermatitis patients. In atopic dermatitis, IL-19 was significantly elevated, correlated with EASI scores, and decreased with skin improvement. Therefore, measurement of serum IL-19 provides clinicians with an objective disease-activity assessment tool for psoriasis and atopic dermatitis patients.
Melanocyte Chitosan/Gelatin Composite Fabrication with Human Outer Root Sheath-Derived Cells to Produce Pigment
Authors: Zhou Xianyu , Ma Yan , Liu Fei , Gu Chuan , Wang Xiuxia , Xia Huitang , Zhou Guangdong , Huang Jinny , Luo Xusong , Yang Jun
Published: March 2019

The hair follicle serves as a melanocyte reservoir for both hair and skin pigmentation. Melanocyte stem cells (MelSCs) and melanocyte progenitors reside in the bulge/sub-bulge region of the lower permanent portion of the hair follicle and play a vital role for repigmentation in vitiligo. It would be beneficial to isolate MelSCs in order to further study their function in pigmentary disorders; however, due to the lack of specific molecular surface markers, this has not yet been successfully accomplished in human hair follicles (HuHF). One potential method for MelSCs isolation is the “side population” technique, which is frequently used to isolate hematopoietic and tumor stem cells. In the present study, we decided to isolate HuHF MelSCs using “side population” to investigate their melanotic function. By analyzing mRNA expression ofTYR,SOX10, andMITF, melanosome structure, and immunofluorescence with melanocyte-specific markers, we revealed that the SP-fraction contained MelSCs with an admixture of differentiated melanocytes. Furthermore, ourin vivostudies indicated that differentiated SP-fraction cells, when fabricated into acell-chitosan/gelatin composite, could transiently repopulate immunologically compromised mice skin to regain pigmentation. In summary, the SP technique is capable of isolating HuHF MelSCs that can potentially be used to repopulate skin for pigmentation.
Crystallization of gas-selective nanoporous graphene by competitive etching and growth: a modeling study
Authors: Dutta Soumajit , Vahdat Mohammad Tohidi , Rezaei Mojtaba , Agrawal Kumar Varoon
Published: March 2019

A robust synthesis methodology for crystallizing nanoporous single-layer graphene hosting a high density of size-selective nanopores is urgently needed to realize the true potential of two-dimensional membranes for gas separation. Currently, there are no controllable etching techniques for single-layer graphene that are self-limiting, and that can generate size-selective nanopores at a high pore-density. In this work, we simulate a unique chemical vapor deposition based crystallization of graphene on Cu(111), in the presence of an etchant, to generate a high density (>1013 cm−2) of sub-nanometer-sized, elongated nanopores in graphene. An equilibrium between the growth rate and the etching rate is obtained, and beyond a critical time, the total number of the carbon atoms and the edge carbon atoms do not change. Using an optimal first-order etching chemistry, a log-mean pore-size of 5.0 ± 1.7 (number of missing carbon atoms), and a pore-density of 3 × 1013 cm−2 was achieved. A high throughput calculation route for estimating gas selectivity from ensembles of thousands of nanopores was developed. The optimized result yielded H2/CO2, H2/N2 and H2/CH4 selectivities larger than 200, attributing to elongated pores generated by the competitive etching and growth. The approach of competitive etching during the crystal growth is quite generic and can be applied to a number of two-dimensional materials.
Antrodia cinnamomea induces anti-tumor activity by inhibiting the STAT3 signaling pathway in lung cancer cells
Authors: Huang Tsung-Teng , Lan Ying-Wei , Chen Chuan-Mu , Ko Yun-Fei , Ojcius David M. , Martel Jan , Young John D. , Chong Kowit-Yu
Published: March 2019

We examined the effects of an Antrodia cinnamomea ethanol extract (ACEE) on lung cancer cells in vitro and tumor growth in vivo. ACEE produced dose-dependent cytotoxic effects and induced apoptosis in Lewis lung carcinoma (LLC) cells. ACEE treatment increased expression of p53 and Bax, as well as cleavage of caspase-3 and PARP, while reducing expression of survivin and Bcl-2. ACEE also reduced the levels of JAK2 and phosphorylated STAT3 in LLC cells. In a murine allograft tumor model, oral administration of ACEE significantly inhibited LLC tumor growth and metastasis without affecting serum biological parameters or body weight. ACEE increased cleavage of caspase-3 in murine tumors, while decreasing STAT3 phosphorylation. In addition, ACEE reduced the growth of human tumor xenografts in nude mice. Our findings therefore indicate that ACEE inhibits lung tumor growth and metastasis by inducing apoptosis and by inhibiting the STAT3 signaling pathway in cancer cells.
Detection of novel fusion-transcripts by RNA-Seq in T-cell lymphoblastic lymphoma
Authors: López-Nieva Pilar , Fernández-Navarro Pablo , Graña-Castro Osvaldo , Andrés-León Eduardo , Santos Javier , Villa-Morales María , Cobos-Fernández María Ángeles , González-Sánchez Laura , Malumbres Marcos , Salazar-Roa María , Fernández-Piqueras José
Published: March 2019

Fusions transcripts have been proven to be strong drivers for neoplasia-associated mutations, although their incidence in T-cell lymphoblastic lymphoma needs to be determined yet. Using RNA-Seq we have selected 55 fusion transcripts identified by at least two of three detection methods in the same tumour. We confirmed the existence of 24 predicted novel fusions that had not been described in cancer or normal tissues yet, indicating the accuracy of the prediction. Of note, one of them involves the proto oncogene TAL1. Other confirmed fusions could explain the overexpression of driver genes such as COMMD3-BMI1, LMO1 or JAK3. Five fusions found exclusively in tumour samples could be considered pathogenic (NFYG-TAL1, RIC3-TCRBC2, SLC35A3-HIAT1, PICALM MLLT10 and MLLT10-PICALM). However, other fusions detected simultaneously in normal and tumour samples (JAK3-INSL3, KANSL1-ARL17A/B and TFG-ADGRG7) could be germ-line fusions genes involved in tumour-maintaining tasks. Notably, some fusions were confirmed in more tumour samples than predicted, indicating that the detection methods underestimated the real number of existing fusions. Our results highlight the potential of RNA-Seq to identify new cryptic fusions, which could be drivers or tumour-maintaining passenger genes. Such novel findings shed light on the searching for new T-LBL biomarkers in these haematological disorders.