bluuebunny/crossref_metadata_2025 huggingface dataset:
The origin of a primordial genome through spontaneous symmetry breaking
Authors: Takeuchi Nobuto , Hogeweg Paulien , Kaneko Kunihiko
Published: August 2017

The heredity of a cell is provided by a small number of non-catalytic templates—the genome. How did genomes originate? Here, we demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness. These conflicting tendencies induce the symmetry breaking, whereby one strand of the molecules remains catalytic and increases its copy number (enzyme-like molecules), whereas the other becomes non-catalytic and decreases its copy number (genome-like molecules). This asymmetry increases the equilibrium cellular fitness by decreasing mutation pressure and increasing intracellular genetic drift. These results implicate conflicting multilevel evolution as a key cause of the origin of genetic complexity.
Vertical ocean heat redistribution sustaining sea-ice concentration trends in the Ross Sea
Authors: Lecomte Olivier , Goosse Hugues , Fichefet Thierry , de Lavergne Casimir , Barthélemy Antoine , Zunz Violette
Published: August 2017

Several processes have been hypothesized to explain the slight overall expansion of Antarctic sea ice over the satellite observation era, including externally forced changes in local winds or in the Southern Ocean’s hydrological cycle, as well as internal climate variability. Here, we show the critical influence of an ocean–sea-ice feedback. Once initiated by an external perturbation, it may be sufficient to sustain the observed sea-ice expansion in the Ross Sea, the region with the largest and most significant expansion. We quantify the heat trapped at the base of the ocean mixed layer and demonstrate that it is of the same order of magnitude as the latent heat storage due to the long-term changes in sea-ice volume. The evidence thus suggests that the recent ice coverage increase in the Ross Sea could have been achieved through a reorganization of energy within the near-surface ice-ocean system.
Perceptions of asthma control in the United Kingdom: a cross-sectional study comparing patient and healthcare professionals’ perceptions of asthma control with validated ACT scores
Authors: Menzies-Gow Andrew , Chiu Gavin
Published: August 2017

Perceptions of asthma control often vary between patients and physicians. This cross-sectional survey provided UK-specific data on actual and perceived asthma control in patients (18–75 years) attending routine asthma reviews in primary, secondary and tertiary settings. Differences between healthcare professionals’ (HCP) and patients’ perceptions of asthma control were evaluated via an online questionnaire and compared to a control—the validated asthma control test (ACT)—which patients completed. Treated patients (at least a short acting ß-agonist) with a documented diagnosis of asthma were enroled and consented within a month of their last appointment. Patients were grouped according to the British Thoracic Society (BTS)/Scottish Intercollegiate Guidelines Network (SIGN) 2014 treatment guidelines (BTS/SIGN steps 1–5). A total of 260 patients were screened: 234 were eligible for enrolment: 33, 52, 50, 49 and 50 patients in steps 1–5, respectively. Seventy per cent (164) were women. The percentage of patients aged 45–64 years was 47.4%. HCPs classed 70% (164) as non-smokers. 84.2% of patients and 73.9% of HCPs perceived that asthma was controlled but ACT results suggest that asthma was only controlled in 54.7% of patients (ACT score ≥20). Patients in steps 4 and 5 had the highest levels of uncontrolled asthma. Correct agreement between ACT score with perceptions of controlled or uncontrolled asthma occurred in 67.9% of patients and 68.8% of HCPs; the poorest levels of agreement occurred in patients in steps 4 and 5. Uncontrolled asthma is common in UK patients. High proportions of patients and HCPs have incorrect perceptions of asthma control, especially in relation to patients with asthma in steps 4 and 5.
The global burden of lower urinary tract symptoms suggestive of benign prostatic hyperplasia: A systematic review and meta-analysis
Authors: Lee Shaun Wen Huey , Chan Esther Mei Ching , Lai Yin Key
Published: August 2017

Benign prostatic hyperplasia is a common non-malignant condition among older men, but the epidemiology is poorly characterised. We summarised and determined the global prevalence of benign prostatic hyperplasia. A systematic search on PubMed, EMBASE and CENTRAL was performed up until 31st July 2016. Studies that described the epidemiology of benign prostatic hyperplasia were included and cumulative plots of prevalence estimates were calculated. A total of 31 prevalence rate estimates from 25 countries were identified. The combined prevalence estimates showed that the lifetime prevalence of BPH was 26.2% (95% CI: 22.8–29.6%). We found that there was an increasing prevalence of BPH with age. However, we found no significant difference between (a) rural, urban or mixed sites, (b) different countries, (c) respondent representativeness. (d) sample size or (e) study quality. We also found no significant change in the prevalence over the past 20 years. While there is substantial variation between sites estimates, results suggest that nearly 1 in 4 men will suffer from BPH over their lifetime. The study revealed there are significant gaps in knowledge, which provides opportunities for future research to further enrich the epidemiological landscape with data.
Plasma GDF15 level is elevated in psychosis and inversely correlated with severity
Authors: Kumar Parvin , Millischer Vincent , Villaescusa J. Carlos , Nilsson Ida A. K. , Östenson Claes-Göran , Schalling Martin , Ösby Urban , Lavebratt Catharina
Published: August 2017

Accumulating evidence suggests that GDF15 is a biomarker for ageing and morbidity of many somatic disorders such as cancer and inflammatory disorders. Recently, elevated serum GDF15 level was proposed as a marker for mood disorder. However, psychosis severity was not investigated in relation to plasma GDF15 levels. In the present study we measured GDF15 levels in plasma of 120 psychosis patients compared to 120 age and gender matched healthy controls. Within the patient cohort GDF15 levels were evaluated for association with age, gender, lifestyle factors, C-reactive protein levels, psychosis severity and metabolic disorder. Psychosis patients had elevated GDF15 levels compared to controls (medianPsychosis = 744 ng/mL, mediancontrols = 516 ng/mL, p < 0.001). Within the psychosis cohort, GDF15 levels, when corrected for age, metabolic health and lifestyle factors, were negatively correlated with psychosis severity (β = −0.218, p = 0.012). While GDF15 levels were elevated in patients versus healthy controls, the negative correlation between psychosis severity and GDF15 suggests a loss of anti-inflammatory GDF15 mediated functionality in severe psychosis. Study replication in larger cohorts will be necessary to assess the potential of GDF15 as a prognostic biomarker in psychosis.
Temozolomide arrests glioma growth and normalizes intratumoral extracellular pH
Authors: Rao Jyotsna U. , Coman Daniel , Walsh John J. , Ali Meser M. , Huang Yuegao , Hyder Fahmeed
Published: August 2017

Gliomas maintain an acidic extracellular pH (pHe), which promotes tumor growth and builds resistance to therapy. Given evidence that acidic pHe beyond the tumor core indicates infiltration, we hypothesized that imaging the intratumoral pHe in relation to the peritumoral pHe can provide a novel readout of therapeutic influence on the tumor microenvironment. We used Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), which utilizes chemical shifts of non-exchangeable protons from macrocyclic chelates (e.g., DOTP8−) complexed with paramagnetic thulium (Tm3+), to generate pHe maps in rat brains bearing U251 tumors. Following TmDOTP5− infusion, T2-weighted MRI provided delineation of the tumor boundary and BIRDS was used to image the pHe gradient between intratumoral and peritumoral regions (ΔpHe) in both untreated and temozolomide treated (40 mg/kg) rats bearing U251 tumors. Treated rats had reduced tumor volume (p < 0.01), reduced proliferation (Ki-67 staining; p < 0.03) and apoptosis induction (cleaved Caspase-3 staining; p < 0.001) when compared to untreated rats. The ΔpHe was significantly higher in untreated compared to treated rats (p < 0.002), suggesting that temozolomide, which induces apoptosis and hinders proliferation, also normalizes intratumoral pHe. Thus, BIRDS can be used to map the ΔpHe in gliomas and provide a physiological readout of the therapeutic response on the tumor microenvironment.
Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation
Authors: Kuang Qie , Purhonen Pasi , Ålander Johan , Svensson Richard , Hoogland Veronika , Winerdal Jens , Spahiu Linda , Ottosson-Wadlund Astrid , Jegerschöld Caroline , Morgenstern Ralf , Hebert Hans
Published: August 2017

Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two aliphatic chains and one glutathione (GSH) molecule. The functional unit is a homotrimer centered on the crystallographic three-fold axes of the unit cell. The GSH substrate binds in an extended conformation at the interface between two subunits of the trimer supported by new in vitro mutagenesis data. Mutation of Arginine 130 to alanine resulted in complete loss of activity consistent with a role for Arginine 130 in stabilizing the strongly nucleophilic GSH thiolate required for catalysis. Based on the new model and an electron diffraction data set from crystals soaked with trinitrobenzene, that forms a dead-end Meisenheimer complex with GSH, a difference map was calculated. The map reveals side chain movements opening a cavity that defines the second substrate site.
Incoherent scattering can favorably influence energy filtering in nanostructured thermoelectrics
Authors: Singha Aniket , Muralidharan Bhaskaran
Published: August 2017

Investigating in detail the physics of energy filtering through a single planar energy barrier in nanostructured thermoelectric generators, we reinforce the non-trivial result that the anticipated enhancement in generated power at a given efficiency via energy filtering is a characteristic of systems dominated by incoherent scattering and is absent in ballistic devices. In such cases, assuming an energy dependent relaxation time τ(E) = kE
r
, we show that there exists a minimum value r
min
beyond which generation can be enhanced by embedding nanobarriers. For bulk generators with embedded nanobarriers, we delve into the details of inter sub-band scattering and show that it has finite contribution to the enhancement in generation. We subsequently discuss the realistic aspects, such as the effect of smooth transmission cut-off and show that for r > r
min
, the optimized energy barrier is just sufficiently wide enough to scatter off low energy electrons, a very wide barrier being detrimental to the performance. Analysis of the obtained results should provide general design guidelines for enhancement in thermoelectric generation via energy filtering. Our non-equilibrium approach is typically valid in the absence of local quasi-equilibrium and hence sets the stage for future advancements in thermoelectric device analysis, for example, Peltier cooling near a barrier interface.
Mapping physiological inputs from multiple photoreceptor systems to dopaminergic amacrine cells in the mouse retina
Authors: Zhao Xiwu , Wong Kwoon Y. , Zhang Dao-Qi
Published: August 2017

In the vertebrate retina, dopamine is synthesized and released by a specialized type of amacrine cell, the dopaminergic amacrine cell (DAC). DAC activity is stimulated by rods, cones, and melanopsin-expressing intrinsically photosensitive retinal ganglion cells upon illumination. However, the relative contributions of these three photoreceptor systems to the DAC light-induced response are unknown. Here we found that rods excite dark-adapted DACs across a wide range of stimulation intensities, primarily through connexin-36-dependent rod pathways. Similar rod-driven responses were observed in both ventral and dorsal DACs. We further found that in the dorsal retina, M-cones and melanopsin contribute to dark-adapted DAC responses with a similar threshold intensity. In the ventral retina, however, the threshold intensity for M-cone-driven responses was two log units greater than that observed in dorsal DACs, and melanopsin-driven responses were almost undetectable. We also examined the DAC response to prolonged adapting light and found such responses to be mediated by rods under dim lighting conditions, rods/M-cones/melanopsin under intermediate lighting conditions, and cones and melanopsin under bright lighting conditions. Our results elucidate the relative contributions of the three photoreceptor systems to DACs under different lighting conditions, furthering our understanding of the role these cells play in the visual system.
CaV1.3 L-type Ca2+ channel contributes to the heartbeat by generating a dihydropyridine-sensitive persistent Na+ current
Authors: Toyoda Futoshi , Mesirca Pietro , Dubel Stefan , Ding Wei-Guang , Striessnig Joerg , Mangoni Matteo E. , Matsuura Hiroshi
Published: August 2017

The spontaneous activity of sinoatrial node (SAN) pacemaker cells is generated by a functional interplay between the activity of ionic currents of the plasma membrane and intracellular Ca2+ dynamics. The molecular correlate of a dihydropyridine (DHP)-sensitive sustained inward Na+ current (Ist), a key player in SAN automaticity, is still unknown. Here we show that Ist and the L-type Ca2+ current (ICa,L) share CaV1.3 as a common molecular determinant. Patch-clamp recordings of mouse SAN cells showed that Ist is activated in the diastolic depolarization range, and displays Na+ permeability and minimal inactivation and sensitivity to ICa,L activators and blockers. Both CaV1.3-mediated ICa,L and Ist were abolished in CaV1.3-deficient (CaV1.3−/−) SAN cells but the CaV1.2-mediated ICa,L current component was preserved. In SAN cells isolated from mice expressing DHP-insensitive CaV1.2 channels (CaV1.2DHP−/−), Ist and CaV1.3-mediated ICa,L displayed overlapping sensitivity and concentration–response relationships to the DHP blocker nifedipine. Consistent with the hypothesis that CaV1.3 rather than CaV1.2 underlies Ist, a considerable fraction of ICa,L was resistant to nifedipine inhibition in CaV1.2DHP−/− SAN cells. These findings identify CaV1.3 channels as essential molecular components of the voltage-dependent, DHP-sensitive Ist Na+ current in the SAN.
Regulation of the Human Phosphatase PTPN4 by the inter-domain linker connecting the PDZ and the phosphatase domains
Authors: Caillet-Saguy Célia , Toto Angelo , Guerois Raphael , Maisonneuve Pierre , di Silvio Eva , Sawyer Kristi , Gianni Stefano , Wolff Nicolas
Published: August 2017

Human protein tyrosine phosphatase non-receptor type 4 (PTPN4) has been shown to prevent cell death. The active form of human PTPN4 consists of two globular domains, a PDZ (PSD-95/Dlg/ZO-1) domain and a phosphatase domain, tethered by a flexible linker. Targeting its PDZ domain abrogates this protection and triggers apoptosis. We previously demonstrated that the PDZ domain inhibits the phosphatase activity of PTPN4 and that the mere binding of a PDZ ligand is sufficient to release the catalytic inhibition. We demonstrate here that the linker connecting the PDZ domain and the phosphatase domain is involved in the regulation of the phosphatase activity in both PDZ-related inhibition and PDZ ligand-related activation events. We combined bioinformatics and kinetic studies to decipher the role of the linker in the PTPN4 activity. By comparing orthologous sequences, we identified a conserved patch of hydrophobic residues in the linker. We showed that mutations in this patch affect the regulation of the PTPN4 bidomain indicating that the PDZ-PDZ ligand regulation of PTPN4 is a linker-mediated mechanism. However, the mutations do not alter the binding of the PDZ ligand. This study strengthens the notion that inter-domain linker can be of functional importance in enzyme regulation of large multi-domain proteins.
Luteolin, a natural flavonoid, inhibits methylglyoxal induced apoptosis via the mTOR/4E-BP1 signaling pathway
Authors: Liu Yi , Huang Jie , Zheng Xian , Yang Xia , Ding Yan , Fang Tongyong , Zhang Yuyun , Wang Shuaishuai , Zhang Xiaofei , Luo Xuan , Guo Anlei , Newell Kelly A. , Yu Yinghua , Huang Xu-Feng
Published: August 2017

Methylglyoxal (MG) accumulation has been observed in human cerebrospinal fluid and body tissues under hyperglycaemic conditions. Recent research has demonstrated that MG-induces neuronal cell apoptosis, which promotes the development of diabetic encephalopathy. Our previous animal study has shown that luteolin, a natural flavonoid, attenuates diabetes-associated cognitive dysfunction. To further explore the neuroprotective properties of luteolin, we investigated the inhibitive effect of luteolin on MG-induced apoptosis in PC12 neuronal cells. We found that MG inhibited cell viability in a dose-dependent manner and induced apoptosis in PC12 cells. Pretreatment with Luteolin significantly elevated cell viability, reduced MG-induced apoptosis, inhibited the activation of the mTOR/4E-BP1 signaling pathway, and decreased pro-apoptotic proteins, Bax, Cytochrome C as well as caspase-3. Furthermore, we found that pretreatment with the mTOR inhibitor, rapamycin, significantly reduced the expression of the pro-apoptotic protein Bax. Therefore, these observations unambiguously suggest that the inhibitive effect of Luteolin against MG-induced apoptosis in PC12 cells is associated with inhibition of the mTOR/4E-BP1 signaling pathway.
Population pharmacokinetics of peginterferon α2a in patients with chronic hepatitis B
Authors: Bi Jingfeng , Li Xingang , Liu Jia , Chen Dawei , Li Shuo , Hou Jun , Zhou Yuxia , Zhu Shanwei , Zhao Zhigang , Qin Enqiang , Wei Zhenman
Published: August 2017

There were significant differences in response and pharmacokinetic characteristics to the peginterferon α2a treatment among Chronic Hepatitis B (CHB) patients. The aim of this study is to identify factors which could significantly impact the peginterferon α2a pharmacokinetic characteristics in CHB patients. There were 208 blood samples collected from 178 patients who were considered as CHB and had been treated with peginterferon α2a followed by blood concentration measurement and other laboratory tests. The covariates such as demographic and clinical characteristics of the patients were retrieved from medical records. Nonlinear mixed-effects modeling method was used to develop the population pharmacokinetic model with NONMEM software. A population pharmacokinetic model for peginterferon α2a has been successfully developed which shows that distribution volume (V) was associated with body mass index (BMI), and drug clearance (CL) had a positive correlation with creatinine clearance (CCR). The final population pharmacokinetic model supports the use of BMI and CCR-adjusted dosing in hepatitis B virus patients.
Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification
Authors: Lv Jianjian , Gao Baoquan , Liu Ping , Li Jian , Meng Xianliang
Published: August 2017

A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, a linkage map was constructed for the swimming crab (Portunus trituberculatus) with 10,963 markers; as far as we know, this number of markers has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM. The de novo assembly based on genome and transcriptome sequencing data enabled 2,378 explicit annotated markers to be anchored to the map. Quantitative trait locus (QTL) mapping revealed 10 growth-related QTLs with a phenotypic variance explained (PVE) range of 12.0–35.9. Eight genes identified from the growth-related QTL regions, in particular, RE1-silencing transcription factor and RNA-directed DNA polymerase genes with nonsynonymous substitutions, were considered important growth-related candidate genes. We have demonstrated that linkage mapping aided by de novo assembly of genome and transcriptome sequencing could serve as an important platform for QTL mapping and the identification of trait-related genes.
Choroidal Remodeling in Age-related Macular Degeneration and Polypoidal Choroidal Vasculopathy: A 12-month Prospective Study
Authors: Ting Daniel Shu Wei , Yanagi Yasuo , Agrawal Rupesh , Teo Hwei Yee , Seen Sophia , Yeo Ian Yew San , Mathur Ranjana , Chan Choi Mun , Lee Shu Yen , Wong Edmund Yick Mun , Wong Doric , Wong Tien Yin , Cheung Gemmy Chui Ming
Published: August 2017

Choroid thinning occurs in age-related macular degeneration (AMD). However, it remains unclear whether the reduction is due to reduction in choroidal vessels or shrinkage of choroidal stroma, or both. The purpose of this study was to evaluate the changes of the choroidal vascular and stromal area in 118 patients with typical AMD (t-AMD) and polypoidal choroidal vasculopathy (PCV) over a 12-month period. We used spectral-domain optical coherence tomography (SD-OCT) with enhanced depth imaging (EDI) mode to measure the subfoveal choroidal thickness (CT), central retinal thickness (CRT) and choroidal vascularity index (CVI - ratio of luminal area to total choroidal area). At baseline, PCV eyes had higher CRT (471.6 µm vs 439.1 µm, p = 0.02), but comparable subfoveal CT and CVI, compared to t-AMD. Eyes with high CVI at baseline showed marked reduction in stromal area compared with eyes with average or low CVI. Over 12 months, CRT and subfoveal CT significantly decreased (p < 0.001) in both subtypes. Eyes with high baseline CVI showed significant CVI reduction from baseline to month 12 (p < 0.001), whereas eyes with average to low baseline CVI showed increase in CVI. These differences in choroidal vascularity may reflect different predominant pathogenic processes and remodeling in AMD eyes with varying spectrum.
Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth
Authors: Baalsrud Helle Tessand , Voje Kjetil Lysne , Tørresen Ole Kristian , Solbakken Monica Hongrø , Matschiner Michael , Malmstrøm Martin , Hanel Reinhold , Salzburger Walter , Jakobsen Kjetill S. , Jentoft Sissel
Published: August 2017

Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments.
Ectodomain shedding of Limbic System-Associated Membrane Protein (LSAMP) by ADAM Metallopeptidases promotes neurite outgrowth in DRG neurons
Authors: Sanz Ricardo L. , Ferraro Gino B. , Girouard Marie-Pier , Fournier Alyson E.
Published: August 2017

IgLONs are members of the immunoglobulin superfamily of cell adhesion proteins implicated in the process of neuronal outgrowth, cell adhesion and subdomain target recognition. IgLONs form homophilic and heterophilic complexes on the cell surface that repress or promote growth depending on the neuronal population, the developmental stage and surface repertoire of IgLON family members. In the present study, we identified a metalloproteinase-dependent mechanism necessary to promote growth in embryonic dorsal root ganglion cells (DRGs). Treatment of embryonic DRG neurons with pan-metalloproteinase inhibitors, tissue inhibitor of metalloproteinase-3, or an inhibitor of ADAM Metallopeptidase Domain 10 (ADAM10) reduces outgrowth from DRG neurons indicating that metalloproteinase activity is important for outgrowth. The IgLON family members Neurotrimin (NTM) and Limbic System-Associated Membrane Protein (LSAMP) were identified as ADAM10 substrates that are shed from the cell surface of DRG neurons. Overexpression of LSAMP and NTM suppresses outgrowth from DRG neurons. Furthermore, LSAMP loss of function decreases the outgrowth sensitivity to an ADAM10 inhibitor. Together our findings support a role for ADAM-dependent shedding of cell surface LSAMP in promoting outgrowth from DRG neurons.
Improvement of a rapid diagnostic application of monoclonal antibodies against avian influenza H7 subtype virus using Europium nanoparticles
Authors: Yeo Seon-Ju , Bao Duong Tuan , Seo Ga-Eun , Bui Cuc Thi , Kim Do Thi Hoang , Anh Nguyen Thi Viet , Tien Trinh Thi Thuy , Linh Nguyen Thi Phuong , Sohn Hae-Jin , Chong Chom-Kyu , Shin Ho-Joon , Park Hyun
Published: August 2017

The development of a sensitive and rapid diagnostic test is needed for early detection of avian influenza (AI) H7 subtype. In this study, novel monoclonal antibodies (mAbs) against influenza A H7N9 recombinant hemagglutinin (rHA)1 were developed and applied to a Europium nanoparticle–based rapid fluorescent immunochromatographic strip test (FICT) to improve the sensitivity of the rapid diagnostic system. Two antibodies (2F4 and 6D7) exhibited H7 subtype specificity in a dot-FICT assay by optimization of the conjugate and the pH of the lysis buffer. The subtype specificity was confirmed by an immunofluorescence assay and Western blot analysis. The limit of detection of the FICT employing novel mAbs 31 ng/mL for H7N9 rHA1 and 40 hemagglutination units/mL for H7 subtype virus. Sensitivity was improved 25-fold using Europium as confirmed by comparison of colloidal gold-based rapid diagnostic kit using the 2F4 and 6D7 mAbs.
Statistical characterization of therapeutic protein modifications
Authors: Tsai Tsung-Heng , Hao Zhiqi , Hong Qiuting , Moore Benjamin , Stella Cinzia , Zhang Jeffrey H. , Chen Yan , Kim Michael , Koulis Theo , Ryslik Gregory A. , Verschueren Erik , Jacobson Fred , Haskins William E. , Vitek Olga
Published: August 2017

Peptide mapping with liquid chromatography–tandem mass spectrometry (LC-MS/MS) is an important analytical method for characterization of post-translational and chemical modifications in therapeutic proteins. Despite its importance, there is currently no consensus on the statistical analysis of the resulting data. In this manuscript, we distinguish three statistical goals for therapeutic protein characterization: (1) estimation of site occupancy of modifications in one condition, (2) detection of differential site occupancy between conditions, and (3) estimation of combined site occupancy across multiple modification sites. We propose an approach, which addresses these goals in terms of summarizing the quantitative information from the mass spectra, statistical modeling, and model-based analysis of LC-MS/MS data. We illustrate the approach using an LC-MS/MS experiment from an antibody-drug conjugate and its monoclonal antibody intermediate. The performance was compared to a ‘naïve’ data analysis approach, by using computer simulation, evaluation of differential site occupancy in positive and negative controls, and comparisons of estimated site occupancy with orthogonal experimental measurements of N-linked glycoforms and total oxidation. The results demonstrated the importance of replicated studies of protein characterization, and of appropriate statistical modeling, for reproducible, accurate and efficient site occupancy estimation and differential analysis.
Effectiveness of a multimodal pain management concept for patients with cervical radiculopathy with focus on cervical epidural injections
Authors: Benditz Achim , Brunner Melanie , Zeman Florian , Greimel Felix , Florian Völlner , Boluki Daniel , Grifka Joachim , Weber Markus , Renkawitz Tobias
Published: August 2017

Cervical radiculopathy has become an increasing problem worldwide. Conservative treatment options have been recommended in many reviews on cervical radiculopathy, ranging from different types of physiotherapy to waiting for remission by natural history. No multimodal pain management concept (MPM) on an inpatient basis has been evaluated. This study aimed at showing the positive short-term effects of an inpatient multimodal pain management concept with focus on cervical translaminar epidural steroid injection for patients with cervical radiculopathy. 54 patients who had undergone inpatient MPM for 10 days were evaluated before and after 10-days treatment. The NRS (0–10) value for arm pain could be reduced from 6.0 (IQR 5.7–6.8) to 2.25 (IQR 2.0–3.1) and from 5.9 (IQR 4.8–6.0) to 2.0 (IQR 1.7–2.6) for neck pain. Neck pain was reduced by 57.4% and arm pain by 62.5%. 2 days after epidural steroid injection, pain was reduced by 40.1% in the neck and by 43.4% in the arms. MPM seems to be an efficient short-term approach to treating cervical radiculopathy. Cervical translaminar epidural steroid injection is an important part of this concept. In the absence of a clear indication for surgery, MPM represents a treatment option.
Recombineering using RecET in Corynebacterium glutamicum ATCC14067 via a self-excisable cassette
Authors: Huang Yuanyuan , Li Lu , Xie Shan , Zhao Nannan , Han Shuangyan , Lin Ying , Zheng Suiping
Published: August 2017

Gene manipulation is essential for metabolic engineering and synthetic biology, but the current general gene manipulation methods are not applicable to the non-model strain Corynebacterium glutamicum (C. glutamicum) ATCC14067, which is used for amino acid production. Here, we report an effective and sequential deletion method for C. glutamicum ATCC14067 using the exonuclease-recombinase pair RecE + RecT (RecET) for recombineering via a designed self-excisable linear double-strand DNA (dsDNA) cassette, which contains the Cre/loxP system, to accomplish markerless deletion. To the best of our knowledge, this is the first effective and simple strategy for recombination with markerless deletion in C. glutamicum ATCC14067. This strategy provides a simple markerless deletion strategy for C. glutamicum and builds a solid basis for producer construction.
Regulation of tumour related genes by dynamic epigenetic alteration at enhancer regions in gastric epithelial cells infected by Epstein-Barr virus
Authors: Okabe Atsushi , Funata Sayaka , Matsusaka Keisuke , Namba Hiroe , Fukuyo Masaki , Rahmutulla Bahityar , Oshima Motohiko , Iwama Atsushi , Fukayama Masashi , Kaneda Atsushi
Published: August 2017

Epstein-Barr virus (EBV) infection is associated with tumours such as Burkitt lymphoma, nasopharyngeal carcinoma, and gastric cancer. We previously showed that EBV(+) gastric cancer presents an extremely high-methylation epigenotype and this aberrant DNA methylation causes silencing of multiple tumour suppressor genes. However, the mechanisms that drive EBV infection-mediated tumorigenesis, including other epigenomic alteration, remain unclear. We analysed epigenetic alterations induced by EBV infection especially at enhancer regions, to elucidate their contribution to tumorigenesis. We performed ChIP sequencing on H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K9me3 in gastric epithelial cells infected or not with EBV. We showed that repressive marks were redistributed after EBV infection, resulting in aberrant enhancer activation and repression. Enhancer dysfunction led to the activation of pathways related to cancer hallmarks (e.g., resisting cell death, disrupting cellular energetics, inducing invasion, evading growth suppressors, sustaining proliferative signalling, angiogenesis, and tumour-promoting inflammation) and inactivation of tumour suppressive pathways. Deregulation of cancer-related genes in EBV-infected gastric epithelial cells was also observed in clinical EBV(+) gastric cancer specimens. Our analysis showed that epigenetic alteration associated with EBV-infection may contribute to tumorigenesis through enhancer activation and repression.
A Novel Aldosterone Antagonist Limits Renal Injury in 5/6 Nephrectomy
Authors: Fujihara Clarice K. , Kowala M. C. , Breyer M. D. , Sena Claudia R. , Rodrigues Mariliza V. , Arias Simone C. A. , Fanelli Camilla , Malheiros Denise M. , Jadhav P. K. , Montrose-Rafizadeh Chahrzad , Krieger Jose E. , Zatz Roberto
Published: August 2017

Aldosterone antagonists slow the progression of chronic kidney disease (CKD), but their use is limited by hyperkalemia, especially when associated with RAS inhibitors. We examined the renoprotective effects of Ly, a novel non-steroidal mineralocorticoid receptor (MR) blocker, through two experimental protocols: In Protocol 1, male Munich-Wistar rats underwent 5/6 renal ablation (Nx), being divided into: Nx+V, receiving vehicle, Nx+Eple, given eplerenone, 150 mg/kg/day, and Nx+Ly, given Ly, 20 mg/kg/day. A group of untreated sham-operated rats was also studied. Ly markedly raised plasma renin activity (PRA) and aldosterone, and exerted more effective anti-albuminuric and renoprotective action than eplerenone. In Protocol 2, Nx rats remained untreated until Day 60, when they were divided into: Nx+V receiving vehicle; Nx+L treated with losartan, 50 mg/kg/day; Nx+L+Eple, given losartan and eplerenone, and Nx+L+Ly, given losartan and Ly. Treatments lasted for 90 days. As an add-on to losartan, Ly normalized blood pressure and albuminuria, and prevented CKD progression more effectively than eplerenone. This effect was associated with strong stimulation of PRA and aldosterone. Despite exhibiting higher affinity for the MR than either eplerenone or spironolactone, Ly caused no hyperkalemia. Ly may become a novel asset in the effort to detain the progression of CKD.
New variant and expression studies provide further insight into the genotype-phenotype correlation in YAP1-related developmental eye disorders
Authors: Holt R. , Ceroni F. , Bax D. A. , Broadgate S. , Diaz D. Gold , Santos C. , Gerrelli D. , Ragge N. K.
Published: August 2017

YAP1, which encodes the Yes-associated protein 1, is part of the Hippo pathway involved in development, growth, repair and homeostasis. Nonsense YAP1 mutations have been shown to co-segregate with autosomal dominantly inherited coloboma. Therefore, we screened YAP1 for variants in a cohort of 258 undiagnosed UK patients with developmental eye disorders, including anophthalmia, microphthalmia and coloboma. We identified a novel 1 bp deletion in YAP1 in a boy with bilateral microphthalmia and bilateral chorioretinal coloboma. This variant is located in the coding region of all nine YAP1 spliceforms, and results in a frameshift and subsequent premature termination codon in each. The variant is predicted to result in the loss of part of the transactivation domain of YAP1, and sequencing of cDNA from the patient shows it does not result in nonsense mediated decay. To investigate the role of YAP1 in human eye development, we performed in situ hybridisation utilising human embryonic tissue, and observed expression in the developing eye, neural tube, brain and kidney. These findings help confirm the role of YAP1 and the Hippo developmental pathway in human eye development and its associated anomalies and demonstrate its expression during development in affected organ systems.
Circulating CD40 and sCD40L Predict Changes in Renal Function in Subjects with Chronic Kidney Disease
Authors: Xie Jeffrey X. , Alderson Helen , Ritchie James , Kalra Philip A. , Xie Yanmei , Ren Kaili , Nguyen Hanh , Chen Tian , Brewster Pamela , Gupta Rajesh , Dworkin Lance D. , Malhotra Deepak , Cooper Christopher J. , Tian Jiang , Haller Steven T.
Published: August 2017

Soluble CD40 ligand (sCD40L) has been implicated in the development of renal injury. The CD40 receptor exists in a soluble form, sCD40R, and has been shown to function as a competitive antagonist against CD40 activation. We analyzed whether plasma levels of sCD40L and sCD40R predict changes in renal function in an all-cause chronic kidney disease (CKD) cohort. Stratification of subjects based on sCD40L and sCD40R individually, as well as in combination, demonstrated that sCD40L was directly associated with declines in estimated glomerular filtration rate (eGFR). sCD40R was negatively associated with declines in eGFR. Baseline characteristics following stratification, including systolic blood pressure, history of diabetes mellitus or peripheral vascular disease, primary renal disease classification, and angiotensin converting enzyme inhibitor or angiotensin receptor blocker usage were not significantly different. High sCD40L and low sCD40R were both found to be independent predictors of a decline in eGFR at 1-year follow-up (−7.57%, p = 0.014; −6.39%, p = 0.044). Our data suggest that circulating levels of sCD40L and sCD40R are associated with changes in renal function in patients with CKD. The CD40 decoy receptor, sCD40R, may serve as a potential therapeutic target to attenuate renal function decline.
Stimulation in primary and secondary metabolism by elevated carbon dioxide alters green tea quality in Camellia sinensis L
Authors: Li Xin , Zhang Lan , Ahammed Golam Jalal , Li Zhi-Xin , Wei Ji-Peng , Shen Chen , Yan Peng , Zhang Li-Ping , Han Wen-Yan
Published: August 2017

Rising CO2 concentration, a driving force of climate change, is impacting global food security by affecting plant physiology. Nevertheless, the effects of elevated CO2 on primary and secondary metabolism in tea plants (Camellia sinensis L.) still remain largely unknown. Here we showed that exposure of tea plants to elevated CO2 (800 µmol mol−1 for 24 d) remarkably improved both photosynthesis and respiration in tea leaves. Furthermore, elevated CO2 increased the concentrations of soluble sugar, starch and total carbon, but decreased the total nitrogen concentration, resulting in an increased carbon to nitrogen ratio in tea leaves. Among the tea quality parameters, tea polyphenol, free amino acid and theanine concentrations increased, while the caffeine concentration decreased after CO2 enrichment. The concentrations of individual catechins were altered differentially resulting in an increased total catechins concentration under elevated CO2 condition. Real-time qPCR analysis revealed that the expression levels of catechins and theanine biosynthetic genes were up-regulated, while that of caffeine synthetic genes were down-regulated in tea leaves when grown under elevated CO2 condition. These results unveiled profound effects of CO2 enrichment on photosynthesis and respiration in tea plants, which eventually modulated the biosynthesis of key secondary metabolites towards production of a quality green tea.
Enhancing NK cell-mediated cytotoxicity to cisplatin-resistant lung cancer cells via MEK/Erk signaling inhibition
Authors: Yang Li , Shen MingJing , Xu Li Jun , Yang Xiaodong , Tsai Ying , Keng Peter C. , Chen Yuhchyau , Lee Soo Ok
Published: August 2017

Major progress has been made clinically in inhibiting the programmed death receptor 1 (PD-1)/PD-L1 interaction to enhance T cell-mediated immune function, yet the effectiveness of anti-PD-L1/PD-1 agents in enhancing natural killer (NK) cell’s function remains largely unknown. Susceptibilities of cisplatin-resistant A549CisR and H157CisR cells vs. parental cells to the cytotoxic action of NK cells were examined. We found cisplatin-resistant cells more resistant to NK cell cytotoxicity than parental cells. There were constitutively higher expressions of PD-L1 in A549CisR and H157CisR cells than in parental cells in vitro, as well as in H157CisR cell-derived tumors than H157P cell-derived tumors. In contrast, we observed that the expression of PD-1 in NK cells was induced after co-culture with cisplatin-resistant cells. We also observed increased susceptibility of cisplatin-resistant cells to NK cell cytotoxicity when neutralizing antibody of PD-1 or PD-L1 was added. Further, we found that the NK group 2, member D (NKG2D) ligand levels were lower in A549CisR and H157CisR cells than in parental cells. Meanwhile, we discovered that the MEK/Erk signaling pathway played a significant role in this regulation, and the addition of a MEK/Erk pathway inhibitor significantly enhanced the PD-L1 Ab effect in enhancing NK cell cytotoxicity to cisplatin-resistant cells.
miR-12 and miR-124 contribute to defined early phases of long-lasting and transient memory
Authors: Michely Julia , Kraft Susanne , Müller Uli
Published: August 2017

MicroRNAs (miRNAs) are important epigenetic regulators of mRNA translation implicated in long-lasting synaptic plasticity and long-term memory (LTM). Since recent findings demonstrated a role of epigenetic regulation of gene expression in early memory phases we investigated whether epigenetic regulation by miRNAs also contributes to early memory phases. We used the olfactory associative learning paradigm in honeybees and addressed the contribution of miRNAs depending on the conditioning strength. We selected miR-12, miR-124, and miR-125 that have been implicated in processes of neuronal plasticity and analysed their contribution to non-associative and associative learning using miRNA inhibitors. Blocking miR-12, miR-124, or miR125 neither affects gustatory sensitivity nor habituation nor sensitization. Blocking the function of miR-12 and miR-124 during and shortly after 3-trial conditioning impairs different early memory phases. Although different, the function of miR-12 and miR-124 is also required for early phases of transient memory that is induced by 1-trial conditioning. Blocking miR-125 has no effect on early memory independent of the conditioning strength. These findings demonstrate that distinct miRNAs contribute to early phases of both, transient memories as well as long-lasting memories.
Inputs of humic fluorescent dissolved organic matter via submarine groundwater discharge to coastal waters off a volcanic island (Jeju, Korea)
Authors: Kim Jeonghyun , Kim Guebuem
Published: August 2017

The abundance of fluorescent dissolved organic matter (FDOM) in the surface ocean plays a critical role in the growth of marine microorganisms and corals by affecting the optical properties (i.e., the penetration of UV radiation) of seawater. In general, it is known that rivers are the main source of FDOM to surface ocean waters. Here, however, we show that the concentrations of FDOM in coastal seawater off a volcanic island, Jeju, Korea, are dependent primarily on submarine groundwater discharge (SGD). Based on a significant correlation between 222Rn and salinity in seawater, fresh groundwater was found to be the main source of groundwater as well as fresh water in the bay. The addition of dissolved organic carbon (DOC) and protein-like FDOM to the bay via SGD was generally negligible or negative. However, SGD enhanced the inventory of humic-like FDOM (FDOMH) in seawater by 2–3 times over all seasons, with conservative behavior of FDOMH in bay seawater. These results suggest that SGD-driven fluxes of FDOM regulate its inventory in seawater and consequently play a significant role in determining the optical properties of coastal waters off islands and associated coastal ecosystems (i.e., corals).
Atomic Force Microscopy Reveals the Dynamic Morphology of Fenestrations in Live Liver Sinusoidal Endothelial Cells
Authors: Zapotoczny B. , Szafranska K. , Owczarczyk K. , Kus E. , Chlopicki S. , Szymonski M.
Published: August 2017

Here, we report an atomic force microscopy (AFM)-based imaging method for resolving the fine nanostructures (e.g., fenestrations) in the membranes of live primary murine liver sinusoidal endothelial cells (LSECs). From data on topographical and nanomechanical properties of the selected cell areas collected within 1 min, we traced the dynamic rearrangement of the cell actin cytoskeleton connected with the formation or closing of cell fenestrations, both in non-stimulated LSECs as well as in response to cytochalasin B and antimycin A. In conclusion, AFM-based imaging permitted the near real-time measurements of dynamic changes in fenestrations in live LSECs.
Effects of disulfide bridges and backbone connectivity on water sorption by protein matrices
Authors: Kim Sang Beom , Singh Rakesh S. , Paul Prem K. C. , Debenedetti Pablo G.
Published: August 2017

Understanding the water sorption behavior of protein powders is important in applications such as the preservation of protein-based pharmaceuticals. Most globular proteins exhibit a characteristic sigmoidal water adsorption isotherm at ambient conditions. However, it is not well understood how water sorption behavior is influenced by intrinsic factors that are related to structural properties of proteins. We investigate computationally how structural constraints on proteins influence the water sorption isotherms of amorphous protein powders. Specifically, we study the effects of non-local disulfide linkages and backbone connectivity using pheromone ER-23 and lysozyme as model proteins. We find that non-local disulfide linkages can significantly restrict structural changes during hydration and dehydration, and this in turn greatly reduces the extent of hysteresis between the adsorption and desorption branches. Upon removing the backbone connectivity by breaking all peptide bonds in lysozyme, we find that the hysteresis shifts towards the lower humidity regime, and the water uptake capacity is significantly enhanced. We attribute these changes to the higher aggregation propensity of the constraint-free amino acids in dehydrated condition, and the formation of a spanning water network at high hydration levels.
Ultra-fast Hygrometer based on U-shaped Optical Microfiber with Nanoporous Polyelectrolyte Coating
Authors: Chen George Y. , Wu Xuan , Kang Yvonne Qiongyue , Yu Li , Monro Tanya M. , Lancaster David G. , Liu Xiaokong , Xu Haolan
Published: August 2017

Real-time measurement of the relative humidity of air has applications ranging from process control to safety. By using a microfiber form-factor, we demonstrate a miniature and fast-response hygrometer with the shortest-ever response time (3 ms). The sensor head consists of an optical microfiber of 10 µm diameter and 2 mm length configured to form a compact U-shaped probe, and functionalized with a polyelectrolyte multilayer coating of 1.0 bilayer. The sensing mechanism is primarily water-absorption-based optical loss. We have measured a response time of 3 ms and a recovery time of 36 ms. The sensitivity is as high as 0.4%/%RH, and the detection limit is as low as 1.6%RH. The maximum relative humidity is 99%RH, before reaching a recoverable dew-point.