bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyper-acidic fusion minipeptides escort the intrinsic antioxidative ability of the pattern recognition receptor CRP in non-animal organisms
Authors: Zhang Mengru , Liu Yanjuan , Liu Zhibin , Wang Jianmei , Gong Ming , Ge Hu , Li Xufeng , Yang Yi , Zou Zhurong
Published: February 2019

C-reactive protein (CRP) is widely used as a biomarker of inflammation. It plays important roles in innate immunity response as a member of pattern recognition receptors, by binding oxidation-specific epitopes including some intermediates of lipid oxidative chain reaction. The inferred antioxidative ability of CRP was ever demonstrated by only fewin vitroevidences, and needs to be clarified especiallyin vivo. Herein, we expressed human CRP in three representative non-animal organisms (Escherichia coli,Saccharomyces cerevisiae, and tobacco) inherently lacking the milieu for CRP signalling, and found CRP did possess an intrinsic antioxidative ability. Heterologous CRP could confer increased oxidative resistance in its recombinantE.coliand yeast cells and transgenic tobaccos. We also revealed a positive correlation between the antioxidative effect of CRP and its solubility. Only soluble CRP could exhibit distinct antioxidative activity, while the CRP aggregates might be instead toxic (probably pro-oxidative) to cells. Moreover, fusion with hyper-acidic minipeptides could remarkably improve CRP solubility, and meanwhile guarantee or enhance CRP antioxidative ability. These results not only provide a new insight for understanding the etiology of CRP-involved inflammations and diseases, and also endorse a potential of CRP biotechnological applications in developing new pharmaceutical therapies and improving plant oxidative resistance.
Key Role of the Ocean Western Boundary currents in shaping the Northern Hemisphere climate
Authors: Omrani Nour-Eddine , Ogawa Fumiaki , Nakamura Hisashi , Keenlyside Noel , Lubis Sandro W. , Matthes Katja
Published: February 2019

The individual impact of North Atlantic and Pacific Ocean Western Boundary Currents (OWBCs) on the tropospheric circulation has recently been studied in depth. However, their simultaneous role in shaping the hemisphere-scale wintertime troposphere/stratosphere-coupled circulation and its variability have not been considered. Through semi-idealized Atmospheric General-Circulation-Model experiments, we show that the North Atlantic and Pacific OWBCs jointly maintain and shape the wintertime hemispheric circulation and its leading mode of variability Northern Annular Mode (NAM). The OWBCs energize baroclinic waves that reinforce quasi-annular hemispheric structure in the tropospheric eddy-driven jetstreams and NAM variability. Without the OWBCs, the wintertime NAM variability is much weaker and its impact on the continental and maritime surface climate is largely insignificant. Atmospheric energy redistribution caused by the OWBCs acts to damp the near-surface atmospheric baroclinicity and compensates the associated oceanic meridional energy transport. Furthermore, the OWBCs substantially weaken the wintertime stratospheric polar vortex by enhancing the upward planetary wave propagation, and thereby affecting both stratospheric and tropospheric NAM-annularity. Whereas the overall impact of the extra-tropical OWBCs on the stratosphere results mainly from the Pacific, the impact on the troposphere results from both the Pacific and Atlantic OWBCs.
Analysis of the Antigenic Properties of Membrane Proteins of Mycobacterium tuberculosis
Authors: Li Haifeng , Liu Liguo , Zhang Wei-jia , Zhang Xiaobing , Zheng Jianhua , Li Li , Zhu Xiuyun , Yang Qianting , Zhang Mingxia , Liu Haiying , Chen Xinchun , Jin Qi
Published: February 2019

Tuberculosis (TB) is a continuing major threat to global health and a leading cause of death, particularly in developing countries. In this study, we aimed to identify a specific and sensitive diagnostic biomarker and develop a vaccine to prevent this disease. We investigated membrane proteins to reveal biomarkers in serum and peripheral blood mononuclear cells (PBMCs) obtained from TB patients. We employed Western blotting to evaluate serological immunoglobulin G levels, and Enzyme Linked Immunospot (ELISpot) to assess the antigen-specific cellular interferon-γ secretion from PBMCs after membrane protein stimulation. A total of 219 membrane proteins were identified, 52 exhibited at a higher levels than the 38-kDa prositive control. Of these 18 exhibited reacted ratios above 1, especially Rv1111c (427–981), with a ratios at 3.38. Accuracy and sensitivity were markedly higher for the top two antigen candidates, Rv0232 and Rv1115, after two rounds of ELISpot tests than ESAT-6 in the commercial kit (42.15 and 43.62%, respectively). These two proteins were administered to mice to detect whether they acted as effective antigens in vivo. These data provide a comprehensive view of the membranes involved in humoural and cellular immune responses that may be used as biomarkers for TB and candidates for a vaccine.
Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae
Authors: Kasari Villu , Margus Tõnu , Atkinson Gemma C. , Johansson Marcus J. O. , Hauryliuk Vasili
Published: February 2019

In addition to the standard set of translation factors common in eukaryotic organisms, protein synthesis in the yeast Saccharomyces cerevisiae requires an ABCF ATPase factor eEF3, eukaryotic Elongation Factor 3. eEF3 is an E-site binder that was originally identified as an essential factor involved in the elongation stage of protein synthesis. Recent biochemical experiments suggest an additional function of eEF3 in ribosome recycling. We have characterised the global effects of eEF3 depletion on translation using ribosome profiling. Depletion of eEF3 results in decreased ribosome density at the stop codon, indicating that ribosome recycling does not become rate limiting when eEF3 levels are low. Consistent with a defect in translation elongation, eEF3 depletion causes a moderate redistribution of ribosomes towards the 5′ part of the open reading frames. We observed no E-site codon- or amino acid-specific ribosome stalling upon eEF3 depletion, supporting its role as a general elongation factor. Surprisingly, depletion of eEF3 leads to a relative decrease in P-site proline stalling, which we hypothesise is a secondary effect of generally decreased translation and/or decreased competition for the E-site with eIF5A.
Rapalog resistance is associated with mesenchymal-type changes in Tsc2-null cells
Authors: Valianou Matthildi , Filippidou Natalia , Johnson Daniel L. , Vogel Peter , Zhang Erik Y. , Liu Xiaolei , Lu Yiyang , Yu Jane J. , Bissler John J. , Astrinidis Aristotelis
Published: February 2019

Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) are caused by inactivating mutations in TSC1 or TSC2, leading to mTORC1 hyperactivation. The mTORC1 inhibitors rapamycin and analogs (rapalogs) are approved for treating of TSC and LAM. Due to their cytostatic and not cytocidal action, discontinuation of treatment leads to tumor regrowth and decline in pulmonary function. Therefore, life-long rapalog treatment is proposed for the control of TSC and LAM lesions, which increases the chances for the development of acquired drug resistance. Understanding the signaling perturbations leading to rapalog resistance is critical for the development of better therapeutic strategies. We developed the first Tsc2-null rapamycin-resistant cell line, ELT3-245, which is highly tumorigenic in mice, and refractory to rapamycin treatment. In vitro ELT3-245 cells exhibit enhanced anchorage-independent cell survival, resistance to anoikis, and loss of epithelial markers. A key alteration in ELT3-245 is increased β-catenin signaling. We propose that a subset of cells in TSC and LAM lesions have additional signaling aberrations, thus possess the potential to become resistant to rapalogs. Alternatively, when challenged with rapalogs TSC-null cells are reprogrammed to express mesenchymal-like markers. These signaling changes could be further exploited to induce clinically-relevant long-term remissions.
High-resolution atmospheric-pressure MALDI mass spectrometry imaging workflow for lipidomic analysis of late fetal mouse lungs
Authors: Garikapati Vannuruswamy , Karnati Srikanth , Bhandari Dhaka Ram , Baumgart-Vogt Eveline , Spengler Bernhard
Published: February 2019

Mass spectrometry imaging (MSI) provides label-free, non-targeted molecular and spatial information of the biomolecules within tissue. Lipids play important roles in lung biology, e.g. as surfactant, preventing alveolar collapse during normal and forced respiration. Lipidomic characterization of late fetal mouse lungs at day 19 of gestation (E19) has not been performed yet. In this study we employed high-resolution atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionization MSI for the lipidomic analysis of E19 mouse lungs. Molecular species of different lipid classes were imaged in E19 lung sections at high spatial and mass resolution in positive- and negative-ion mode. Lipid species were characterized based on accurate mass and on-tissue tandem mass spectrometry. In addition, a dedicated sample preparation protocol, homogenous deposition of matrices on tissue surfaces and data processing parameters were optimized for the comparison of signal intensities of lipids betweendifferenttissue sections of E19 lungs of wild type andPex11β-knockout mice. Our study provides lipid information of E19 mouse lungs, optimized experimental and data processing strategies for the direct comparison of signal intensities of metabolites (lipids) among the tissue sections from MSI experiments. To best of our knowledge, this is the first MSI and lipidomic study of E19 mouse lungs.
MiR-494 acts as a tumor promoter by targeting CASP2 in non-small cell lung cancer
Authors: Zhang Qiao , Li Yan , Zhao Mei , Lin Hong , Wang Wenjie , Li Dongdong , Cui Wei , Zhou Caihong , Zhong Jialing , Huang Changzhi
Published: February 2019

MiR-494 plays an important role in several types of human cancers, including non-small cell lung cancer (NSCLC). Although the role of miR-494 has been investigated in several studies, the expression profile and underlying mechanism are still poorly understood. In this study, we found that overexpression of miR-494 promoted the proliferation and colony formation of NSCLC cells and reduced their sensitivity to cisplatin-induced apoptosis. By using microarray and Dual luciferase reporter assays, we further showed that caspase-2 (CASP2) is a functional target of miR-494, and the expression of CASP2 is inversely associated with miR-494 in vitro. In addition, miR-494 promoted the proliferation and colony formation of NSCLC cells and reduced their sensitivity to cisplatin-induced apoptosis by targeting CASP2. Therefore, our results suggest that miR-494 plays an oncomiR role in NSCLC cells and may be a candidate biomarker for malignant transformation and a therapeutic target of NSCLC.
Improving lupeol production in yeast by recruiting pathway genes from different organisms
Authors: Qiao Weibo , Zhou Zilin , Liang Qin , Mosongo Isidore , Li Changfu , Zhang Yansheng
Published: February 2019

Lupeol is a pentacyclic triterpene that shows a variety of pharmacological properties. Compared to engineering the production of sesquiterpenes and diterpenes, it is much more challenging to engineer the biosynthesis of triterpenes in microbial platforms. This study showed our efforts on engineering the triterpene pathway in Escherichia coli and Saccharomyces cerevisiae cells by recruiting the codon-optimized three lupeol pathway genes from different organisms. By comparing their activities with their respective counterparts, the squalene synthase from Thermosynechococcus elongates (tSQS), the squalene epoxidase from Rattus norvegicus (rSE) and the lupeol synthase from Olea europaea (OeLUP) were introduced into E. coli BL21(DE3), a break-through from zero was observed for lupeol biosynthesis in a prokaryotic host. We also assessed the lupeol pathway under two different yeast backgrounds-WAT11 and EPY300, and have found that the engineered strains based on EPY300, named ECHHOe, processed the best lupeol-producing ability with the maximum lupeol titer being 200.1 mg l−1 at 30 °C in a 72 h-flask culture, which so far was the highest amount of lupeol obtained by a microbial system and provides a basis for further industrial application of lupeol in the future.
Dynamic protein changes in the perihaemorrhagic zone of Surgically Treated Intracerebral Haemorrhage Patients
Authors: Tobieson Lovisa , Ghafouri Bijar , Zsigmond Peter , Rossitti Sandro , Hillman Jan , Marklund Niklas
Published: February 2019

The secondary injury cascades exacerbating the initial brain injury following intracerebral haemorrhage (ICH) are incompletely understood. We used dual microdialysis (MD) catheters placed in the perihaemorrhagic zone (PHZ) and in seemingly normal cortex (SNX) at time of surgical ICH evacuation in ten patients (range 26–70 years). Routine interstitial MD markers (including glucose and the lactate/pyruvate ratio) were analysed and remaining microdialysate was analysed by two-dimensional gel electrophoresis (2-DE) and nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS). Two time intervals were analysed; median 2–10 hours post-surgery (time A) and median 68–76 hours post-ICH onset (time B). Using 2-DE, we quantified 232 ± 31 different protein spots. Two proteins differed between the MD catheters at time A, and 12 proteins at time B (p < 0.05). Thirteen proteins were significantly altered between time A and time B in the SNX and seven proteins in the PHZ, respectively. Using nLC-MS/MS ca 800 proteins were identified out of which 76 were present in all samples. At time A one protein was upregulated and two downregulated, and at time B, seven proteins were upregulated, and four downregulated in the PHZ compared to the SNX. Microdialysis-based proteomics is feasible for study of secondary injury mechanisms and discovery of biomarkers after ICH.
Control of Multiferroic properties in BiFeO3 nanoparticles
Authors: Carranza-Celis Diego , Cardona-Rodríguez Alexander , Narváez Jackeline , Moscoso-Londono Oscar , Muraca Diego , Knobel Marcelo , Ornelas-Soto Nancy , Reiber Andreas , Ramírez Juan Gabriel
Published: February 2019

BiFeO3 (BFO) nanoparticles (NPs) were synthesized using the sol-gel method at different calcination temperatures from 400 °C to 600 °C. XRD studies have confirmed that all BFO NPs show distorted rhombohedral crystals that match the R3c space group. We found evidence of local structural strain that develops with increasing particle size as suggested by TEM and Raman spectroscopy measurements. Magnetic measurements suggest that NPs have two distinct regimes: a ferromagnetic-like one at low temperatures and a superparamagnetic-like one at room temperature. The crossover temperature increases with NPs size, suggesting a size-dependent blocking magnetic regime. Similarly, local piezoelectric measurements at room temperature in single NP have confirmed a ferroelectric order with a NP size-dependent d33 coefficient. An analysis of both the ferroelectric and the magnetic results suggest that ferromagnetism and ferroelectricity coexist at room temperature in NPs. Our results lead to the possibility of tailoring the ferroic order in multifunctional materials by means of NP size.
Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking
Authors: Martin H. Christian , Ibáñez Roberto , Nothias Louis-Félix , Boya P. Cristopher A. , Reinert Laura K. , Rollins-Smith Louise A. , Dorrestein Pieter C. , Gutiérrez Marcelino
Published: February 2019

Amphibian populations worldwide have declined and in some cases become extinct due to chytridiomycosis, a pandemic disease caused by the fungus Batrachochytrium dendrobatidis; however, some species have survived these fungal epidemics. Previous studies have suggested that the resistance of these species is due to the presence of cutaneous bacteria producing antifungal metabolites. As our understanding of these metabolites is still limited, we assessed the potential of such compounds against human-relevant fungi such as Aspergillus. In this work we isolated 201 bacterial strains from fifteen samples belonging to seven frog species collected in the highlands of Panama and tested them against Aspergillus fumigatus. Among the 29 bacterial isolates that exhibited antifungal activity, Pseudomonas cichorii showed the greatest inhibition. To visualize the distribution of compounds and identify them in the inhibition zone produced by P. cichorii, we employed MALDI imaging mass spectrometry (MALDI IMS) and MS/MS molecular networking. We identified viscosin and massetolides A, F, G and H in the inhibition zone. Furthermore, viscosin was isolated and evaluated in vitro against A. fumigatus and B. dendrobatidis showing MIC values of 62.50 µg/mL and 31.25 µg/mL, respectively. This is the first report of cyclic depsipeptides with antifungal activity isolated from frog cutaneous bacteria.
Elucidating the Contribution of Skeletal Muscle Ion Channels to Amyotrophic Lateral Sclerosis in search of new therapeutic options
Authors: Camerino Giulia Maria , Fonzino Adriano , Conte Elena , De Bellis Michela , Mele Antonietta , Liantonio Antonella , Tricarico Domenico , Tarantino Nancy , Dobrowolny Gabriella , Musarò Antonio , Desaphy Jean-Francois , De Luca Annamaria , Pierno Sabata
Published: February 2019

The discovery of pathogenetic mechanisms is essential to identify new therapeutic approaches in Amyotrophic Lateral Sclerosis (ALS). Here we investigated the role of the most important ion channels in skeletal muscle of an ALS animal model (MLC/SOD1G93A) carrying a mutated SOD1 exclusively in this tissue, avoiding motor-neuron involvement. Ion channels are fundamental proteins for muscle function, and also to sustain neuromuscular junction and nerve integrity. By a multivariate statistical analysis, using machine learning algorithms, we identified the discriminant genes in MLC/SOD1G93A mice. Surprisingly, the expression of ClC-1 chloride channel, present only in skeletal muscle, was reduced. Also, the expression of Protein Kinase-C, known to control ClC-1 activity, was increased, causing its inhibition. The functional characterization confirmed the reduction of ClC-1 activity, leading to hyperexcitability and impaired relaxation. The increased expression of ion channel coupled AMPA-receptor may contribute to sustained depolarization and functional impairment. Also, the decreased expression of irisin, a muscle-secreted peptide protecting brain function, may disturb muscle-nerve connection. Interestingly, the in-vitro application of chelerythrine or acetazolamide, restored ClC-1 activity and sarcolemma hyperexcitability in these mice. These findings show that ion channel function impairment in skeletal muscle may lead to motor-neuron increased vulnerability, and opens the possibility to investigate on new compounds as promising therapy.
A transgenic inducible GFP extracellular-vesicle reporter (TIGER) mouse illuminates neonatal cortical astrocytes as a source of immunomodulatory extracellular vesicles
Authors: Neckles Victoria N. , Morton Mary C. , Holmberg Jennie C. , Sokolov Aidan M. , Nottoli Timothy , Liu Don , Feliciano David M.
Published: February 2019

Extracellular vesicles (EVs) are cellular derived particles found throughout the body in nearly all tissues and bodily fluids. EVs contain biological molecules including small RNAs and protein. EVs are proposed to be transferred between cells, notably, cells of the immune system. Tools that allow for in vivo EV labeling while retaining the ability to resolve cellular sources and timing of release are required for a full understanding of EV functions. Fluorescent EV fusion proteins are useful for the study of EV biogenesis, release, and identification of EV cellular recipients. Among the most plentiful and frequently identified EV proteins is CD9, a tetraspanin protein. A transgenic mouse containing a CRE-recombinase inducible CAG promoter driven CD9 protein fused to Turbo-GFP derived from the copepod Pontellina plumata was generated as an EV reporter. The transgenic inducible GFP EV reporter (TIGER) mouse was electroporated with CAG-CRE plasmids or crossed with tamoxifen inducible CAG-CRE-ERT2 or nestin-CRE-ERT2 mice. CD9-GFP labeled cells included glutamine synthetase and glial fibrillary acidic protein positive astrocytes. Cortical astrocytes released ~136 nm EVs that contained CD9. Intraventricular injected EVs were taken up by CD11b/IBA1 positive microglia surrounding the lateral ventricles. Neonatal electroporation and shRNA mediated knockdown of Rab27a in dorsal subventricular zone NSCs and astrocytes increased the number of CD11b/IBA1 positive rounded microglia. Neonatal astrocyte EVs had a unique small RNA signature comprised of morphogenic miRNAs that induce microglia cytokine release. The results from this study demonstrate that inducible CD9-GFP mice will provide the EV community with a tool that allows for EV labeling in a cell-type specific manner while simultaneously allowing in vivo experimentation and provides evidence that EVs are required immunomodulators of the developing nervous system.
Quantitative Analysis of Objective Forward Scattering and Its Relevant Factors in Eyes with Cataract
Authors: Kamiya Kazutaka , Fusako Fujimura , Takushi Kawamorita , Takahashi Masahide , Ando Wakako , Iida Yoshihiko , Shoji Nobuyuki
Published: February 2019

This study was aimed to quantitatively assess objective forward scattering and its relevant factors in eyes having cataract. Our study comprised 192 eyes of 192 patients (mean age, 71.3 ± 9.2 (standard deviation) years) who have cataract formation for surgical consultation. We determined uncorrected and corrected distance visual acuities (UDVA and CDVA), manifest refraction, the grade of nuclear sclerosis, objective scattering index (OSI) with the OQAS II (Visiometrics, Spain), log(s) with the C-Quant (Oculus, Germany), and ocular higher-order aberrations (HOAs) using the wavefront sensor (KR-1W, Topcon, Japan). The mean OSI was 5.11 ± 3.19 (0.90 to 20.90). We found explanatory variables relevant to the OSI to be, logMAR CDVA (p < 0.0001, partial regression coefficient B = 5.917) and log(s) (p = 0.0006, B = 0.911) (adjusted R2 = 0.333), in order of influence. No significant correlation was found with other clinical factors such as gender, age, manifest refraction, UDVA, ocular HOAs, or nuclear sclerosis. Eyes with worse CDVA and higher log(s) are more predisposed to show higher OSI in cataractous eyes. It is suggested that objective forward scattering was associated, not only with CDVA, but also with subjective forward scattering, in cataractous subjects.
Evaluation of dental arch dimensions in 12 year-old Vietnamese children - A cross-sectional study of 4565 subjects
Authors: Dung Truong Manh , Ngoc Vo Truong Nhu , Hiep Nguyen Hung , Khoi Truong Dinh , Xiem Vu Van , Chu-Dinh Thien , Cieslar-Pobuda Artur , Stoufi Eleana , Show Pau Loke , Tao Yang , Bac Nguyen Duy , Van Ba Nguyen , Le Quynh-Anh , Pham Van-Huy , Chu Dinh-Toi
Published: February 2019

This study aimed to define the width and length of the dental arch in 12-year-old Vietnamese children, and to elucidate differences between genders and among ethnic groups. A cross-sectional study was conducted in 4565 12 years-old children from the 4 major ethnic groups in Vietnam (Kinh, Muong, Thai, and Tay), with a healthy and full set of 28 permanent teeth that had never had any orthodontic treatment and with no reconstructive materials at the measured points. The mean variables in all subjects were 36.39 mm for upper inter-canine width; 46.88 mm for upper inter-first molar width; 59.43 mm for upper inter-second molar width; 10.41 mm for upper anterior length; 32.15 mm for upper posterior length 1; 45.52 mm for upper posterior length 2; 28.31 mm for lower inter-canine width; 41.63 mm for lower inter-first molar width; 54.57 mm for lower inter-second molar width (LM2W); 7.06 mm for lower anterior length (LAL); 26.87 mm for lower posterior length 1 (LP1L); and 41.29 mm for lower posterior length 2. Significant differences in these parameters between genders were found in all ethnic groups, except for LAL in the Kinh and Thai groups, and LP1L in the Tay group. Significant ethnic differences were also found in almost all parameters except LM2W in both males and females. Taken together, the representative sizes of dental arches of 12-year-old Vietnamese children have been defined. Our data indicate that there are some variations in dental arch dimensions among ethnic groups and between genders.
Transcriptome analysis of two cultivars of tobacco in response to Cucumber mosaic virus infection
Authors: Liu Dan , Zhao Qiang , Cheng Yazeng , Li Dandan , Jiang Caihong , Cheng Lirui , Wang Yuanying , Yang Aiguo
Published: February 2019

Cucumber mosaic virus (CMV) is among the most important plant virus infections, inducing a variety of disease symptoms. However, the molecular mechanisms underlying plant responses to CMV infection remain poorly understood. In this study, we performed RNA sequencing analysis of tolerant (Taiyan8) and susceptible (NC82) tobacco cultivars on CMV-infected plants, using mock-inoculated plants as a control. The propagation of CMV in inoculated leaves did not show obvious difference between two cultivars, whereas virus accumulation in systemic leaves of Taiyan8 was smaller than those of NC82 at the same time point. We observed 765 and 1,011 differentially expressed genes (DEGs) in Taiyan8 and NC82, respectively, in CMV-inoculated leaves. DEGs related to reactive oxygen species, salicylic acid signal transduction, and plant–pathogen interaction were upregulated or downregulated in Taiyan8, which indicates that defense response pathways to CMV were activated in the tolerant cultivar. In addition, we identified several DEGs related to disease defense and stress resistance showing opposing expression patterns in the two cultivars. Our comparative transcriptome analysis will improve our understanding of the mechanisms of CMV tolerance in plants, and will be of great importance in the molecular breeding of CMV- tolerant genotypes.
Identification of S-nitrosylation sites based on multiple features combination
Authors: Li Taoying , Song Runyu , Yin Qian , Gao Mingyue , Chen Yan
Published: February 2019

Protein S-nitrosylation (SNO) is a typical reversible, redox-dependent and post-translational modification that involves covalent modification of cysteine residues with nitric oxide (NO) for the thiol group. Numerous experiments have shown that SNO plays a major role in cell function and pathophysiology. In order to rapidly analysis the big sets of data, the computing methods for identifying the SNO sites are being considered as necessary auxiliary tools. In this study, multiple features including Parallel correlation pseudo amino acid composition (PC-PseAAC), Basic kmer1 (kmer1), Basic kmer2 (kmer2), General parallel correlation pseudo amino acid composition (PC-PseAAC_G), Adapted Normal distribution Bi-Profile Bayes (ANBPB), Double Bi-Profile Bayes (DBPB), Bi-Profile Bayes (BPB), Incorporating Amino Acid Pairwise (IAAPair) and Position-specific Tri-Amino Acid Propensity(PSTAAP) were employed to extract the sequence information. To remove information redundancy, information gain (IG) was applied to evaluate the importance of amino acids, which is the information entropy of class after subtracting the conditional entropy for the given amino acid. The prediction performance of the SNO sites was found to be best by using the cross-validation and independent tests. In addition, we also calculated four commonly used performance measurements, i.e. Sensitivity (Sn), Specificity (Sp), Accuracy (Acc), and the Matthew’s Correlation Coefficient (MCC). For the training dataset, the overall Acc was 83.11%, the MCC was 0.6617. For an independent test dataset, Acc was 73.17%, and MCC was 0.3788. The results indicate that our method is likely to complement the existing prediction methods and is a useful tool for effective identification of the SNO sites.
Thermal conductivity enhancement in electrospun poly(vinyl alcohol) and poly(vinyl alcohol)/cellulose nanocrystal composite nanofibers
Authors: Park Yeongcheol , You Myungil , Shin Jihoon , Ha Sumin , Kim Dukeun , Heo Min Haeng , Nah Junghyo , Kim Yoong Ahm , Seol Jae Hun
Published: February 2019

The thermal conductivity enhancement of neat poly(vinyl alcohol) and poly(vinyl alcohol) (PVA)/cellulose nanocrystal (CNC) composite was attempted via electrospinning. The suspended microdevice technique was applied to measure the thermal conductivity of electrospun nanofibers (NFs). Neat PVA NFs and PVA/CNC NFs with a diameter of approximately 200 nm showed thermal conductivities of 1.23 and 0.74 W/m-K, respectively, at room temperature, which are higher than that of bulk PVA by factors of 6 and 3.5, respectively. Material characterization by Fourier transform infrared spectroscopy, differential scanning calorimetry, and thermogravimetric analysis confirmed that the thermal conductivity of the PVA/CNC NFs was enhanced by the reinforcement of their backbone rigidity, while that of the neat PVA NFs was attributed to the increase in their crystallinity that occurred during the electrospinning.
Fabry–Pérot resonances and a crossover to the quantum Hall regime in ballistic graphene quantum point contacts
Authors: Ahmad Nurul Fariha , Komatsu Katsuyoshi , Iwasaki Takuya , Watanabe Kenji , Taniguchi Takashi , Mizuta Hiroshi , Wakayama Yutaka , Hashim Abdul Manaf , Morita Yoshifumi , Moriyama Satoshi , Nakaharai Shu
Published: February 2019

We report on the observation of quantum transport and interference in a graphene device that is attached with a pair of split gates to form an electrostatically-defined quantum point contact (QPC). In the low magnetic field regime, the resistance exhibited Fabry–Pérot (FP) resonances due to np’n(pn’p) cavities formed by the top gate. In the quantum Hall (QH) regime with a high magnetic field, the edge states governed the phenomena, presenting a unique condition where the edge channels of electrons and holes along a p–n junction acted as a solid-state analogue of a monochromatic light beam. We observed a crossover from the FP to QH regimes in ballistic graphene QPC under a magnetic field with varying temperatures. In particular, the collapse of the QH effect was elucidated as the magnetic field was decreased. Our high-mobility graphene device enabled observation of such quantum coherence effects up to several tens of kelvins. The presented device could serve as one of the key elements in future electronic quantum optic devices.
Novel anticoagulants versus vitamin K antagonists for cardioversion of non- valvular atrial fibrillation – a meta-analysis of more than 17000 patients
Authors: Mincu Raluca Ileana , Mahabadi Amir Abbas , Totzeck Matthias , Rassaf Tienush
Published: February 2019

Non-vitamin K antagonist oral anticoagulants (NOACs) have proven a favorable risk-benefit profile compared to vitamin K antagonists (VKAs) for preventing stroke and systemic embolism in patients with non-valvular atrial fibrillation (AF), but actual data are not sufficiently powered to extend this profile on patients with AF that undergo cardioversion. We aimed to compare outcomes after cardioversion of AF under NOACs vs. VKAs. We systematically searched Pubmed, Cochrane, SCOPUS, and Web of Science databases for studies published until October 2017. A total of 17506 patients from 11 studies were included. Treatment with NOACs was associated with similar relative risks (RR) of stroke and systemic embolism, hemorrhagic stroke, myocardial infarction, cardiovascular death, and all cause death compared to VKAs treatment. The RR of ischemic stroke was lower in the NOACs group. The risk of major bleeding was similar across treatment groups. Treatment with NOACs in patients with non-valvular AF that undergo cardioversion seems to be as safe and effective as the use of classical VKAs, with a better profile for ischemic stroke. Clinical Trial Registration: PROSPERO Registry, CRD42018086181 https://www.crd.york.ac.uk/prospero/display_record.php?RecordID = 86181.
De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing
Authors: Taheri Sima , Abdullah Thohirah Lee , Rafii M. Y. , Harikrishna Jennifer Ann , Werbrouck Stefaan P. O. , Teo Chee How , Sahebi Mahbod , Azizi Parisa
Published: February 2019

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, ‘Chiang Mai Pink’ and ‘UB Snow 701’, to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.
Identification and Characterization of a Dominant Sulfolane-Degrading Rhodoferax sp. via Stable Isotope Probing Combined with Metagenomics
Authors: Kasanke Christopher Paul , Collins R. Eric , Leigh Mary Beth
Published: February 2019

Sulfolane is an industrial solvent and emerging organic contaminant affecting groundwater around the world, but little is known about microbes capable of biodegrading sulfolane or the pathways involved. We combined DNA-based stable isotope probing (SIP) with genome-resolved metagenomics to identify microorganisms associated with sulfolane biodegradation in a contaminated subarctic aquifer. In addition to 16S rRNA gene amplicon sequencing, we performed shotgun metagenomics on the 13C-labeled DNA to obtain functional and taxonomic information about the active sulfolane-degrading community. We identified the primary sulfolane degrader, comprising ~85% of the labeled community in the amplicon sequencing dataset, as closely related to Rhodoferax ferrireducens strain T118. We obtained a 99.8%-complete metagenome-assembled genome for this strain, allowing us to identify putative pathways of sulfolane biodegradation. Although the 4S dibenzothiophene desulfurization pathway has been proposed as an analog for sulfolane biodegradation, we found only a subset of the required genes, suggesting a novel pathway specific to sulfolane. DszA, the enzyme likely responsible for opening the sulfolane ring structure, was encoded on both the chromosome and a plasmid. This study demonstrates the power of integrating DNA-SIP with metagenomics to characterize emerging organic contaminant degraders without culture bias and expands the known taxonomic distribution of sulfolane biodegradation.
Asymmetric paralog evolution between the “cryptic” gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4
Authors: Feiner Nathalie , Motone Fumio , Meyer Axel , Kuraku Shigehiro
Published: February 2019

The vertebrate gene repertoire is characterized by “cryptic” genes whose identification has been hampered by their absence from the genomes of well-studied species. One example is the Bmp16 gene, a paralog of the developmental key genes Bmp2 and -4. We focus on the Bmp2/4/16 group of genes to study the evolutionary dynamics following gen(om)e duplications with special emphasis on the poorly studied Bmp16 gene. We reveal the presence of Bmp16 in chondrichthyans in addition to previously reported teleost fishes and reptiles. Using comprehensive, vertebrate-wide gene sampling, our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution. We confirm that Bmp16 genes were lost independently in at least three lineages (mammals, archelosaurs and amphibians) and report that they have elevated rates of sequence evolution. This finding agrees with their more “flexible” deployment during development; while Bmp16 has limited embryonic expression domains in the cloudy catshark, it is broadly expressed in the green anole lizard. Our study illustrates the dynamics of gene family evolution by integrating insights from sequence diversification, gene repertoire changes, and shuffling of expression domains.
Metabolite-based mutualism enhances hydrogen production in a two-species microbial consortium
Authors: Wang Shaojie , Tang Hongzhi , Peng Fei , Yu Xijia , Su Haijia , Xu Ping , Tan Tianwei
Published: February 2019

Sustainable hydrogen production from renewable and low-cost substrates is very important to mitigate environmental and energy-related issues. Microbial consortia are promising for diverse bioenergy and environmental applications, yet microbial interactions are not fully understood. Here, we present comprehensive investigation on how two species in an artificial microbial consortium, consisting of Bacillus cereus A1 and Brevundimonas naejangsanensis B1, mutually cooperate to achieve an overall enhancement in hydrogen production and starch utilization. In this consortium, strains A1 and B1 secrete α-amylase and glucoamylase that are functionally complementary in starch hydrolysis. Moreover, strain A1 converts starch into lactate as a carbon source and electron donor, supporting the cell growth and hydrogen generation of strain B1. In return, strain B1 produces formate as an electron shuttle to strain A1 to enhance hydrogen production. The co-culture re-directs the overall metabolic flux, facilitates the cell growth, and up-regulates the key genes of hydrogen production and starch hydrolysis.
Crystal-engineering and luminescence studies of 1,3,5-tris(3-pyridylethynyl)benzene or 1,3,5-tris(4-pyridylethynyl)benzene with copper(i) iodides
Authors: Tzeng Biing-Chiau , Lin Jun-Fu
Published: February 2019

The interlocking of 1-D frameworks into the 28-membered rings of the adjacent chains generates a novel 1-D (1-D → 1-D) polyrotaxane framework of 3.
Total generalized variation regularization for multi-modal electron tomography
Authors: Huber Richard , Haberfehlner Georg , Holler Martin , Kothleitner Gerald , Bredies Kristian
Published: February 2019

Multi-modal TGV reconstruction of 3D EDX elemental maps.
Large Kondo effect in assemblies of Au nanoparticles linked with alkanedithiol electron bridges
Authors: Tie Monique , Gravelsins Steven , Niewczas Marek , Dhirani Al-Amin
Published: February 2019

The controllable, functional architectures of nanostructures represent a target of opportunity as a versatile means for introducing localized, magnetic impurities (unpaired spins) and generating the Kondo effect in nanostructure assemblies.
Multifunctional Zn doped hollow mesoporous silica/polycaprolactone electrospun membranes with enhanced hair follicle regeneration and antibacterial activity for wound healing
Authors: Zhang Yu , Chang Mengling , Bao Feng , Xing Min , Wang Endian , Xu Qing , Huan Zhiguang , Guo Feng , Chang Jiang
Published: February 2019

Hollow CiH-HMZS nanospheres exert a synergistic antibacterial effect, stimulate cell migration and angiogenesis, and enhance hair follicle regeneration.
Recent advances in the asymmetric synthesis of pharmacology-relevant nitrogen heterocyclesviastereoselective aza-Michael reactions
Authors: Vinogradov Maxim G. , Turova Olga V. , Zlotin Sergei G.
Published: February 2019

In this review, recent applications of a stereoselective aza-Michael reaction for asymmetric synthesis of naturally occurringN-containing heterocyclic scaffolds and their usefulness to pharmacology are summarized.
Synthesis of high molecular weight isobutylene-α-methylstyrene copolymers containing alkenyl groups with a half sandwich scandium initiator system under mild conditions
Authors: Yang Ke , Niu Hui , Yu Hui , Dong Jinghan , Wang Jing , Yu Jialin , Shen Kaihua , Li Yang
Published: February 2019

Copolymerizations of isobutylene and two alkenyl functionalized α-MeSt derivatives respectively, catalyzed by [(C5Me4SiMe3)Sc(CH2SiMe3)2THF], at −35 °C produced high Mn random copolymers with pendant alkenyl groups.
Direct access to 2-aryl substituted pyrrolinium salts for carbon centre based radicals without pyrrolidine-2-ylidene alias cyclic(alkyl)(amino)carbene (CAAC) as a precursor
Authors: Mandal Debdeep , Sobottka Sebastian , Dolai Ramapada , Maiti Avijit , Dhara Debabrata , Kalita Pankaj , Narayanan Ramakirushnan Suriya , Chandrasekhar Vadapalli , Sarkar Biprajit , Jana Anukul
Published: February 2019

A new strategy to synthesise 2-substituted pyrrolinium salts.
Strain effects determine the performance of artificial allosteric systems: calixarenes as models
Authors: Schneider Hans-Jörg
Published: February 2019

Many published allosteric systems show a small efficiency, with a limited concentration range and slow response. As illustrated with calixarenes and some other allosteric systems, strain energy differences ΔGS between equilibrating conformers and the interconversion transition ΔG# determine the performance.
A CO2 photoreduction heterogeneous cobalt-based cocatalyst constructed via in situ electrostatic adsorption deposition
Authors: Li Qinghe , Lin Feng , Liu Feng , Wang Xinchen
Published: February 2019

The photocatalytic reduction of carbon dioxide to carbon monoxide could be achieved through the use of a cobalt based heterogeneous cocatalyst constructed via an in situ electrostatic adsorption deposition method.
An Sn doped 1T–2H MoS2 few-layer structure embedded in N/P co-doped bio-carbon for high performance sodium-ion batteries
Authors: Zeng Lingxing , Luo Fenqiang , Xia Xinshu , Yang Min-Quan , Xu Lihong , Wang Jianbiao , Feng Xiaoshan , Qian Qingrong , Wei Mingdeng , Chen Qinghua
Published: February 2019

A facile route for fabrication of an Sn doped 1T–2H MoS2 few-layer structure embedded in N/P co-doped bio-carbon is initially developed using natural chlorella as an adsorbent and a nanoreactor.
The vibrational CD spectra of propylene oxide in liquid xenon: a proof-of-principle CryoVCD study that challenges theory
Authors: Kreienborg Nora M. , Bloino Julien , Osowski Tobias , Pollok Corina H. , Merten Christian
Published: February 2019

Propylene oxide (PO) is the ideal candidate to benchmark both new experimental and theoretical approaches. Herein it is used to demonstrate the feasibility of measurements of VCD spectra in liquid rare gases (CryoVCD) and to test recent theoretical developments in the prediction of anharmonic IR and VCD spectra.
Simple and reactive Ir(i) N-heterocyclic carbene complexes for alkyne activation
Authors: Gatus Mark R. D. , Pernik Indrek , Tompsett Joshua A. , Binding Samantha C. , Peterson Matthew B. , Messerle Barbara A.
Published: February 2019

Two simple unsymmetrical monometallic Ir(i) complexes with an N-heterocyclic carbene ligand were effective catalysts for C–X (X = N or O) and Si–N bond formation reactions compared to an analogous Ir(i) bimetallic complex.
Effectively immobilizing lead through a melanotekite structure using low-temperature glass-ceramic sintering
Authors: Zhou Ying , Liao Changzhong , Zhou Zhengyuan , Chang ChungKai , Shih Kaimin
Published: February 2019

An energy-efficient and reliable Pb immobilization strategy was developed for the beneficial use of Pb-laden wastes through low-temperature thermal stabilization.
Quantum transport properties of single-crystalline Ag2Se0.5Te0.5 nanowires as a new topological material
Authors: Kim Minjin , Kim Jihwan , Lee In-Ho , Han Woo Hyun , Park Yun Chang , Kim Woo Youn , Kim Bongsoo , Suh Junho
Published: February 2019

Ternary Ag-chalcogenide nanowires as a new topological material exhibit improved quantum transport properties compared to binary counterparts, indicating reduced bulk contribution due to the modified band structure.
An ALP-activatable and mitochondria-targeted probe for prostate cancer-specific bimodal imaging and aggregation-enhanced photothermal therapy
Authors: Yao Defan , Yang Shuyan , Wang Yanshu , Bian Kexin , Yang Weitao , Wang Dengbin , Zhang Bingbo
Published: February 2019

We developed a mitochondria-targeted near-infrared activatable fluorescent/photoacoustic (NIR FL/PA) probe for the selective detection of prostate cancer-derived ALP and aggregation-enhanced photothermal therapy.
Physically cross-linked polyethyleneviareactive extrusion
Authors: Zych Arkadiusz , Verdelli Alice , Soliman Maria , Pinalli Roberta , Vachon Jérôme , Dalcanale Enrico
Published: February 2019

Ureidopyrimidinone (UPy) is introduced into various polyethylenes (PEs) bearing hydroxyl groups by solution grafting, affording physically cross-linked PEviamultiple H-bonding.
Constructing new metal–organic frameworks with complicated ligands from “One-Pot” in situ reactions
Authors: Kong Xiang-Jing , He Tao , Zhang Yong-Zheng , Wu Xue-Qian , Wang Si-Nan , Xu Ming-Ming , Si Guang-Rui , Li Jian-Rong
Published: February 2019

A “One-Pot” strategy has been developed to construct new metal–organic frameworks with complicated ligands from simple precursors by integrating organic and coordination chemistry.
Carbon monoxide insertion at a heavy p-block element: unprecedented formation of a cationic bismuth carbamoyl
Authors: Ramler Jacqueline , Poater Jordi , Hirsch Florian , Ritschel Benedikt , Fischer Ingo , Bickelhaupt F. Matthias , Lichtenberg Crispin
Published: February 2019

The first insertion reaction of CO with a molecular complex of the heavy p-block elements is reported (principal quantum number > 4).
Temporal and spatial pinhole constraints in small-molecule hole transport layers for stable and efficient perovskite photovoltaics
Authors: Niu Xiuxiu , Li Nengxu , Zhu Cheng , Liu Lang , Zhao Yizhou , Ge Yang , Chen Yihua , Xu Ziqi , Lu Yue , Sui Manling , Li Yujing , Tarasov Alexey , Goodilin Eugene A. , Zhou Huanping , Chen Qi
Published: February 2019

We introduced hydrophobic P4VP to substantially reduce the undesired HTL pinholes in temporal and spatial perspectives for more stable PSCs.
Electromagnetic plasmonic field of nanoparticles tune the band gap of two-dimensional semiconducting materials
Authors: Obiakara Chinedu , Mahmoud Mahmoud A.
Published: February 2019

The electromagnetic field of the plasmonic nanoparticles altered the spin–orbital coupling in the MoS2 2D-material thus changed its optical properties.