bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference genes for accessing differential expression among developmental stages and analysis of differential expression of OBP genes in Anastrepha obliqua
Authors: Nakamura Aline Minali , Chahad-Ehlers Samira , Lima André Luís A. , Taniguti Cristiane Hayumi , Sobrinho Iderval , Torres Felipe Rafael , de Brito Reinaldo Alves 
Published: January 2016

AbstractThe West Indian fruit fly,Anastrepha obliqua, is an important agricultural pest in the New World. The use of pesticide-free methods to control invasive species such as this reinforces the search for genes potentially useful in their genetic control. Therefore, the study of chemosensory proteins involved with a range of responses to the chemical environment will help not only on the understanding of the species biology but may also help the development of environmentally friendly pest control strategies. Here we analyzed the expression patterns of three OBP genes,Obp19d_2,Obp56aandObp99c, across different phases ofA. obliquadevelopment byqPCR. In order to do so, we tested eight and identified three reference genes for data normalization,rpl17,rpl18andef1a, which displayed stability for the conditions here tested. All OBPs showed differential expression on adults and some differential expression among adult stages.Obp99chad an almost exclusive expression in males andObp56ashowed high expression in virgin females. Thereby, our results provide relevant data not only for other gene expression studies in this species, as well as for the search of candidate genes that may help in the development of new pest control strategies.
Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells
Authors: Massart Renaud , Dymov Sergiy , Millecamps Magali , Suderman Matthew , Gregoire Stephanie , Koenigs Kevin , Alvarado Sebastian , Tajerian Maral , Stone Laura S. , Szyf Moshe 
Published: January 2016

AbstractWe tested the hypothesis that epigenetic mechanisms in the brain and the immune system are associated with chronic pain. Genome-wide DNA methylation assessed in 9 months post nerve-injury (SNI) and Sham rats, in the prefrontal cortex (PFC) as well as in T cells revealed a vast difference in the DNA methylation landscape in the brain between the groups and a remarkable overlap (72%) between differentially methylated probes in T cells and prefrontal cortex. DNA methylation states in the PFC showed robust correlation with pain score of animals in several genes involved in pain. Finally, only 11 differentially methylated probes in T cells were sufficient to distinguish SNI or Sham individual rats. This study supports the plausibility of DNA methylation involvement in chronic pain and demonstrates the potential feasibility of DNA methylation markers in T cells as noninvasive biomarkers of chronic pain susceptibility.
Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis
Authors: Luitz Manuel P. , Bomblies Rainer , Ramcke Evelyn , Itzen Aymelt , Zacharias Martin 
Published: January 2016

AbstractThe pathogenic pathway of Legionella pneumophila exploits the intercellular vesicle transport system via the posttranslational attachment of adenosine monophosphate (AMP) to the Tyr77 sidechain of human Ras like GTPase Rab1b. The modification, termed adenylylation, is performed by the bacterial enzyme DrrA/SidM, however the effect on conformational properties of the molecular switch mechanism of Rab1b remained unresolved. In this study we find that the adenylylation of Tyr77 stabilizes the active Rab1b state by locking the switch in the active signaling conformation independent of bound GTP or GDP and that electrostatic interactions due to the additional negative charge in the switch region make significant contributions. The stacking interaction between adenine and Phe45 however, seems to have only minor influence on this stabilisation. The results may also have implications for the mechanistic understanding of conformational switching in other signaling proteins.
Individual Restriction Of Fine Specificity Variability In Anti-GM1 IgG Antibodies Associated With Guillain-Barré Syndrome
Authors: Lardone Ricardo D. , Yuki Nobuhiro , Irazoqui Fernando J. , Nores Gustavo A. 
Published: January 2016

AbstractElevated titers of serum antibodies against GM1 ganglioside are associated with a variety of autoimmune neuropathies. Much evidence indicates these autoantibodies play a primary role in the disease processes, but the mechanism for their appearance is unclear. We studied the fine specificity of anti-GM1 antibodies of the IgG isotype present in sera from patients with Guillain-Barré syndrome (GBS), using thin-layer chromatogram-immunostaining of GM1, asialo-GM1 (GA1), GD1b and GM1-derivatives with small modifications on the oligosaccharide moiety. We were able to distinguish populations of antibodies with different fine specificity. Remarkably, individual patients presented only one or two of them and different patients had different populations. This restriction in the variability of antibody populations suggests that the appearance of the anti-GM1 antibodies is a random process involving restricted populations of lymphocytes. With the origin of disease-associated anti-GM1 antibodies as a context, this finding could provide explanation for the “host susceptibility factor” observed in GBS following enteritis with GM1 oligosaccharide-carrying strains of Campylobacter jejuni.
Tape Stripping Technique for Stratum Corneum Protein Analysis
Authors: Clausen Maja-Lisa , Slotved H.-C. , Krogfelt Karen A. , Agner Tove 
Published: January 2016

AbstractThe aim of this study was to investigate the amount of protein in stratum corneum in atopic dermatitis (AD) patients and healthy controls, using tape stripping technique. Furthermore, to compare two different methods for protein assessment. Tape stripping was performed in AD patients and healthy controls to collect stratum corneum samples and subsequently analysed with two different methods: Squame Scan, which gives an estimate of total protein (soluble and insoluble) and Micro BCA protein determination kit which measures soluble protein. Significant differences in cumulative protein content between AD lesional, AD non-lesional and healthy control skin was found using the Squame Scan as well as the Micro BCA protein determination kit. AD patients had significantly lower amount of protein, both total protein and soluble protein compared to healthy controls. Furthermore, soluble protein formed 82% of total protein in AD lesional skin, compared to 17–24% for AD non-lesional skin and healthy control. A decreasing amount of total protein with increasing stratum corneum depth was found for all skin types. Significant differences in stratum corneum protein content between AD lesional, AD non-lesional and healthy control skin were revealed, independent of method used.
Interactions and exchange of CO2 and H2O in coals: an investigation by low-field NMR relaxation
Authors: Sun Xiaoxiao , Yao Yanbin , Liu Dameng , Elsworth Derek , Pan Zhejun 
Published: January 2016

AbstractThe mechanisms by which CO2and water interact in coal remain unclear and these are key questions for understanding ECBM processes and defining the long-term behaviour of injected CO2. In our experiments, we injected helium/CO2to displace water in eight water-saturated samples. We used low-field NMR relaxation to investigate CO2and water interactions in these coals across a variety of time-scales. The injection of helium did not change theT2spectra of the coals. In contrast, theT2spectra peaks of micro-capillary water gradually decreased and those of macro-capillary and bulk water increased with time after the injection of CO2. We assume that the CO2diffuses through and/or dissolves into the capillary water to access the coal matrix interior, which promotes desorption of water molecules from the surfaces of coal micropores and mesopores. The replaced water mass is mainly related to the Langmuir adsorption volume of CO2and increases as the CO2adsorption capacity increases. Other factors, such as mineral composition, temperature and pressure, also influence the effective exchange between water and CO2. Finally, we built a quantified model to evaluate the efficiency of water replacement by CO2injection with respect to temperature and pressure.
Recombinant pre-miR-29b for Alzheimer´s disease therapeutics
Authors: Pereira Patrícia A. , Tomás Joana F. , Queiroz João A. , Figueiras Ana R. , Sousa Fani 
Published: January 2016

AbstractMicroRNAs are arising as the next generation of diagnostic and therapeutic tools for gene silencing. Studies demonstrated that the miR-29 expression is decreased in Alzheimer’s disease (AD) patients displaying high levels of human β-secretase (hBACE1). Recent advances toward an effective therapy for AD intend to employ miR-29 to suppress hBACE1 expression and subsequent Amyloid-β (Aβ) peptide. However, delivery of mature miRNA has demonstrated modest efficacy in vitro; therefore, the preparation of highly pure and biologically active pre-miRNA arises as one of the most important challenges in the development of these therapeutic strategies. Recently, we described a new strategy based arginine-affinity chromatography to specifically purify the recombinant pre-miR-29b. Following this strategy, the purified pre-miR-29b was successfully encapsulated into polyplexes that were further delivered in cytoplasm. It was verified that Chitosan/pre-miR-29b and Polyethylenimine/pre-miR-29b systems efficiently delivered pre-miR-29b to N2a695 cells, thus reducing the hBACE1 protein expression (around 78% and 86%, respectively) and Aβ42 levels (approximately 44% and 47%, respectively). Furthermore, pre-miR-29b downregulates the hBACE1 mRNA expression in 80%. Overall, it was demonstrated that the recombinant pre-miR-29b using polyplexes allowed to decrease the hBACE1 and Aβ42 expression levels, improving the currently available methodologies of miRNA-based therapeutics.
Self-Styled ZnO Nanostructures Promotes the Cancer Cell Damage and Supresses the Epithelial Phenotype of Glioblastoma
Authors: Wahab Rizwan , Kaushik Neha , Khan Farheen , Kaushik Nagendra Kumar , Choi Eun Ha , Musarrat Javed , Al-Khedhairy Abdulaziz A. 
Published: January 2016

AbstractExtensive researches have been done on the applications of zinc oxide nanoparticles (ZnO-NPs) for the biological purposes. However, the role and toxicity mechanisms of ZnO nanostructures (ZnO-NSts) such as nanoplates (NPls), nanorods (NRs), nanosheets (NSs), nanoflowers (NFs) on cancer cells are not largely known. Present study was focused to investigate the possible mechanisms of apoptosis induced by self-designed ZnO-NSts, prepared at fix pH via solution process and exposed against human T98G gliomas including various cancers and non-malignant embryonic kidney HEK293, MRC5 fibroblast cells. NSts were used for the induction of cell death in malignant human T98G gliomas including various cancers and compared with the non-malignant cells. Notably, NRs were found to induce higher cytotoxicity, inhibitory effects on cancer and normal cells in a dose dependent manner. We also showed that NRs induced cancer cell death through oxidative stress and caspase-dependent pathways. Furthermore, quantitative and qualitative analysis of ZnO-NSts have also been confirmed by statistical analytical parameters such as precision, accuracy, linearity, limits of detection and limit of quantitation. These self-styled NSts could provide new perception in the research of targeted cancer nanotechnology and have potentiality to improve new therapeutic outcomes with poor diagnosis.
Mirror-backed Dark Alumina: A Nearly Perfect Absorber for Thermoelectronics and Thermophotovotaics
Authors: Farhat Mohamed , Cheng Tsung-Chieh , Le Khai. Q. , Cheng Mark Ming-Cheng , Bağcı Hakan , Chen Pai-Yen 
Published: January 2016

AbstractWe present here a broadband, wide-angle and polarization-independent nearly perfect absorber consisting of mirror-backed nanoporous alumina. By electrochemically anodizing the disordered multicomponent aluminum and properly tailoring the thickness and air-filling fraction of nanoporous alumina, according to the Maxwell-Garnet mixture theory, a large-area dark alumina can be made with excellent photothermal properties and absorption larger than 93% over a wide wavelength range spanning from near-infrared to ultraviolet light, i.e. 250 nm–2500 nm. The measured absorption is orders of magnitude greater than other reported anodized porous alumina, typically semi-transparent at similar wavelengths. This simple yet effective approach, however, does not require any lithography, nano-mixture deposition, pre- and post-treatment. Here, we also envisage and theoretically investigate the practical use of proposed absorbers and/or photothermal converters in integrated thermoelectronic and/or thermophotovoltaic energy conversion devices, which make efficient use of the entire spectrum of ambient visible to near-infrared radiation.
The solution configurations of inactive and activated DntR have implications for the
sliding dimer mechanism of LysR transcription factors
Authors: Lerche Michael , Dian Cyril , Round Adam , Lönneborg Rosa , Brzezinski Peter , Leonard Gordon A. 
Published: January 2016

AbstractLysR Type Transcriptional Regulators (LTTRs) regulate basic metabolic pathways or
virulence gene expression in prokaryotes. Evidence suggests that the activation of
LTTRs involves a conformational change from an inactive compact apo-
configuration that represses transcription to an active, expanded holo- form
that promotes it. However, no LTTR has yet been observed to adopt both
configurations. Here, we report the results of structural studies of various forms
of the LTTR DntR. Crystal structures of apo-DntR and of a partially
autoinducing mutant H169T-DntR suggest that active and inactive DntR maintain a
compact homotetrameric configuration. However, Small Angle X-ray Scattering (SAXS)
studies on solutions of apo-, H169T- and inducer-bound holo-DntR
indicate a different behaviour, suggesting that while apo-DntR maintains a
compact configuration in solution both H169T- and holo-DntR adopt an expanded
conformation. Models of the SAXS-obtained solution conformations of apo- andholo-DntR homotetramers in complex with promoter-operator region DNA are
consistent with previous observations of a shifting of LTTR DNA binding sites upon
activation and a consequent relaxation in the bend of the promoter-operator region
DNA. Our results thus provide clear evidence at the molecular level which strongly
supports the ‘sliding dimer’ hypothesis concerning LTTR
activation mechanisms.
An Injectable Enzymatically Crosslinked Carboxymethylated Pullulan/Chondroitin Sulfate Hydrogel for Cartilage Tissue Engineering
Authors: Chen Feng , Yu Songrui , Liu Bing , Ni Yunzhou , Yu Chunyang , Su Yue , Zhu Xinyuan , Yu Xiaowei , Zhou Yongfeng , Yan Deyue 
Published: January 2016

AbstractIn this study, an enzymatically cross-linked injectable and biodegradable hydrogel system comprising carboxymethyl pullulan-tyramine (CMP-TA) and chondroitin sulfate-tyramine (CS-TA) conjugates was successfully developed under physiological conditions in the presence of both horseradish peroxidase (HRP) and hydrogen peroxide (H2O2) for cartilage tissue engineering (CTTE). The HRP crosslinking method makes this injectable system feasible, minimally invasive and easily translatable for regenerative medicine applications. The physicochemical properties of the mechanically stable hydrogel system can be modulated by varying the weight ratio and concentration of polymer as well as the concentrations of crosslinking reagents. Additionally, the cellular behaviour of porcine auricular chondrocytes encapsulated into CMP-TA/CS-TA hydrogels demonstrates that the hydrogel system has a good cyto-compatibility. Specifically, compared to the CMP-TA hydrogel, these CMP-TA/CS-TA composite hydrogels have enhanced cell proliferation and increased cartilaginous ECM deposition, which significantly facilitate chondrogenesis. Furthermore, histological analysis indicates that the hydrogel system exhibits acceptable tissue compatibility by using a mouse subcutaneous implantation model. Overall, the novel injectable pullulan/chondroitin sulfate composite hydrogels presented here are expected to be useful biomaterial scaffold for regenerating cartilage tissue.
siRNAmod: A database of experimentally validated chemically modified siRNAs
Authors: Dar Showkat Ahmad , Thakur Anamika , Qureshi Abid , Kumar Manoj 
Published: January 2016

AbstractSmall interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.
Xuefu Zhuyu decoction, a traditional Chinese medicine, provides neuroprotection in a rat model of traumatic brain injury via an anti-inflammatory pathway
Authors: Xing Zhihua , Xia Zian , Peng Weijun , Li Jun , Zhang Chunhu , Fu Chunyan , Tang Tao , Luo Jiekun , Zou Yong , Fan Rong , Liu Weiping , Xiong Xingui , Huang Wei , Sheng Chenxia , Gan Pingping , Wang Yang 
Published: January 2016

AbstractNeuroinflammation is central to the pathology of traumatic brain injury (TBI). Xuefu Zhuyu decoction (XFZY) is an effective traditional Chinese medicine to treat TBI. To elucidate its potential molecular mechanism, this study aimed to demonstrate that XFZY functions as an anti-inflammatory agent by inhibiting the PI3K-AKT-mTOR pathway. Sprague-Dawley rats were exposed to controlled cortical impact to produce a neuroinflammatory response. The treatment groups received XFZY (9 g/kg and 18 g/kg), Vehicle group and Sham group were gavaged with equal volumes of saline. The modified neurologic severity score (mNSS) and the Morris water maze test were used to assess neurological deficits. Arachidonic acid (AA) levels in brain tissue were measured using tandem gas chromatography-mass spectrometry. TNF-α and IL-1β levels in injured ipsilateral brain tissue were detected by ELISA. AKT and mTOR expression were measured by western blot analysis. The results indicated that XFZY significantly enhanced spatial memory acquisition. XFZY (especially at a dose of 9 g/kg) markedly reduced the mNSS and levels of AA, TNF-α and IL-1β. Significant downregulation of AKT/mTOR/p70S6K proteins in brain tissues was observed after the administration of XFZY (especially at a dose of 9 g/kg). XFZY may be a promising therapeutic strategy for reducing inflammation in TBI.
Divergent variations in concentrations of chemical elements among shrub organs in a temperate desert
Authors: He Mingzhu , Song Xin , Tian Fuping , Zhang Ke , Zhang Zhishan , Chen Ning , Li Xinrong 
Published: January 2016

AbstractDesert shrubs, a dominant component of desert ecosystems, need to maintain sufficient levels of nutrients in their different organs to ensure operation of various physiological functions for the purpose of survival and reproduction. In the present study, we analyzed 10 elements in leaves, stems and roots of 24 dominant shrub species from 52 sites across a temperate desert ecosystem in northwestern China. We found that concentrations of all 10 elements were higher in leaves than in stems and roots, that non-legumes had higher levels of leaf Na and Mg than did legumes and that Na was more concentrated in C4 leaves than in C3 leaves. Scaling relationships of elements between the photosynthetic organ (leaf) and non-photosynthetic organs (stem and root) were allometric. Results of principal components analysis (PCA) highlighted the important role of the elements responsible for osmoregulation (K and Na) in water utilization of desert shrubs. Soil properties and taxonomy explained most variation of element concentrations in desert shrubs. Desert shrubs may not be particularly susceptible to future change in climate factors, because most elements (including N, P, K, Ca, Mn, Zn and Cu) associated with photosynthesis, osmoregulation, enzyme activity and water use efficiency primarily depend on soil conditions.
Identification of the Fluvirucin B2 (Sch 38518) Biosynthetic Gene Cluster from Actinomadura fulva subsp. indica ATCC 53714: substrate Specificity of the β-Amino Acid Selective Adenylating Enzyme FlvN
Authors: Miyanaga Akimasa , Hayakawa Yuki , Numakura Mario , Hashimoto Junko , Teruya Kuniko , Hirano Takashi , Shin-ya Kazuo , Kudo Fumitaka , Eguchi Tadashi 
Published: January 2016

Abstract
Fluvirucins are 14-membered macrolactam polyketides that show antifungal and antivirus activities. Fluvirucins have the β-alanine starter unit at their polyketide skeletons. To understand the construction mechanism of the β-alanine moiety in fluvirucin biosyntheses, we have identified the biosynthetic cluster of fluvirucin B2 produced from Actinomadura fulva subsp. indica ATCC 53714. The identified gene cluster contains three polyketide synthases, four characteristic β-amino acid-carrying enzymes, one decarboxylase, and one amidohydrolase. We next investigated the activity of the adenylation enzyme FlvN, which is a key enzyme for the selective incorporation of a β-amino acid substrate. FlvN showed strong preference for l-aspartate over other amino acids such as β-alanine. Based on these results, we propose a biosynthetic pathway for fluvirucin B2.
Biomechanics and functional morphology of a climbing monocot
Authors: Hesse Linnea , Wagner Sarah T. , Neinhuis Christoph 
Published: January 2016

AbstractPlants with a climbing growth habit possess unique biomechanical properties arising from adaptations to changing loading conditions connected with close attachment to mechanical supports. In monocot climbers, mechanical adaptation is restricted by the absence of a bifacial vascular cambium. Flagellaria indica was used to investigate the mechanical properties and adaptations of a monocot climber that, uniquely, attaches to the surrounding vegetation via leaf tendrils. Biomechanical methods such as three-point bending and torsion tests were used together with anatomical studies on tissue development, modification and distribution. In general, the torsional modulus was lower than the bending modulus; hence, torsional stiffness was less than flexural stiffness. Basal parts of mature stems showed the greatest stiffness while that of more apical stem segments levelled off. Mechanical properties were modulated via tissue maturation processes mainly affecting the peripheral region of the stem. Peripheral vascular bundles showed a reduction in the amount of conducting tissue while the proportion and density of the bundle sheath increased. Furthermore, adjacent bundle sheaths merged resulting in a dense ring of fibrous tissue. Although F. indica lacks secondary cambial growth, the climbing habit is facilitated by a complex interaction of tissue maturation and attachment.