bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive evolution of proteins in hepatitis B virus during divergence of genotypes
Authors: Li Shengdi , Wang Zhen , Li Yixue , Ding Guohui 
Published: May 2017

AbstractHepatitis B virus (HBV) is classified into several genotypes, correlated with different geographic distributions, clinical outcomes and susceptible human populations. It is crucial to investigate the evolutionary significance behind the diversification of HBV genotypes, because it improves our understanding of their pathological differences and pathogen-host interactions. Here, we performed comprehensive analysis of HBV genome sequences collected from public database. With a stringent criteria, we generated a dataset of 2992 HBV genomes from eight major genotypes. In particular, we applied a specified classification of non-synonymous and synonymous variants in overlapping regions, to distinguish joint and independent gene evolutions. We confirmed the presence of selective constraints over non-synonymous variants in consideration of overlapping regions. We then performed the McDonald-Kreitman test and revealed adaptive evolutions of non-synonymous variants during genotypic differentiation. Remarkably, we identified strong positive selection that drove the differentiation of PreS1 domain, which is an essential regulator involved in viral transmission. Our study presents novel evidences for the adaptive evolution of HBV genotypes, which suggests that these viruses evolve directionally for maintenance or improvement of successful infections.
Structure Based docking studies towards exploring potential anti-androgen activity of selected phytochemicals against Prostate Cancer
Authors: Singh Anshika N. , Baruah Meghna M. , Sharma Neeti 
Published: May 2017

AbstractProstate cancer (PCa) is the second most common malignancy amongst men worldwide. Under PCa maintenance therapy drugs acting as antagonists/partial agonists of hormone receptors against the prostate tissue are used in clinical practices. Prominent drugs being Cyproterone acetate, Flutamide, Bicalutamide, they not only cause acute and long-term toxicity, but also develops drug resistance among patients. Our focus has been on phytochemicals which do not exhibit any cytotoxicity and have significant androgen receptor (AR) inhibition activity. As Protein- Ligand interactions play a key role in structure based drug design, so by using molecular docking, we screened 803 phytochemicals and investigated their binding affinity against AR. The three dimensional (3D) structure of AR was retrieved from Protein Data Bank, and docked with 3D Pubchem structures of 803 phytochemicals using Argus Lab. Molecular docking and drug likeness studies were made using ADMET properties while Lipinski’s rule of five was performed for the phytochemicals to evaluate their anti-prostate cancer activity. The results showed that Isobavachin exhibited best binding affinity of −13.73 kcal/mol with AR followed by Glabranin, Anthocyanin and Eriosemation. Our studies therefore reveal that these four phytochemicals could be promising candidates for further evaluation for PCa prevention or management.
Restoration of the growth of Escherichia coli under K+-deficient conditions by Cs+ incorporation via the K+ transporter Kup
Authors: Kato Souichiro , Kanata Yoshiki , Kitagawa Wataru , Sone Teruo , Asano Kozo , Kamagata Yoichi 
Published: May 2017

AbstractBiological incorporation of cesium ions (Cs+) has recently attracted significant attention in terms of the possible applications for bioremediation of radiocesium and their significant roles in biogeochemical cycling. Although high concentrations of Cs+ exhibit cytotoxicity on microorganisms, there are a few reports on the promotive effects of Cs+ on microbial growth under K+-deficient conditions. However, whether this growth-promoting effect is a common phenomenon remains uncertain, and direct correlation between growth promotion and Cs+ uptake abilities has not been confirmed yet. Here, we validated the growth promotive effects of Cs+ uptake under K+-deficient conditions using an Escherichia coli strain with an inducible expression of the Kup K+ transporter that has nonspecific Cs+ transport activities (strain kup-IE). The strain kup-IE exhibited superior growth under the Cs+-supplemented and K+-deficient conditions compared to the wild type and the kup null strains. The intracellular Cs+ levels were significantly higher in strain kup-IE than in the other strains, and were well correlated with their growth yields. Furthermore, induction levels of the kup gene, intracellular Cs+ concentrations, and the growth stimulation by Cs+ also correlated positively. These results clearly demonstrated that Cs+ incorporation via Kup transporter restores growth defects of E. coli under K+-deficient conditions.
Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent
Authors: Zhang Jian , Sun Qing-lei , Luan Zhen-dong , Lian Chao , Sun Li 
Published: May 2017

AbstractShrimp of the family Alvinocarididae are the predominant megafauna of deep-sea hydrothermal vents. However, genome information on this family is currently unavailable. In the present study, by employing Illumina sequencing, we performed the first de novo transcriptome analysis of the gills of the shrimp Rimicaris sp. from the hydrothermal vent in Desmos, Manus Basin. The analysis was conducted in a comparative manner with the shrimp taken directly from the vent (GR samples) and the shrimp that had been maintained for ten days under normal laboratory condition (mGR samples). Among the 128,938 unigenes identified, a large number of differentially expressed genes (DEGs) between the GR and mGR samples were detected, including 2365 and 1607 genes significantly upregulated and downregulated, respectively, in GR. The DEGs covered diverse functional categories. Most of the DEGs associated with immunity were downregulated in GR, while most of the DEGs associated with sulfur metabolism and detoxification were upregulated in GR. These results provide the first comprehensive transcriptomic resource for hydrothermal vent Rimicaris and revealed varied categories of genes likely involved in deep-sea survival.
Maternal antioxidant provisioning mitigates pollutant-induced oxidative damage in embryos of the temperate sea urchin Evechinus chloroticus
Authors: Lister Kathryn N. , Lamare Miles D. , Burritt David J. 
Published: May 2017

AbstractOne mechanism of pollution resistance in marine populations is through transgenerational plasticity, whereby offspring capacity to resist pollution reflects parental exposure history. Our study aimed to establish correlations between oxidative stress biomarkers and key reproductive fitness parameters in the temperate sea urchin Evechinus chloroticus following exposure to dietary polycyclic aromatic hydrocarbons (PAHs). PAH-exposed adults exhibited total gonad tissue concentrations of PAHs in excess of 4 and 5 times baseline levels, for females and males respectively. Antioxidant enzymes were upregulated and oxidative lipid and protein damage to gonad tissues occurred. In addition, early stage offspring reflected maternal antioxidant status, with progeny derived from exposed females demonstrating significantly higher baselines than those derived from control females. Maternal exposure history enhanced the capacity of embryos to minimise oxidative damage to lipids and proteins following exposure to additional PAHs, but provided less of an advantage in protection against oxidative DNA damage. Abnormal embryonic development was largely independent of oxidative damage, remaining high in all embryo populations regardless of parental PAH-history. Overall, results document evidence for maternal transfer of antioxidant potential in E. chloroticus, but imply that a short-term inherited resilience against oxidative stress may not necessarily translate to a fitness or survival gain.
The influence of statistical properties of Fourier coefficients on random Gaussian surfaces
Authors: de Castro C. P. , Luković M. , Andrade R. F. S. , Herrmann H. J. 
Published: May 2017

AbstractMany examples of natural systems can be described by random Gaussian surfaces. Much can be learned by analyzing the Fourier expansion of the surfaces, from which it is possible to determine the corresponding Hurst exponent and consequently establish the presence of scale invariance. We show that this symmetry is not affected by the distribution of the modulus of the Fourier coefficients. Furthermore, we investigate the role of the Fourier phases of random surfaces. In particular, we show how the surface is affected by a non-uniform distribution of phases.
Delayed epidural transplantation of human induced pluripotent stem cell-derived neural progenitors enhances functional recovery after stroke
Authors: Lee I-Hui , Huang Shiang-Suo , Chuang Ching-Yu , Liao Ko-Hsun , Chang Li-Hsin , Chuang Chia-Chi , Su Yu-Shih , Lin Hung-Jui , Hsieh Jui-Yu , Su Shu-Han , Lee Oscar Kuang-Sheng , Kuo Hung-Chih 
Published: May 2017

AbstractInduced pluripotent stem cell-derived neural progenitor cells (iPSC-NPCs) are a promising source of tailor-made cell therapy for neurological diseases. However, major obstacles to clinical use still exist. To circumvent complications related to intracerebral administration, we implanted human iPSC-NPCs epidurally over the peri-infarct cortex 7 days after permanent middle cerebral artery occlusion in adult rats. Compared to controls, cell-treated rats showed significant improvements in paretic forelimb usage and grip strength from 10 days post-transplantation (dpt) onwards, as well as reductions in lesion volumes, inflammatory infiltration and astrogliosis at 21 dpt. Few iPSC-NPCs migrated into rat peri-infarct cortices and exhibited poor survival in tissue. To examine the paracrine therapeutic mechanisms of epidural iPSC-NPC grafts, we used transmembrane co-cultures of human iPSC-NPCs with rat cortical cells subjected to oxygen-glucose deprivation. Compared to other human stem cells, iPSC-NPCs were superior at promoting neuronal survival and outgrowth, and mitigating astrogliosis. Using comparative whole-genome microarrays and cytokine neutralization, we identified a neurorestorative secretome from iPSC-NPCs, and neutralizing enriched cytokines abolished neuroprotective effects in co-cultures. This proof-of-concept study demonstrates a relatively safe, yet effective epidural route for delivering human iPSC-NPCs, which acts predominately through discrete paracrine effects to promote functional recovery after stroke.
Tacrolimus Blood Level Fluctuation Predisposes to Coexisting BK Virus Nephropathy and Acute Allograft Rejection
Authors: Shen Chia-Lin , Yang An-Hang , Lien Tse-Jen , Tarng Der-Cherng , Yang Chih-Yu 
Published: May 2017

AbstractBK virus nephropathy (BKVN) and allograft rejection are two distinct disease entities which occur at opposite ends of the immune spectrum. However, they coexist in renal transplant recipients. Predisposing factors for this coexistence remain elusive. We identified nine biopsy-proven BKVN patients with coexisting acute rejection, and 21 patients with BKVN alone. We retrospectively analyzed the dosage and blood concentrations of immunosuppressants during the 3-month period prior to the renal biopsy between the two patient groups. Compared to the BKVN alone group, renal function was noticeably worse in the coexistence group (p = 0.030). Regarding the dose and average drug level of immunosuppressants, there was no difference between the two groups. Interestingly, the coefficient of variance of tacrolimus trough blood level was noticeably higher during the 3-month period prior to the renal biopsy in the coexistence group (p = 0.010). Our novel findings suggest that a higher variability of tacrolimus trough level may be associated with the coexistence of BKVN and acute rejection. Since the prognosis is poor and the treatment is challenging in patients with coexisting BKVN and acute rejection, transplant clinicians should strive to avoid fluctuations in immunosuppressant drug levels in patients with either one of these two disease entities.
Genetic load makes cancer cells more sensitive to common drugs: evidence from Cancer Cell Line Encyclopedia
Authors: Pavel Ana B. , Korolev Kirill S. 
Published: May 2017

AbstractGenetic alterations initiate tumors and enable the evolution of drug resistance. The pro-cancer view of mutations is however incomplete, and several studies show that mutational load can reduce tumor fitness. Given its negative effect, genetic load should make tumors more sensitive to anticancer drugs. Here, we test this hypothesis across all major types of cancer from the Cancer Cell Line Encyclopedia, which provides genetic and expression data of 496 cell lines together with their response to 24 common anticancer drugs. We found that the efficacy of 9 out of 24 drugs showed significant association with genetic load in a pan-cancer analysis. The associations for some tissue-drug combinations were remarkably strong, with genetic load explaining up to 83% of the variance in the drug response. Overall, the role of genetic load depended on both the drug and the tissue type with 10 tissues being particularly vulnerable to genetic load. We also identified changes in gene expression associated with increased genetic load, which included cell-cycle checkpoints, DNA damage and apoptosis. Our results show that genetic load is an important component of tumor fitness and can predict drug sensitivity. Beyond being a biomarker, genetic load might be a new, unexplored vulnerability of cancer.
Structure-based prediction and identification of 4-epimerization activity of phosphate sugars in class II aldolases
Authors: Lee Seon-Hwa , Hong Seung-Hye , An Jung-Ung , Kim Kyoung-Rok , Kim Dong-Eun , Kang Lin-Woo , Oh Deok-Kun 
Published: May 2017

AbstractSugar 4-epimerization reactions are important for the production of rare sugars and their derivatives, which have various potential industrial applications. For example, the production of tagatose, a functional sweetener, from fructose by sugar 4-epimerization is currently constrained because a fructose 4-epimerase does not exist in nature. We found that class II d-fructose-1,6-bisphosphate aldolase (FbaA) catalyzed the 4-epimerization of d-fructose-6-phosphate (F6P) to d-tagatose-6-phosphate (T6P) based on the prediction via structural comparisons with epimerase and molecular docking and the identification of the condensed products of C3 sugars. In vivo, the 4-epimerization activity of FbaA is normally repressed. This can be explained by our results showing the catalytic efficiency of d-fructose-6-phosphate kinase for F6P phosphorylation was significantly higher than that of FbaA for F6P epimerization. Here, we identified the epimerization reactions and the responsible catalytic residues through observation of the reactions of FbaA and l-rhamnulose-1-phosphate aldolases (RhaD) variants with substituted catalytic residues using different substrates. Moreover, we obtained detailed potential epimerization reaction mechanism of FbaA and a general epimerization mechanism of the class II aldolases l-fuculose-1-phosphate aldolase, RhaD, and FbaA. Thus, class II aldolases can be used as 4-epimerases for the stereo-selective synthesis of valuable carbohydrates.
Water-Assisted Synthesis of Molybdenum Disulfide Film with Single Organic Liquid Precursor
Authors: Choi Soo Ho , Stephen Boandoh , Park Ji-Hoon , Lee Joo Song , Kim Soo Min , Yang Woochul , Kim Ki Kang 
Published: May 2017

AbstractWe report on the synthesis of large-area molybdenum disulfide (MoS2) film on an insulating substrate by means of chemical vapor deposition. A single mixture of molybdenum hexacarbonyl (Mo(CO)6) and dimethyl disulfide (C2H6S2) was utilized as an organic liquid precursor for the synthesis of MoS2 film. Carbon impurities stemming from the dissociation of the organic precursor are effectively removed by water oxidation, and hydrogen gas, which is a by-product of the oxidation of carbon impurities, inhibits the formation of molybdenum oxides. The use of a liquid precursor assisted with water oxidation ensures high reproducibility and full-coverage of MoS2 film for large area, which is not typically achieved with solid precursors such as molybdenum oxide and sulfur powder. We believe that our approach will advance the synthesis of transition metal dichalcogenides.
Near Infrared Quantum Cutting Luminescence of Er3+/Tm3+ Ion Pairs in a Telluride Glass
Authors: Chen Xiaobo , Li Song , Hu Lili , Wang Kezhi , Zhao Guoying , He Lizhu , Liu Jinying , Yu Chunlei , Tao Jingfu , Lin Wei , Yang Guojian , Salamo Gregory J. 
Published: May 2017

AbstractThe multiphoton near-infrared, quantum cutting luminescence in Er3+/Tm3+ co-doped telluride glass was studied. We found that the near-infrared 1800-nm luminescence intensity of (A) Er3+(8%)Tm3+(0.5%):telluride glass was approximately 4.4 to 19.5 times larger than that of (B) Tm3+(0.5%):telluride glass, and approximately 5.0 times larger than that of (C) Er3+(0.5%):telluride glass. Additionally, the infrared excitation spectra of the 1800 nm luminescence, as well as the visible excitation spectra of the 522 nm and 652 nm luminescence, of (A) Er3+(8%)Tm3+(0.5%):telluride glass are very similar to those of Er3+ ions in (C) Er3+(0.5%):telluride glass, with respect to the shapes of their excitation spectral waveforms and peak wavelengths. Moreover, we found that there is a strong spectral overlap and energy transfer between the infrared luminescence of Er3+ donor ions and the infrared absorption of Tm3+ acceptor ions. The efficiency of this energy transfer {4I13/2(Er3+) → 4I15/2(Er3+), 3H6(Tm3+) → 3F4(Tm3+)} between the Er3+ and Tm3+ ions is approximately 69.8%. Therefore, we can conclude that the observed behaviour is an interesting multiphoton, near-infrared, quantum cutting luminescence phenomenon that occurs in novel Er3+-Tm3+ ion pairs. These findings are significant for the development of next-generation environmentally friendly germanium solar cells, and near-to-mid infrared (1.8–2.0 μm) lasers pumped by GaN light emitting diodes.
Lactic acid bacteria-specific induction of CD4+Foxp3+T cells ameliorates shrimp tropomyosin-induced allergic response in mice via suppression of mTOR signaling
Authors: Fu Linglin , Peng Jixiang , Zhao Shushu , Zhang Yan , Su Xiurong , Wang Yanbo 
Published: May 2017

AbstractThe beneficial effects of probiotics have been described in allergic sensitization and diseases; however, many questions remain unanswered, such as characteristics of the most effective strains in modulation of allergic responses and how orally administered probiotics affect the systemic immune system. In the present work, oral administration of five lactic acid bacteria strains showed variable effects on protection against the allergic reaction in a mouse model of food allergy to shrimp tropomyosin (ST). The most effective anti-allergic strain, Bacillus coagulans 09.712 (Bc), greatly improved epithelial barrier function and increased lymphocytes proliferation. Moreover, Bc suppresses ST sensitization by altering Th1/Th2/Treg balance as a result of strong induction of CD4+Foxp3+Tregs in combination with IL-10 producing. Bc-specific induction of CD4+Foxp3+ Tregs also suppresses Th17 pro-inflammatory response in this mouse model. Finally, the intake of Bc suppresses mTOR activation and thus the phosphorylation of downstream factors. Inhibition of mTOR signaling by Bc further results in FOXP3 up-regulation and GATA-3 down-regulation, which, in turn, facilitate to control Th2-predominant and Th17 pro-inflammatory responses caused by ST. Our work provides further characterization of the anti-allergic effects of probiotic LAB strains, and identifies new targets for preventive and curative treatment of food allergies.
The Rhizobium tropici CIAT 899 NodD2 protein regulates the production of Nod factors under salt stress in a flavonoid-independent manner
Authors: del Cerro Pablo , Pérez-Montaño Francisco , Gil-Serrano Antonio , López-Baena Francisco Javier , Megías Manuel , Hungria Mariangela , Ollero Francisco Javier 
Published: May 2017

AbstractIn the symbiotic associations between rhizobia and legumes, NodD promotes the expression of the nodulation genes in the presence of appropriate flavonoids. This set of genes is implied in the synthesis of Nodulation factors, which are responsible for launching the nodulation process. Rhizobium tropici CIAT 899 is the most successful symbiont of Phaseolus vulgaris and can nodulate a variety of legumes. This strain produces Nodulation factors under abiotic stress such as acidity or high concentration of salt. Genome sequencing of CIAT 899 allowed the identification of five nodD genes. Whereas NodD1 is essential to nodulate Leucaena leucocephala, Lotus japonicus and Macroptilium atropurpureum, symbiosis with P. vulgaris and Lotus burtii decreased the nodule number but did not abolish the symbiotic process when NodD1 is absent. Nodulation factor synthesis under salt stress is not regulated by NodD1. Here we confirmed that NodD2 is responsible for the activation of the CIAT 899 symbiotic genes under salt stress. We have demonstrated that NodD1 and NodD2 control the synthesis of the Nod factor necessary for a successful symbiosis with P. vulgaris and L. burtii. This is the first time that NodD is directly implied in the activation of the symbiotic genes under an abiotic stress.
Thermal conductivity and dielectric properties of bismaleimide/cyanate ester copolymer
Authors: Wan Lin , Zhang Xia , Wu Guanglei , Feng Ailing 
Published: May 2017

The blend was synthesised with bismaleimide (BMI) resin and bisphenol A‐based cyanate ester (BADCy) resin. The BMI/BADCy copolymer showed excellent dielectric and thermal conductivity properties. The volume resistivity of the copolymer was a little lower than BADCy system. The volume resistivity of blend was 7.8 × 1015 Ω·cm when the BMI content was 20 wt%, which still showed good insulation performance. The dielectric property of modified BADCy copolymer remained the good stability from 0.1 Hz to 1 MHz. Compared to pure BADCy system, the breakdown property of BMI/BADCy blend reached the maximum value of 77.9 kV/mm when the content of BMI was 20 wt%, which was still about 1.22 times. The thermal property and thermal conductivity property of the copolymer were higher than BADCy system.